Cactvs Toolkit Standard Property Definition Summary
| Name | Datatype | Description | Literature | Enumerations | Fields | Parameters | Computation | Dependencies | Invalidation | CompModule |
|---|---|---|---|---|---|---|---|---|---|---|
| A_3D_BONDING_VECTOR | floatvector | 3D bonding vector (i.e. next open ligand shell position in VSEPR model to attach a ligand to). The length of this vector is always 1.0 regardless of the elements involved - this value is only to be used for directions, not as a bond length. Currently, the implementatiion is limited to s/sp/sp2/sp3 geometries. |
Compiled C module | A_XYZ | atomchange bondchange merge 3drelative 3dabsolute hadd | mod_a_3d_bonding_vector.so | ||||
| A_ALCHEMY_TYPE | shortstring | Atom type as used in the Alchemy program | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC | atomchange bondchange | a_alchemy_type.xpd | ||||
| A_ALIHETERO_SUBSTITUENT_COUNT | int | Count the number of hetero (not C or H) ligands around a central atom which are not part of an aroamtic system | Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ISAROMATIC | atomchange bondchange | mod_a_alihetero_substituent_count.so | ||||
| A_ALIRING_COUNT | short | Number of aliphatic rings the atom is member of | countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
|
Compiled C module | R_AROMATIC R_TYPE | atomchange bondchange ring | mod_a_aliring_count.so | |||
| A_ALKYL_SUBSTITUENT_COUNT | short | Number of alkyl substituents (carbon sp3 ligand with no hetero atoms except possibly the atom for which this property is computed). This follows the Lhasa definition of alkyl substituent groups. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 36 | Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER A_HETERO_SUBSTITUENT_COUNT | atomchange bondchange atom bond | mod_a_alkyl_substituent_count.so | |||
| A_ALLENE | byte | Flag for atoms in allenic system | no:terminal:odd:even |
(builtin) | A_VALENCE B_TYPE B_ORDER | atomchange bondchange | ||||
| A_ALLYLIC | byte | An allylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to a carbon-carbon double bond. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER B_ARORING_COUNT | atomchange bondchange atom bond | mod_a_allylic.so | |||
| A_ALPHA_ARO_COUNT | int | Number of aromatic systems in alpha position, without the atom being a member of these. | Compiled C module | A_ISAROMATIC B_TYPE | atomchange bondchange | mod_a_alpha_aro_count.so | ||||
| A_ALPHA_UNSAT_COUNT | int | Number of vinyl, aliphatic systems in alpha position, without the atom being a member of these. This corresponds to the Lilly SMARTS extension "AG>0" and is used to implement the /IWVy extension. | Compiled C module | A_ARORING_COUNT A_UNSATURATION B_TYPE B_ORDER | atomchange bondchange | mod_a_alpha_unsat_count.so | ||||
| A_ANNOTATION | string | Atom annotation string for 2D rendering, containing, for example, charge and radical information | chargerepeatlimit: { value: 2 datatype: string} stereogroups: { value: 1 datatype: string} stereo: { value: 7 datatype: string} isotope: { value: 1 datatype: string} radical: { value: 1 datatype: string} mapping: { value: 1 datatype: string} query: { value: 1 datatype: string} flags: { value: 1 datatype: string} nostereo: { value: 0 datatype: string} auxproperty: { value: {} datatype: string} auxfilter: { value: {} datatype: string} auxpropertyprefix: { value: {} datatype: string} auxpropertysuffix: { value: {} datatype: string} style: { value: default datatype: string} label: { value: 0 datatype: string} |
(builtin) | A_TYPE A_ISOTOPE A_FORMAL_CHARGE A_FREE_ELECTRONS A_ELEMENT A_LABEL_STEREO A_CIP_STEREO A_FLAGS A_DL_STEREO A_QUERY A_HASH_STEREO A_MAP_STEREO A_RADICAL A_STEREO_GROUP | atomchange bondchange stereochange | ||||
| A_AROBOND_COUNT | byte | Number of aromatic bonds atom participates in | Compiled C module | B_ISAROMATIC | atomchange bondchange | mod_a_arobond_count.so | ||||
| A_AROCONDENSED | boolean | Flags for atoms in condensed aromatic ring systems (i.e. atoms which are member in two or more aromatic rings that are connected by an overlapping ring portion, or share an annealed aromatic bond) | Compiled C module | R_TYPE R_AROMATIC | atomchange bondchange | mod_a_arocondensed.so | ||||
| A_ARORING_COUNT | short | Number of aromatic rings the atom is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | R_AROMATIC R_TYPE | atomchange bondchange ring | ||||
| A_ARORING_SIZE_BITS | bitset | Bit mask for aromatic ring sizes the atom participates in | ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
|
Compiled C module | R_SIZE R_TYPE B_TYPE A_ARORING_COUNT R_AROMATIC | bondchange ring | mod_a_aroring_size_bits.so | |||
| A_AUTODOCK4_TYPE | shortstring | Atom type as used in the Autodock 4 program | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC | atomchange bondchange | a_autodock4_type.xpd | ||||
| A_BENZYLIC | byte | A benzylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to an aromatic carbon atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER A_ARORING_COUNT | atomchange bondchange atom bond | mod_a_benzylic.so | |||
| A_BONDORDER_COUNT | bytevector | Count of different bond orders around an atom (array). | (builtin) | B_ORDER | atomchange bondchange | |||||
| A_BOND_RANGE | intpair | Ids of first and last bond atom is bonded to | (builtin) | B_SEQUENCE_NUMBER | atomchange bondchange merge shuffle hadd mol | |||||
| A_BRICS_LINKER_TYPE | short | BRICS fragmentation scheme linker type | ChemMedChem 2008, 3, 1503-1507 | none:C-R1:N-R2:O-R3:C-R4:N-R5:C-R6:C-R7:C-R8:n-R9:N-R10:S-R11:S-R12:C-R13:C-R14:C-R15:C-R16 |
never | |||||
| A_BRIDGEHEAD | boolean | Flag indicating atom is a ring system bridgehead | Compiled C module | A_RING_COUNT | atomchange bondchange | mod_a_bridgehead.so | ||||
| A_C13_NMRSHIFT | float | C13 NMR shift, measured in ppm. | atomchange bondchange stereochange atom bond | |||||||
| A_CARBOCYCLE | boolean | Flag indicating an atom in a carbocycle ESSSR ring | Compiled C module | R_TYPE R_HETEROATOM_COUNT | atomchange bondchange atom bond | mod_a_carbocycle.so | ||||
| A_CARBON_FRAGMENT_SIZE | int | Size of the carbon skeleton the atom looked at is member of | Compiled C module | B_TYPE A_ELEMENT A_TYPE | atomchange bondchange | mod_a_carbon_fragment_size.so | ||||
| A_CENTRALITY | double | Centrality rating of the atom (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN) | Compiled C module | A_TOPO_DISTANCE M_SPAN | atomchange bondchange atom bond | mod_a_centrality.so | ||||
| A_CGR_CHANGE | intpair | Atom change when interpreting a CGR-encoded structure. The values are a flag for addition/removal (-1: delete in product, 0: no change, 1:add in product) and the formal charge delta when going from reagent to product | presence int charge int |
atomchange bondchange 3dabsolute atom bond reaction | ||||||
| A_CH2_CHAIN_LENGTH | int | The length of the unbranched CH2/CH3 chain the atom is a member of. Hetero or carbon atoms that do not have 2 or more hydrogen neighbors have a 0 value. Hydrogen atoms are assigned the value of their bonding partner. | Compiled C module | A_TYPE A_ELEMENT B_TYPE A_RING_COUNT A_HEAVY_SUBSTITUENT_COUNT | atomchange bondchange atom bond | mod_a_ch2_chain_length.so | ||||
| A_CHAIN_LENGTH | int | The size of the chain-heavy-atoms-only fragment the atom is a member of. Ring atoms have value 0. Hydrogen atoms inherit the value of their bond partner. | Compiled C module | A_TYPE A_RING_COUNT B_TYPE | atomchange bondchange atom bond | mod_a_chain_length.so | ||||
| A_CHARGE_STABILIZATION | shortvector | Stabilization for negative charges, radicals and positive charges (in this order) on carbon atom (potentially after cutting a bond which is not the source of a stabilizing effect) according to the Lhasa formula | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 43 | minus int plus int radical int |
Compiled C module | atomchange bondchange atom bond | mod_a_charge_stabilization.so | |||
| A_CIP_STEREO | byte | Stereo descriptor for atoms, based on CIP (R/S) rules | SS=-2:S=-1:undef=0:R=1:RR=2 |
(builtin) | atomchange bondchange | |||||
| A_CL_COUNT | int | Count the number of chlorine substituents around the atoms | Tcl script | A_ELEMENT A_TYPE | atomchange bondchange | a_cl_count.xpd | ||||
| A_COLOR | color | Atom rendering color | mode: { value: light datatype: string} labellist: { value: 1 datatype: string} colorlist: { value: green datatype: string} defaultcolor: { value: gray20 datatype: string} |
(builtin) | A_ELEMENT A_TYPE | never | ||||
| A_COLOR_SCALE | color | Get color values in different coloration models useing some atom property as data | property: { value: A_SIGMA_CHARGE datatype: string constraints: property} maxintensity: { value: 255 datatype: int} minintensity: { value: 0 datatype: int} maxvalue: { value: auto datatype: string} minvalue: { value: auto datatype: string} colorspace: { value: rgb enumeration: red:green:blue:grey,gray:rgb:fixed datatype: int} invert: { value: 0 datatype: boolean} rootscale: { value: 0 datatype: boolean} zerobalance: { value: 0 datatype: boolean} filter: { value: {} datatype: string constraints: filterlist} rangecolors: { value: red 1 green 0 blue datatype: string} |
Tcl script | atomchange bondchange | a_color_scale.xpd | ||||
| A_COMMENT | string | free-form atom comment. This is used for exampole in reading PubChem ASN.1 structure data. | never | |||||||
| A_CONFORMER | xyzvector | Conformers of the ensemble, created by various methods | maxconformers: { value: 10 description: Maximum number of conformers to generate or store minvalue: 1 maxvalue: 99999 datatype: int}
|
Tcl script | A_ELEMENT A_MOL_NUMBER A_TYPE B_TYPE A_FREE_ELECTRONS A_LABEL_STEREO B_LABEL_STEREO B_ORDER A_FLAGS A_FORMAL_CHARGE | atomchange bondchange merge | a_conformer.xpd | |||
| A_CONJUGATED | boolean | A conjugated atom according to the Lhasa definition. Conjugated atoms are those alpha to a multiply bonded atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | Compiled C module | A_TYPE B_TYPE A_FG_PARTICIPATION B_ORDER | atomchange bondchange atom bond | mod_a_conjugated.so | |||
| A_CONJUGATED_SYSTEM_SIZE | int | The size of the conjugated system the atom participates in according to the Shoichet definition (see literature reference). Atoms not in such a system get value 0. | J. Med. Chem. 2003, 46, 4477-4486 | Compiled C module | A_TYPE A_SP2 A_INAMIDE A_ARORING_COUNT B_TYPE | atomchange bondchange atom bond | mod_a_conjugated_system_size.so | |||
| A_COVALENCY_RADIUS | float | Default covalence radius | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_CSP2_0H | boolean | Flag for carbon atoms with sp2 hybridization and no hydrogen substituents | Tcl script | A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp2_0h.xpd | ||||
| A_CSP2_1H | boolean | Flag for carbon atoms with sp2 hybridization and one hydrogen substituent | Tcl script | A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp2_1h.xpd | ||||
| A_CSP2_2H | boolean | Flag for carbon atoms with sp2 hybridization and two hydrogen substituents | Tcl script | A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp2_2h.xpd | ||||
| A_CSPECIAL | boolean | Flag for carbon atoms plotted with symbols by common agreement | triplebond: { value: 1 datatype: string} allene: { value: 1 datatype: string} charged: { value: 1 datatype: string} isotope: { value: 1 datatype: string} specialbonds: { value: 1 datatype: string} onlyhligands: { value: 1 datatype: string} onlyterminalxligands: { value: 1 datatype: string} never: { value: 0 datatype: string} |
(builtin) | B_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER A_TERMINAL_DISTANCE A_ISOTOPE A_TEXTLABEL | atomchange bondchange merge hadd | ||||
| A_CSP_0H | boolean | Flag for carbon atoms with sp hybridization and no hydrogen substituents | Tcl script | A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp_0h.xpd | ||||
| A_CSP_1H | boolean | Flag for carbon atoms with sp hybridization and one hydrogen substituent | Tcl script | A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp_1h.xpd | ||||
| A_DAYLIGHT_ALIRING_COUNT | short | Number of aliphatic rings the atom is member of, with Daylight definition of aromaticity | countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
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Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE | atomchange bondchange ring | mod_a_daylight_aliring_count.so | |||
| A_DAYLIGHT_ARORING_COUNT | short | Number of aromatic rings the atom is member of, using Daylight aromaticity from R_DAYLIGHT_AROMATIC instead of globally configurable R_AROMATIC | countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
|
Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE | atomchange bondchange ring | mod_a_daylight_aroring_count.so | |||
| A_DAYLIGHT_ARORING_SIZE_BITS | bitset | Bit mask for aromatic ring sizes the atom participates in, using always Daylight aromaticity | ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
|
Compiled C module | R_SIZE R_TYPE B_TYPE A_DAYLIGHT_ARORING_COUNT R_DAYLIGHT_AROMATIC | bondchange ring | mod_a_daylight_aroring_size_bits.so | |||
| A_DEGREE | byte | Number of explicit valences around atom. This corresponds to the absurdly impractical and dangerous 'D' attribute in SMILES and should be avoided to be used for anything else. | ignorequeryatoms: { value: 0 description: If set, query atoms are not counted to the degree value in the atom neighbor sphere datatype: boolean} ignorestereoh: { value: 1 description: If set, non-implicit H at stereo centers is treated as implicit, assuming it was only added for stereochemistry encoding, not to make a structural statement datatype: boolean} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT A_LABEL_STEREO | atomchange bondchange | mod_a_degree.so | |||
| A_DISTANCE | floatvector | Interatomic 3D distances | (builtin) | A_XYZ | atomchange bondchange stereochange 3drelative shuffle hadd | |||||
| A_DL_STEREO | byte | Stereo descriptor for atoms, based on D/L nomenclature rules | L=-1:undef=0:D=1 |
(builtin) | atomchange bondchange | |||||
| A_EC_FRAGMENTS | dataset | Structure fragments associated with the different spheres of the EC hashcode Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction) |
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int} debug: { value: 0 description: If set, print debug info datatype: boolean} usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean} includehydrogens: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean} lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange atom bond | mod_a_ec_fragments.so | |||
| A_EC_HASH | uint64vector | Base atoms hashcodes for ECFP-style fingerprints. Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction) |
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int} debug: { value: 0 description: If set, print debug info datatype: boolean} usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean} includeh: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean} properties: { value: A_ELEMENT A_SUBSTITUENT_COUNT A_HCOUNT description: List of properties to use in the atom seed, values cast to integer datatype: string constraints: propertylist} boolproperties: { value: A_RING_COUNT description: List of properties to use in the atom seed, values cast to boolean datatype: string constraints: propertylist} exprproperties: { value: A_EQUILIBRATED_CHARGE*10 description: List of property expressions to use in the atom seed, values cast to int datatype: string constraints: list} lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange atom bond | mod_a_ec_hash.so | |||
| A_ELEMENT | byte | Atomic number (periodic table of elements index, H=1) | (builtin) | A_SYMBOL | never | |||||
| A_ENOLIZABLE | boolean | An enolizable atom by the Lhasa definition. An enolizable atom must be saturated, non-bridgehead, have at least one hydrogen and be activated by a withdrawing bond. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 48 | Compiled C module | A_TYPE A_ELEMENT A_BRIDGEHEAD A_HCOUNT B_TYPE B_ORDER A_FG_SUBSTITUENTS | atomchange bondchange atom bond | mod_a_enolizable.so | |||
| A_EQUILIBRATED_CHARGE | float | Equilibrated nominal charge | fixnoxides: { value: 1 datatype: string}
|
(builtin) | B_TYPE A_FORMAL_CHARGE A_PICENTER | atomchange bondchange hadd | ||||
| A_EXPLICIT_VALENCE | byte | Sum of bond orders of bonds which do not lead to implicit atoms (property A_IMPLICIT). Use with extreme caution, this is not a generally useful property. This maps to the "nbonds" property in Bruns/Watson query processing. | ignoreallh: { value: 1 description: If set, all hydrogens are assumed to be implicit datatype: boolean}
|
Compiled C module | B_TYPE B_ORDER A_IMPLICIT A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_a_explicit_valence.so | |||
| A_EXTENDED_GROUPHASH | uint64 | Perturbed group hashcode | usebondorder: { value: aro description: Whether to mix in bond orders within group: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string} usesubstitution: { value: none description: none: pure group, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string} |
Compiled C module | A_TYPE A_FRAMEWORK A_ELEMENT | atomchange bondchange groupchange hadd group | mod_a_extended_grouphash.so | |||
| A_EXTENDED_GROUPHASH_GROUP | index | Hash group id index for atom group hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *group* indexing, the ensemble part is used as in A_HASHGROUP for global grouping. | Compiled C module | A_GROUP_NUMBER A_EXTENDED_GROUPHASH | atomchange bondchange groupchange merge hadd group | mod_a_extended_grouphash_group.so | ||||
| A_EXTENDED_RINGHASH | uint64 | Perturbed ringsystem hashcode | usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string} usesubstitution: { value: none description: none: pure ring system, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string} |
Compiled C module | A_TYPE A_FRAMEWORK A_ELEMENT | atomchange bondchange hadd ring | mod_a_extended_ringhash.so | |||
| A_EXTENDED_RINGHASH_GROUP | index | Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping. | Compiled C module | A_RINGSYSTEM_NUMBER A_EXTENDED_RINGHASH | atomchange bondchange merge hadd ring | mod_a_extended_ringhash_group.so | ||||
| A_FG_CHECK | bitvector | Functional group test (for example, in Patran FGS/FGNOT clauses) of atoms as per the LHASA definition, If the atom is a carbon atom and the FG is carbon-centric, this is the A_FG_PARTICIPATION flag, otherwise a test for A_FG_SUBSTITUIENTS>1 |
none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide 1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving |
ketone boolean aldehyde boolean acid boolean thioacid boolean ester boolean amide*1 boolean amide*2 boolean amide*3 boolean sulfonamide*1 boolean sulfonamide*2 boolean sulfonamide*3 boolean carbonium boolean isocyanate boolean acid*halide boolean thioester boolean amine*3 boolean aziridine boolean amine*2 boolean amine*1 boolean nitroso boolean diazo boolean haloamine boolean hydrazone boolean oxime boolean imine boolean thiocyanate boolean isocyanide boolean nitrile boolean azo boolean hydroxylamine boolean nitro boolean enamine boolean amine*oxide boolean thiol boolean episulfide boolean sulfide boolean sulfoxide boolean sulfone boolean c*sulfonate boolean anhydride boolean lactam boolean phosphine boolean phosphonate boolean epoxide boolean ether boolean peroxide boolean alcohol boolean enol*ether boolean nitrite boolean o*sulfonate boolean fluoride boolean chloride boolean bromide boolean iodide boolean gem*dihalide boolean trihalide boolean acetylene boolean olefin boolean vic*dihalide boolean halohydrin boolean glycol boolean hydrate boolean hemiketal boolean ketal boolean hemiacetal boolean acetal boolean azide boolean disulfide boolean allene boolean vinylsilane boolean lactone boolean vinylw boolean vinyld boolean esterx boolean amidz boolean methylene boolean carbonyl boolean carboxyl boolean halide boolean amine boolean amide boolean sulfonamide boolean selenide boolean trialkylsilyl boolean trialkylsiloxy boolean silylenolether boolean n*urea*h boolean n*urea*c boolean carbamate*h boolean carbamate*c boolean o*carbamate boolean n*carbamate boolean o*carbonate boolean dithioacetal boolean dithioketal boolean requested boolean withdrawing boolean expandable*withdrawing boolean nonexpandable*withdrawing boolean donating boolean leaving boolean good*leaving boolean |
Compiled C module | A_FG_PARTICIPATION A_FG_SUBSTITUENTS A_ELEMENT A_TYPE | atomchange bondchange atom bond | mod_a_fg_check.so | ||
| A_FG_PARTICIPATION | bitvector | Functional group participation of atoms as per the LHASA definition | none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide,sulphonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving:origin |
ketone boolean aldehyde boolean acid boolean thioacid boolean ester boolean amide*1 boolean amide*2 boolean amide*3 boolean sulfonamide*1 boolean sulfonamide*2 boolean sulfonamide*3 boolean carbonium boolean isocyanate boolean acid*halide boolean thioester boolean amine*3 boolean aziridine boolean amine*2 boolean amine*1 boolean nitroso boolean diazo boolean haloamine boolean hydrazone boolean oxime boolean imine boolean thiocyanate boolean isocyanide boolean nitrile boolean azo boolean hydroxylamine boolean nitro boolean enamine boolean amine*oxide boolean thiol boolean episulfide boolean sulfide boolean sulfoxide boolean sulfone boolean c*sulfonate boolean anhydride boolean lactam boolean phosphine boolean phosphonate boolean epoxide boolean ether boolean peroxide boolean alcohol boolean enol*ether boolean nitrite boolean o*sulfonate boolean fluoride boolean chloride boolean bromide boolean iodide boolean gem*dihalide boolean trihalide boolean acetylene boolean olefin boolean vic*dihalide boolean halohydrin boolean glycol boolean hydrate boolean hemiketal boolean ketal boolean hemiacetal boolean acetal boolean azide boolean disulfide boolean allene boolean vinylsilane boolean lactone boolean vinylw boolean vinyld boolean esterx boolean amidz boolean methylene boolean carbonyl boolean carboxyl boolean halide boolean amine boolean amide boolean sulfonamide boolean selenide boolean trialkylsilyl boolean trialkylsiloxy boolean silylenolether boolean n*urea*h boolean n*urea*c boolean carbamate*h boolean carbamate*c boolean o*carbamate boolean n*carbamate boolean o*carbonate boolean dithioacetal boolean dithioketal boolean requested boolean withdrawing boolean expandable*withdrawing boolean nonexpandable*withdrawing boolean donating boolean leaving boolean good*leaving boolean origin boolean |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER A_FORMAL_CHARGE | atomchange bondchange atom bond | mod_a_fg_participation.so | ||
| A_FG_SUBSTITUENTS | shortvector | Functional group substituents on carbon as per the LHASA definition | ketone short aldehyde short acid short thioacid boolean ester short amide*1 short amide*2 short amide*3 short sulfonamide*1 boolean sulfonamide*2 boolean sulfonamide*3 boolean carbonium short isocyanate short acid*halide short thioester short amine*3 short aziridine short amine*2 short amine*1 short nitroso short diazo short haloamine short hydrazone short oxime short imine short thiocyanate short isocyanide short nitrile short azo short hydroxylamine short nitro short enamine short amine*oxide short thiol short episulfide short sulfide short sulfoxide short sulfone short c*sulfonate short anhydride short lactam short phosphine short phosphonate short epoxide short ether short peroxide short alcohol short enol*ether short nitrite short o*sulfonate short fluoride short chloride short bromide short iodide short gem*dihalide short trihalide short acetylene short olefin short vic*dihalide short halohydrin short glycol short hydrate short hemiketal short ketal short hemiacetal short acetal short azide short disulfide short allene short vinylsilane short lactone short vinylw short vinyld short esterx short amidz short methylene short carbonyl short carboxyl short halide short amine short amide short sulfonamide boolean selenide short trialkylsilyl short trialkylsiloxy short silylenolether short n*urea*h short n*urea*c short carbamate*h short carbamate*c short o*carbamate short n*carbamate short o*carbonate short dithioacetal short dithioketal short requested short withdrawing short expandable*withdrawing short nonexpandable*withdrawing short donating short leaving short good*leaving short |
Compiled C module | A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE | atomchange bondchange atom bond | mod_a_fg_substituents.so | |||
| A_FLAGS | bitset | Display attributes for atom like boxing, marks, Fisher center | ^none:starred,star:inverted,inverse,invert:boxed:groupbox1,gbox1:groupbox2,gbox2:invisible,invis:secondary:bold,dgrey,dgray,dark:greyed,mgrey,mgray,medium:italic,light,lgrey,lgray:fischer,fischercenter,fisher:nosym,nosymbol:circled,circle:alpha:beta:gamma:label:top:bottom:left:right:core:ligand,coreligand:highlight:diamond:triangle:cross:active:nostereo:protected:interfering:participating:hshowhetero:hshowterminal:hshowall:ballstick:capped:spacefill:wireframe:selected:expanded:spare1:spare2:spare3:node:symbol:insuperatom,insuper:hidden:firsthidden:groupsymbol |
starred boolean inverted boolean boxed boolean groupbox1 boolean groupbox2 boolean invisible boolean secondary boolean bold boolean greyed boolean italic boolean fischercenter boolean nosymbol boolean circled boolean alpha boolean beta boolean gamma boolean label boolean top boolean bottom boolean left boolean right boolean core boolean ligand boolean highlight boolean diamon boolean triangle boolean cross boolean active boolean nostereo boolean protected boolean interfering boolean participating boolean hshowheterolboolean boolean hshowterminal boolean hshowall boolean ballstick boolean capped boolean spacefill boolean wireframe boolean selected boolean expanded boolean spare1 boolean spare2 boolean spare3 boolean node boolean symbol boolean insuperatom boolean hidden boolean firsthidden boolean groupsymbol boolean |
(builtin) | never | ||||
| A_FMC0 | float | Fragment molecular connectivity level #0 | Compiled C module | atomchange bondchange | mod_a_fmc0.so | |||||
| A_FMC1 | float | Fragment molecular connectivity level #1 | Compiled C module | atomchange bondchange | mod_a_fmc1.so | |||||
| A_FMC2 | float | Fragment molecular connectivity level #2 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc2.so | ||||
| A_FMC3 | float | Fragment molecular connectivity level #3 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc3.so | ||||
| A_FMC4 | float | Fragment molecular connectivity level #4 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc4.so | ||||
| A_FMC5 | float | Fragment molecular connectivity level #5 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc5.so | ||||
| A_FORMAL_CHARGE | byte | Nominal atom charge | (builtin) | A_FREE_ELECTRONS | never | |||||
| A_FRACTIONAL_XYZ | floatvector | Fractional/reciprocal atomic 3D-coordinates. This is used in the CIF I/O module. | x float y float z float |
A_XYZ E_UNIT_CELL | atomchange bondchange stereochange merge 3drelative 3dabsolute | |||||
| A_FRAGMENT_ID | string | Fragment identifier for original atom source. This is used in D_CHEMDRAW_PAGE. | never | |||||||
| A_FRAMEWORK | byte | Framework classification 0=ring, 1=sidechain, 2=linker | ring:sidechain,chain:linker,bridge |
(builtin) | B_TYPE | atomchange bondchange hadd ring | ||||
| A_FREE_ELECTRONS | byte | Number of free electrons | (builtin) | A_FORMAL_CHARGE | never | |||||
| A_FREE_VALENCE | byte | Number of free valences | (builtin) | A_ELEMENT A_FORMAL_CHARGE A_VALENCE | atomchange bondchange hadd | |||||
| A_F_COUNT | int | Count the number of fluorine substituents around a central atom | Tcl script | A_ELEMENT A_TYPE | atomchange bondchange | a_f_count.xpd | ||||
| A_GENERIC_FORCEFIELD_TYPE | string | Generic Force Field atom type- Used in the IFF I/O module. Computation of this property is linked to various program-specific variants, which can be selected by a parameter. | forcefield: { value: none description: If set to none, use the first type alread present on structure, or fallback to Sybyl2 as last resort enumeration: tinker:macromodel:sybyl2:sybyl:alchemy:babel datatype: string}
|
Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_generic_forcefield_type.xpd | |||
| A_GEOMETRY | byte | Enumerated value of the geometry of an atom (terminal, tetrahedral, etc.) | none:terminal,end,s:linear,sp:trigonalplanar,planar,sp2:tetrahedral,tetraeder,sp3:bipyramidal,tbp,trigonalbipyramidal,bipyramid,sp3d,dsp3:sawhorse,seesaw:tshaped,t-shaped:octahedral,octaeder,sp3d2,d2sp3:squarepyramidal:squareplanar,sp2d,dsp2:other |
Compiled C module | A_VERTEX_DEGREE A_FREE_ELECTRONS A_TYPE B_TYPE A_FORMAL_CHARGE A_ISAROMATIC A_PICENTER A_IUPAC_GROUP | atomchange bondchange | mod_a_geometry.so | |||
| A_GROUP_FRAMEWORK | byte | Framework classification 0=group, 1=sidechain, 2=linker, using groups as core elements instead of rings as in standard A_FRAMEWORK | group:sidechain:linker |
Compiled C module | B_TYPE | atomchange bondchange groupchange hadd group | mod_a_group_framework.so | |||
| A_GROUP_NUMBER | int | Number (1-indexed group list position) of atoms, with 0 for atoms which are not in a group. This property assumes that an atom is only a member in a single group, if any. | Compiled C module | atomchange bondchange groupchange atom bond group | mod_a_group_number.so | |||||
| A_H1_NMRSHIFT | float | Proton NMR shift, measured in ppm. | atomchange bondchange stereochange atom bond | |||||||
| A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY | double | The absolute electrophilic reactivity as computed by a simple Hammet calculation. Used in Lhasa transforms. | delta: { value: 1 datatype: double} rho: { value: -5 datatype: double} |
Compiled C module | A_HUCKEL_PI_ELECTRON_DENSITY | atomchange bondchange pi | mod_a_hammet_absolute_electrophilic_reactivity.so | |||
| A_HAMMET_ABSOLUTE_NUCLEOPHILIC_REACTIVITY | double | The absolute nucleophilic reactivity as computed by a simple Hammet calculation. Used in Lhasa transforms. | delta: { value: 1 datatype: double} rho: { value: -5 datatype: double} |
Compiled C module | A_HUCKEL_PI_ELECTRON_DENSITY | atomchange bondchange pi | mod_a_hammet_absolute_nucleophilic_reactivity.so | |||
| A_HAMMET_DIFFERENTIAL_ELECTROPHILIC_REACTIVITY | double | The differential electrophilic reactivity as computed by a simple Huckel calculation. Used in Lhasa transforms. | Compiled C module | A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY | atomchange bondchange pi | mod_a_hammet_differential_electrophilic_reactivity.so | ||||
| A_HAMMET_RELATIVE_ELECTROPHILIC_REACTIVITY | double | The relative electrophilic reactivity as computed by a simple Huckel calculation, expressed as percent of max reactivity in the structure. Used in Lhasa transforms. | Compiled C module | A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY | atomchange bondchange pi | mod_a_hammet_relative_electrophilic_reactivity.so | ||||
| A_HAMMET_RELATIVE_NUCLEOPHILIC_REACTIVITY | double | The relative nucleophilic reactivity as computed by a simple Huckel calculation, expressed as percent of max reactivity in the structure. Used in Lhasa transforms. | Compiled C module | A_HAMMET_ABSOLUTE_NUCLEOPHILIC_REACTIVITY | atomchange bondchange pi | mod_a_hammet_relative_nucleophilic_reactivity.so | ||||
| A_HASH | uint64 | Basic atomic hashcode | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 0 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE | atomchange bondchange hadd | ||||
| A_HASHGROUP | index | Hash group id index for basic hash code | (builtin) | A_MOL_NUMBER A_HASH | atomchange bondchange merge hadd | |||||
| A_HASH_STEREO | byte | Stereo descriptor for atoms, based on atomic hashcodes | M=-1:undef=0:P=1 |
useisotope: { value: 0 datatype: string}
|
(builtin) | A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange hadd | |||
| A_HCOUNT | byte | Number of classically bonded hydrogen atoms | useimplicith: { value: 0 datatype: string}
|
(builtin) | B_TYPE A_ELEMENT | atomchange bondchange hadd | ||||
| A_HEAVY_SUBSTITUENT_COUNT | byte | Number of classically bonded non-hydrogen atoms | (builtin) | B_TYPE A_ELEMENT | atomchange bondchange | |||||
| A_HETERO_SUBSTITUENT_COUNT | byte | Count the number of hetero (not C or H) ligands around a central atom | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange | mod_a_hetero_substituent_count.so | ||||
| A_HSPECIAL | byte | Flag for hydrogen atoms plotted with symbols by common agreement: 0: no, 1:yes, 2:at cis/trans db, 3:at stereocenter, but not wedge | never: { value: 0 datatype: string}
|
(builtin) | B_STEREOINFO A_STEREOINFO A_ELEMENT A_TERMINAL_DISTANCE B_ORDER A_CSPECIAL B_FLAGS A_FLAGS A_ISOTOPE A_RING_COUNT | atomchange bondchange merge hadd | ||||
| A_HUCKEL_ELECTROPHILIC_LOCALIZATION_ENERGY | double | The electrophilic localization energy as computed by a simple Huckel calculation. Used in Lhasa transforms. | Compiled C module | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | mod_a_huckel_electrophilic_localization_energy.so | ||||
| A_HUCKEL_HOMO_COEFFICIENT | double | The HOMO coefficient as computed by a simple Huckel method. Used in Lhasa transforms. | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | ||||||
| A_HUCKEL_HOMO_ENERGY | double | The LUMO energy of the pi system on this atom as computed by a simple Huckel method | Compiled C module | P_HUCKEL_HOMO_ENERGY | atomchange bondchange pi | mod_a_huckel_homo_energy.so | ||||
| A_HUCKEL_LUMO_COEFFICIENT | double | The LUMO coefficient as computed by a simple Huckel method. Used in Lhasa transforms. | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | ||||||
| A_HUCKEL_LUMO_ENERGY | double | The LUMO energy of the pi system on this atom as computed by a simple Huckel method | Compiled C module | P_HUCKEL_LUMO_ENERGY | atomchange bondchange pi | mod_a_huckel_lumo_energy.so | ||||
| A_HUCKEL_NUCLEOPHILIC_LOCALIZATION_ENERGY | double | The nucleophilic localization energy as computed by a simple Huckel calculation. Used in Lhasa transforms. | Compiled C module | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | mod_a_huckel_nucleophilic_localization_energy.so | ||||
| A_HUCKEL_PI_ELECTRON_DENSITY | double | Pi elektron density (sum of electron count in occupied orbitals multiplied with atomic MO coefficient) according to plain Huckel model | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange atom bond pi | ||||||
| A_HYBRIDIZATION | byte | Hybridization of atom | none:s:sp3:sp2:sp:sp3d:sp3d2 |
Compiled C module | never | mod_a_hybridization.so | ||||
| A_HYDROGENS_NEEDED | byte | Number of hydrogen atoms missing to fill up to standard valency | maxsulphurvalence: { value: 2 datatype: string} maxchlorinevalence: { value: 1 datatype: string} maxphosphorvalence: { value: 3 datatype: string} hypervalentaddition: { value: 0 datatype: string} |
(builtin) | B_TYPE A_IUPAC_GROUP A_FORMAL_CHARGE A_FREE_ELECTRONS A_VALENCE A_RADICAL | atomchange bondchange shuffle | ||||
| A_HYDROGEN_BONDING | byte | Classification of H-Bonding Donor/Acceptor Potential | none:acidic:donor:acceptor:basic |
Compiled C module | A_FORMAL_CHARGE A_ELEMENT B_TYPE B_ORDER A_FREE_ELECTRONS A_SIGMA_CHARGE A_ISAROMATIC R_AROMATIC A_IUPAC_GROUP | atomchange bondchange | mod_a_hydrogen_bonding.so | |||
| A_IMPLICIT | boolean | Flag for implicitly added atoms. This information is internally maintained by hydrogen addition etc. subroutines. The compute function copies this internal data into a property. | Compiled C module | atomchange | mod_a_implicit.so | |||||
| A_IMPLICIT_HCOUNT | byte | Number of implicit (automatically added) hydrogens around atom. This is computed from the internal hydrogen origin memory of structures. If this information has been deleted, the result is always zero. | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange | mod_a_implicit_hcount.so | ||||
| A_INAMIDE | boolean | Flags for atoms in amide-type system (set for n,o,c). Or'ed bits 'extended 1' allow C=S, 'extended 2' allow C=N | extended: { value: 1 datatype: string}
|
(builtin) | A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||
| A_INDEX | int | Index of atom in internal atom list, not ordered into blocked molecules | Compiled C module | atomchange bondchange merge shuffle hadd atom | mod_a_index.so | |||||
| A_ISAROMATIC | boolean | Flag whether atom is member of aromatic ring or not | (builtin) | R_AROMATIC R_TYPE | atomchange bondchange ring | |||||
| A_ISMETAL | boolean | Flag for metal atoms, as determined by the column in the built-in element table, where the criterion could be modified if necessary. | Compiled C module | A_ELEMENT | atomchange bondchange | mod_a_ismetal.so | ||||
| A_ISOLATED_RING | boolean | Flag indicating atom is part of an isolated ring | Compiled C module | Y_RING_COUNT | atomchange bondchange atom bond | mod_a_isolated_ring.so | ||||
| A_ISOTOPE | short | Absolute isotopic mass (12C=12.0000) | never | |||||||
| A_ISOTOPE_HASH | uint64 | Atomic hashcode with isotopes | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 1 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange hadd | ||||
| A_ISOTOPE_HASHGROUP | index | Hash group id index for isotope hash code | (builtin) | A_MOL_NUMBER A_ISOTOPE_HASH | atomchange bondchange merge | |||||
| A_ISOTOPE_LABELLING_DEGREE | float | Isotope labelling degree (0.0..1.0) | A_ISOTOPE | atomchange | ||||||
| A_ISOTOPE_STEREO_HASH | uint64 | Stereospecific and isotope-aware atomic hashcode | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 1 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange stereochange hadd | ||||
| A_ISOTOPE_STEREO_HASHGROUP | index | Hash group id index for stereospecific isotope hash code | (builtin) | A_MOL_NUMBER A_ISOTOPE_STEREO_HASH | atomchange bondchange merge | |||||
| A_IS_CHARGED_METAL_ION | boolean | Boolean flag indicating an unbonded, charged metal ion | Tcl script | A_TYPE A_ELEMENT A_FORMAL_CHARGE | atomchange bondchange | a_is_charged_metal_ion.xpd | ||||
| A_IUPAC_GROUP | byte | New IUPAC group number in range 1-18, 19=lanthanides, 20=actinides | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_JSTDATA | intquad | Extended fields in JST-type molfile | atomchange bondchange stereochange merge | |||||||
| A_LABEL | int | Arbitrary atom label | (builtin) | never | ||||||
| A_LABELCOLOR | color | X11 style color name of atom labels | Tcl script | never | a_labelcolor.xpd | |||||
| A_LABEL_STEREO | byte | Stereo descriptor for atoms, based on atomic labels | M,-=-1:undef=0:P,+=1:U,C=2:Z,N=3:X=4 |
(builtin) | never | |||||
| A_LHASA_PATH_LABEL | byte | Path atom label (1-based) for matched Lhasa patterns | X_LHASA_SCORE | atomchange bondchange atom bond | ||||||
| A_LIGAND_ANGLE_SUM | float | Allred/Rochow ligand angle sum for phosphor atoms | Tcl script | atomchange bondchange 3drelative | a_ligand_angle_sum.xpd | |||||
| A_LIGAND_ENEG_SUM | float | Tcl script | atomchange bondchange | a_ligand_eneg_sum.xpd | ||||||
| A_LIGAND_RANK | intvector | Priority-sorted list of ligands around stereocenters according to CIP rules. The vector fields are label values of the stereo-defining root substituents (which may be distand in case of atom-stereogenic allenes). The ligand with highest priority is listed first. Stereogenic electron pairs are not listed, and for such compounds there are only three listed ligands on the stereo atom. Atoms without stereo potential have an empty vector. | Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER A_CIP_STEREO B_CIP_STEREO A_LABEL A_ALLENE | atomchange bondchange stereochange hadd | mod_a_ligand_rank.so | ||||
| A_LILLY_SPINACH | boolean | Boolean flag whether the atom is part of what in Eli Lilly lingo is defined "molecular spinach". Atoms which are a ring atom, a ring bridge atom, or connected via a multiple bond to a ring or ring bridge are part of the scaffold and not spinach. | J. Med. Chem. 2012, 55, 9763-9772 | Compiled C module | A_FRAMEWORK B_TYPE B_ORDER | atomchange bondchange atom bond ring | mod_a_lilly_spinach.so | |||
| A_LINEAR_CHAIN_LENGTH | int | The size of the linear-chain-heavy-atoms-only fragment the atom is a member of. Ring atoms or branch atoms have value 0. Hydrogen atoms inherit the value of their bond partner. | Compiled C module | A_TYPE A_RING_COUNT B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange atom bond | mod_a_linear_chain_length.so | ||||
| A_MACROMODEL_TYPE | short | MacroModel atom type. Used for example in the MMD and MAESTRO I/O modules. | none:C1:C2:C3:CA:CB:CC:CD:CE:CF:CM:CP:CR:unused:C0:O2:O3:OA:OM:OW:OP:OQ:unused:O0:N1:N2:N3:NA:NB:NC:ND:N4:N5:NE:NF:NG:NH:NI:NM:NP:N0:H1:H2:H3:H4:H5:unused:unused:unused:H0:S1:SA:SM:S0:P0:B2:B3:F0:Cl:Br:I0:Si:Z0:Lp:00:Li:Na:K0:Rb:Cs:Ca:Ba:Mg:M2:M3:M4:M5:M6:M7:f2:f3:o2:o3:n2:n3:c1:c2:Zn:m3:m4:m5:m6:unused:unused:unused:unused:unused:unused:unused:unused:SP:S2:Cm:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:PI |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | a_macromodel_type.xpd | |||
| A_MAPPING | int | Atom mapping (for example for reactions), linking to same-value A_MAPPING atoms of complementary structure (reagent <-> product), 0 for unmapped atoms. A_MAPPING has no direct relationship to atom labels A_LABEL. | ignoreexpandedcarbon: { value: 0 datatype: string} ignoreexpandedhetero: { value: 0 datatype: string} ignoreexpandedhydrogen: { value: 0 datatype: string} ignoreexpandedalicarbon: { value: 0 datatype: string} ignoreexpandedarocarbon: { value: 0 datatype: string} |
(builtin) | atomchange bondchange merge atom bond reaction | |||||
| A_MAP_STEREO | byte | Atom stereo descriptor based on reaction mapping | M,-=-1:undef=0:P,+=1 |
(builtin) | A_MAPPING | never | ||||
| A_MDL_VALUE | string | Custom atom value in MDL files ('V' data lines in Molfiles) | never | |||||||
| A_MOL_LABEL | int | Label of molecule atom belongs to | (builtin) | A_MOL_NUMBER M_LABEL | atomchange bondchange merge shuffle hadd mol | |||||
| A_MOL_NUMBER | short | Number (index+1) of molecule atom belongs to | (builtin) | B_TYPE | atomchange bondchange merge shuffle hadd | |||||
| A_MORGAN | uint64 | Morgan numbering value (not the atom rank in the Morgan number, this is the full raw value) | includeh: { value: 1 datatype: boolean} useelement: { value: 0 datatype: boolean} |
Compiled C module | A_TYPE B_TYPE A_ELEMENT A_VERTEX_DEGREE | atomchange bondchange hadd bond | mod_a_morgan.so | |||
| A_MORGAN_RANK | int | Ranking of atoms according to Morgan code value (rank 1 has highest rating) | Tcl script | A_MORGAN | atomchange bondchange merge hadd atom bond | a_morgan_rank.xpd | ||||
| A_N15_NMRSHIFT | float | Proton NMR shift, measured in ppm. | atomchange bondchange stereochange atom bond | |||||||
| A_NCBI_MMDB | compound | MMDB source information | mmdb-id int molecule-id int molecule-name stringvector residue-id int residue-name string atom-id int atom-name string |
never | ||||||
| A_NCICADD_NORM_CHARGE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| A_NCICADD_RESONANCE_STEREO_DELETED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| A_NCICADD_TAUTO_STEREO_DELETED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| A_NEIGHBOR_COUNT | byte | Number of ALL bonded neighbor atoms | (builtin) | bondchange hadd | ||||||
| A_NH2_COUNT | int | Count the number of -NH2 substituents around an atom | Tcl script | A_ELEMENT A_HCOUNT | atomchange bondchange | a_nh2_count.xpd | ||||
| A_NMRSHIFT | float | True shift values, computed from shielding parameters and method string | Tcl script | A_SHIELDING | atomchange bondchange stereochange 3drelative | a_nmrshift.xpd | ||||
| A_NORMAL_VIBRATIONS | xyzvector | Raman and IR normal vibrations of the structure | A_XYZ | atomchange bondchange stereochange merge 3drelative mol atom bond | ||||||
| A_OSAWA_C13_NMRSHIFT | float | C13 NMR spectrum chemical shift., as computed by a simple QSAR function. This is defined only for simple alkanes and more a demo property than of practical use. | Osawa, FMC wo mochiita 13C-NMR kagakushifto no yosoku ni kan suru kenkyuu; master thesis; TUT 1993 | Tcl script | A_FMC0 A_FMC1 A_FMC2 A_FMC3 A_FMC4 A_FMC5 | atomchange bondchange | a_osawa_c13_nmrshift.xpd | |||
| A_P31_NMRSHIFT | float | P31 NMR shift values, by default computed from A_SHIELDING shielding parameters | Tcl script | A_SHIELDING | atomchange bondchange stereochange 3drelative | a_p31_nmrshift.xpd | ||||
| A_PATTY_TYPE | string | Programmable atom typer | patternfile: { value: patty.sma datatype: diskfile constraints: readable} trace: { value: 0 datatype: boolean} |
Tcl script | A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange hadd atom bond | a_patty_type.xpd | |||
| A_PHENYL_COUNT | int | Count for the number or ESSSR phenyl rings the atom is part of | Compiled C module | R_TYPE R_AROMATIC R_HETEROATOM_COUNT | atomchange bondchange atom bond ring | mod_a_phenyl_count.so | ||||
| A_PICENTER | byte | Flag for atoms with pi system (1:free electrons, 2:multibond or epair) | (builtin) | A_PSE_ROW A_FREE_ELECTRONS B_TYPE A_FORMAL_CHARGE B_ORDER | atomchange bondchange hadd | |||||
| A_PISYSTEM_ELECTRON_COUNT | short | Number of pi electrons in largest pi system the atom is a member of | Compiled C module | P_ELECTRON_COUNT | atomchange bondchange atom bond pi | mod_a_pisystem_electron_count.so | ||||
| A_PISYSTEM_SIZE | short | Size (atom count) of the largest pi system the atom is a member of | Compiled C module | atomchange bondchange atom bond pi | mod_a_pisystem_size.so | |||||
| A_PI_CHARGE | float | Gasteiger Pi charges | A_TYPE A_SIGMA_CHARGE | atomchange bondchange hadd | ||||||
| A_PI_ELECTRONEGATIVITY | float | Gasteiger Pi Eneg value | A_TYPE A_PI_CHARGE | atomchange bondchange hadd | ||||||
| A_POLARIZABILITY | float | Atom polarizablities by the Kang & Jhon (sic) algorithm | Y. K. Kang, M. S. Jhon, Theor. Chim. Acta 61, 41 (1982) | Compiled C module | A_VB_NEIGHBOR_COUNT A_ELEMENT A_FREE_ELECTRONS A_FORMAL_CHARGE A_ISAROMATIC A_AROCONDENSED | atomchange bondchange | mod_a_polarizability.so | |||
| A_PSE_ROW | byte | Row number in PSE (1 for H,He, 2 for Li ..) | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_QNA_DESCRIPTORS | floatpair | Filimonov/Zakharov/Lagunin/Poroikov QNA atomic descriptors. The p value correlates with partial atomic hardness, and q with electronegativity. The use of the matrix exponent of the adjaceny matrix ensures a decreasing neighbor influence with increasing topological distance. Further literature references: Chemical Research in Toxicology, 2012, 25, 2378-2385, DOI 10.1021/tx300247r SAR and QSAR in Environmental Research, 2009, 20, 679-709, DOI 10.1080/10629360903438370 |
Molecular Informatics 30, 2011, 241-250 | p double q double |
Compiled C module | A_TYPE A_ELEMENT E_EXP_CONNECTIVITY_MATRIX | atomchange bondchange atom bond | mod_a_qna_descriptors.so | ||
| A_QUERY | compound | Atom query attributes | element,std,normal,standard:any,*,?:list,whitelist:excllist,neglist,blacklist:hetero,q:halogen,x:noth,noh:heteroh,qh,notc,noc:metal,m:pull1,y:pull2,z:hdonor,hd:hacceptor,ha:insulator,r:terminator,t,ref,reference:anyh,ah:metalh,mh:halogenh,xh:g,group:gh,grouph:g*,groupx:gh*,grouphx:acy:ach:abc:abh:ayl:ayh:alk:alh:ael:aeh:ahc:ahh:aox:aoh:aam:aah:amox:amoxh:cyc:cyh:cbc:cbh:ary:arh:cal:cah:cel:ceh:chc:chh:har:hah:cxx:cxh:1a:2a:3a:4a:5a:6a:7a:8a:1b:2b:3b:4b:5b:6b:7b:8b:8x:8y:8z:1m:2m:3m:tr:ln:ac,an:4m:nm:alk*,*alk,allalk:alh*,*alh,allalh:chk:hea:hef:het:spinach:spinachh:xspinach:xspinachh:cspinach:cspinachh:spinach2:spinach2h:xspinach2:xspinach2h:cspinach2:cspinach2h ^none:stereo:charge:unsaturated,unsat,insaturated,insat:dontmatch,exclude:aromatic:aliphatic,inaromatic:mustmap:picenter:aroneighbor,aroneighbour:noaroneighbor,noaroneighbour:substituted:unsubstituted:fgneighbor,fgneighbor:nofgneighbor,nofgneighbour:aroneighbor_unmatched,aroneighbour_unmatched:noaroneighbor_unmatched,noaroneighbour_unmatched:substituted_unmatched:unsubstituted_unmatched:fgneighbor_unmatched,fgneighbor_unmatched:nofgneighbor_unmatched,nofgneighbour_unmatched:nostereook:nomappingok:nooverlap:exactchange:noextrah:noextrac:noextrax:stereoinversion,inversion:stereoretention,retention:saturated:branched:linear,chain:nochargeok:explicitzerocharge:noextrarings:filledvalence:unfilledvalence:stereochangeofpresence,changeofpresence:noisotopeok:offpath:rgroup:groupsaturated,gsaturated:groupunsaturated,groupinsaturated,gunsaturated,ginsaturated:groupacyclic,gacyclic:groupmonocyclic,gmonocyclic:grouppolycyclic,gpolycyclic:groupcyclic,gcyclic:groupsimple,groupnotpolycyclic,gsimple,gnotpolycyclic:wbond,withdrawingbond:nowbond,nowithdrawingbond,no_withdrawing_bond,no_wbond:branched:unbranched:tertbranched,tbranched:heterocyclic:carbocylic none:H:He:Li:Be:B:C:N:O:F:Ne:Na:Mg:Al:Si:P:S:Cl:Ar:K:Ca:Sc:Ti:V:Cr:Mn:Fe:Co:Ni:Cu:Zn:Ga:Ge:As:Se:Br:Kr:Rb:Sr:Y:Zr:Nb:Mo:Tc:Ru:Rh:Pd:Ag:Cd:In:Sn:Sb:Te:I:Xe:Cs:Ba:La:Ce:Pr:Nd:Pm:Sm:Eu:Gd:Tb:Dy:Ho:Er:Tm:Yb:Lu:Hf:Ta:W:Re:Os:Ir:Pt:Au:Hg:Tl:Pb:Bi:Po:At:Rn:Fr:Ra:Ac:Th:Pa:U:Np:Pu:Am:Cm:Bk:Cf:Es:Fm:Md:No:Lr |
type byte flags bitset list intvector substituentcount bitset valencecount bitset neighborcount bitset hydrogencount bitset ringsize bitset ringcount bitset rganchor int rgmember int rginstance int rgattach int tclproc string fuzz int query querytree component int heterosubstituentcount bitset rbcount bitset repeat bitset charge bitset pyfunction string ringid int ringsystemid int fgs bitvector fgnot bitvector aliheterosubstituentcount bitset freeelectroncount bitset pielectroncount bitset rgroupid int pathid int altpathid int formula formulamatch piformula formulamatch |
never | |||||
| A_RACEMATE | byte | Racemate distribution of stereocenter | undefined,undef:rac,racemat:pure |
atomchange bondchange | ||||||
| A_RADICAL | byte | Flag for radical center | none,no:singlet:doublet,yes:triplet:quartet:quintet |
(builtin) | A_FREE_ELECTRONS | never | ||||
| A_RADIOACTIVE | boolean | Marker for radioactive isotope labels. | Tcl script | A_ISOTOPE A_ELEMENT | atomchange bondchange atom bond | a_radioactive.xpd | ||||
| A_RECAP_LINKER_TYPE | byte | Connection type on this placeholder atom in the RECAP algorithm. The original paper abuses isotope labels for this. | J. Chem. Inf. Comput. Sci. 1998, 38, 511-522 | none:urea:amide:ester:amines:cyclicamines:ether:olefin:aronitroalicarbon:lactam:arocarbonarocarbon:sulphonamide:aronitroarocarbon |
never | |||||
| A_RENDER_XY | floatpair | Render coordinate of atoms on images, etc. Only set by render functions is specifically requested. | A_XY E_STDBLE A_FLAGS | atomchange bondchange groupchange mol atom bond ring group | ||||||
| A_RESIDUE | compound | Residue information, esp. for proteins from PDB | atomtag string grouptag string groupindex int segmentid string resid string chain string weight double hetatm boolean |
atomchange bondchange | ||||||
| A_RINGHASH | uint64 | Atom hash code for atoms which are part of ring systems | usebondorder: { value: none datatype: string}
|
(builtin) | A_TYPE A_FRAMEWORK A_ELEMENT B_TYPE | atomchange bondchange 3drelative 3dabsolute ring | ||||
| A_RINGHASH_GROUP | index | Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping. | Compiled C module | A_RINGSYSTEM_NUMBER A_RINGHASH | atomchange bondchange merge hadd ring | mod_a_ringhash_group.so | ||||
| A_RINGLABEL | int | Renumbered labels of atoms in ring system- Atoms not in ring get label 0, the ring atoms start with one. The order of the labelled atoms follows their standard atom label rank. | Tcl script | A_LABEL | ring | a_ringlabel.xpd | ||||
| A_RINGS | intvector | Labels of the rings the atom is member in | (builtin) | R_LABEL A_RING_COUNT R_TYPE | atomchange bondchange merge ring | |||||
| A_RINGSYSTEM_NUMBER | int | Number (1-indexed ringsystem list position) of atoms, with 0 for atoms which are not in a ringsystem. | Compiled C module | Y_LABEL | atomchange bondchange atom bond ring | mod_a_ringsystem_number.so | ||||
| A_RINGSYSTEM_SIZE | short | Number of ESSSR rings in the ringsystem the atom is a member of, 0 for chain atoms | Compiled C module | atomchange bondchange ring | mod_a_ringsystem_size.so | |||||
| A_RING_BOND_COUNT | byte | Number of ring bonds atom is participating in | Compiled C module | B_RING_COUNT | bondchange ring | mod_a_ring_bond_count.so | ||||
| A_RING_COUNT | short | Number of simple (non-envelope) rings an atom is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | R_TYPE | atomchange bondchange ring | ||||
| A_RING_HETEROATOM_COUNT_BITS | bitset | A bit is set at bit position n for any ESSSR ring the atom is a member of which has n hetero atoms. Chain atoms have value 0. If the atom is a member of a carbocyclic ESSSR ring, bit position 0 is set. | Compiled C module | R_HETEROATOM_COUNT R_TYPE | atomchange bondchange atom bond | mod_a_ring_heteroatom_count_bits.so | ||||
| A_RING_SIZE_BITS | bitset | Bit mask for ring sizes the atom participates in | ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
|
Compiled C module | R_SIZE R_TYPE B_TYPE A_RING_COUNT | bondchange ring | mod_a_ring_size_bits.so | |||
| A_RING_SUBSTITUENT_SIZE | intpair | Number of atoms and maximum bond distance in ring substituent | size int depth int |
(builtin) | A_FRAMEWORK | ring | ||||
| A_SCIDEX_DATA | dictionary | Scidex-specific atom attribute support for MDL SD-files. Handles data encoded in "S SDX" lines. | atomchange bondchange atom bond | |||||||
| A_SEQUENCE_NUMBER | int | Sequential atom number (trad. atoms only) | (builtin) | A_MOL_NUMBER M_ATOM_RANGE A_TYPE | atomchange bondchange merge shuffle hadd mol | |||||
| A_SHELL_ELECTRONS | byte | Number of shell electrons in unbonded atom | (builtin) | A_ELEMENT A_TYPE | atomchange bondchange | |||||
| A_SHIELDING | float | Isotropic magnetic shielding (NMR spectroscopy). This is a field in the SHARC spectroscopy archive format. | atomchange bondchange stereochange merge 3drelative hadd | |||||||
| A_SHIELD_TENSOR | tensor | Anisotropic magnetic shielding tensor. Used as data field in the SHARC NMR archive format. | atomchange bondchange stereochange merge 3drelative hadd | |||||||
| A_SIGMA_CHARGE | float | Gasteiger sigma charges | Compiled C module | A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 | atomchange bondchange | mod_a_sigma_charge.so | ||||
| A_SIGMA_ELECTRONEGATIVITY | float | Gasteiger sigma electronegativities | A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_SP A_SP2 | atomchange bondchange | ||||||
| A_SIMILARITY_PATTERN | float | Quantitative evaluation of fragment-bit similarity | cmplist: { value: {} datatype: string}
|
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | a_similarity_pattern.xpd | |||
| A_SMALLEST_RING | int | Size of smallest ESSSR ring the atom is a member of (0 for non-ring atoms) | Compiled C module | R_SIZE | ring | mod_a_smallest_ring.so | ||||
| A_SMILES_INDEX | int | Atom index in SMILES string (-1 for implicit atoms not explicitly encoded in the SMILES string). The result data is automatically set when computing E_SMILES, which has many options which influence the atom sequence in the string. | E_SMILES A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL_STEREO B_LABEL_STEREO A_ISOTOPE A_MAPPING A_QUERY B_QUERY | atomchange bondchange merge hadd mol | ||||||
| A_SMILES_RANK | int | Unique SMILES ranking of atoms | Compiled C module | A_ELEMENT B_TYPE A_TYPE B_ORDER A_FORMAL_CHARGE | atomchange bondchange merge hadd | mod_a_smiles_rank.so | ||||
| A_SP | boolean | Flags for atoms forced into sp hybridisation by charge equilibration or aromaticity | useimplicith: { value: 1 datatype: boolean}
|
Compiled C module | A_ELEMENT B_TYPE B_ORDER A_HYDROGENS_NEEDED | atomchange bondchange | mod_a_sp.so | |||
| A_SP2 | boolean | Flags for atoms forced into sp2 hybridisation by charge equilibration or aromaticity | useimplicith: { value: 1 datatype: boolean}
|
Compiled C module | A_FORMAL_CHARGE B_ORDER B_TYPE A_HYDROGENS_NEEDED A_ELEMENT | atomchange bondchange | mod_a_sp2.so | |||
| A_SPAN | float | Largest distance of this atom to any atom in molecule, divided by molecule span | Compiled C module | B_TYPE M_SPAN A_TOPO_DISTANCE | atomchange bondchange hadd atom bond | mod_a_span.so | ||||
| A_SPIRO | byte | Number of spiro ring joins atom is participating in ESSSR ring set | (builtin) | A_RING_COUNT R_TYPE | atomchange bondchange ring | |||||
| A_SSMATCH | int | Ensemble is structure, property data encodes labels of matching substructure atoms, 0 for unmatched parts | sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
|
Tcl script | never | a_ssmatch.xpd | ||||
| A_SSMATCH_COUNT | int | Atom match count for structure matching. This is set on the *structure* ensemble when specific match flags are set in the substructure match routine. | sshandle: { value: {} datatype: substructure}
|
Tcl script | never | a_ssmatch_count.xpd | ||||
| A_SSMATCH_ENVIRONMENT | datatree | Classigied unmatched structure environment of the substructure atoms, i.e. data on the characteristics of the unmatched structure atoms sprouting from the structure atom matched by this substructure atom. Set by a substructure hit option, not directly computable. | atomchange bondchange atom bond | |||||||
| A_STANDARD_GROUP_LABEL | int | Label of group which contains the atoms which form a standard group | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| A_STEREOGENIC | byte | Can this atom be a stereocenter ? | no:maybe:checkno:yes,checkyes:ringct |
(builtin) | atomchange bondchange hadd | |||||
| A_STEREOINFO | byte | Stereo descriptor availability info: 1:Label,2:R/S,4:D/L:8:hash,16:map | ^none,st_none:label,st_label:cip,st_cip:dl,st_dl:hash,st_hash:map,st_map |
(builtin) | A_HASH_STEREO A_LABEL_STEREO A_CIP_STEREO A_DL_STEREO A_MAP_STEREO | atomchange bondchange stereochange | ||||
| A_STEREO_CHANGE | byte | Stereo change during course of reaction | unknown:inversion:retention:changeofpresence |
atomchange bondchange atom bond | ||||||
| A_STEREO_GROUP | short | MDL-style stereo group. The enumeration values correspond to the official MDL names of these groups. They are read and set by SDF3000/RXN3000 file format modules, and also used in PubChem I/O via ASN. | abs=99:or15=-15:or14=-14:or13=-31:or12=-12:or11=-11:or10=-10:or9=-9:or8=-8:or7=-7:or6=-6:or5=-5:or4=-4:or3=-3:or2=-2:or1=-1:none=0:&1,and1=1:&2,and2=2:&3,and3=3:&4,and4=4:&5,and5=5:&6,and6=6:&7,and7=7:&8,and8=8:&9,and9=9:&10,and10=10:&11,and11=11:&12,and12=12:&13,and13=13:&14,and14=14:&15,and15=15 |
A_TYPE B_TYPE | atomchange bondchange stereochange | |||||
| A_STEREO_HASH | uint64 | Stereospecific basic atomic hashcode | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 0 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE | atomchange bondchange stereochange hadd | ||||
| A_STEREO_HASHGROUP | index | Hash group id index for basic stereospecific hash code | (builtin) | A_MOL_NUMBER A_STEREO_HASH | atomchange bondchange merge hadd | |||||
| A_STMATCH | int | Ensemble is substructure, property data encodes labels of matching structure atoms, 0 for unmatched parts | sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
|
Tcl script | never | a_stmatch.xpd | ||||
| A_STMATCH_COUNT | int | Atom match count for structure matching. This is set on the *substructure* ensemble when specific match flags are set in the substructure match routine. | sthandle: { value: {} datatype: structure}
|
Tcl script | never | a_stmatch_count.xpd | ||||
| A_SUBSTITUENT_COUNT | int | Count the number of non-H neighbors around a central atom | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange | mod_a_substituent_count.so | ||||
| A_SUBSTITUENT_VECTOR | float | Angle of the mid of the largest gap in the 2D layout of the substituent sphere | excludeatoms: { value: {} datatype: string}
|
(builtin) | A_XY | atomchange bondchange hadd | ||||
| A_SUPERATOMSTRING | string | Descriptive string for atoms and especially superatoms | never | |||||||
| A_SUPERATOM_SSMATCH | string | A_SUPERATOMSTRING of matching substructure superatom, empty for unmatched parts. This is set by the substructure match routine if suitable flags are set. | sshandle: { value: {} datatype: structure}
|
Tcl script | never | a_superatom_ssmatch.xpd | ||||
| A_SURFACE_AREA | double | Estimated surface area from simple intersection of bonded VdW spheres on A_XYZ coordinates | P. Labute, Methods in Molecular Biology, 275, 261ff | vdwscale: { value: 0.8 description: scaling parameter for VdW radii datatype: double} bondsonly: { value: 1 description: if set, only compute sphere intersections of bonded atoms datatype: boolean} |
Compiled C module | A_XYZ A_TYPE A_ELEMENT A_ISAROMATIC A_VDW_RADIUS | atomchange bondchange 3dabsolute hadd atom bond | mod_a_surface_area.so | ||
| A_SURFACE_SPHERE_RADIUS | float | Radius of sphere used for surface calculation | A_XYZ | atomchange bondchange stereochange 3drelative | ||||||
| A_SYBYL2_TYPE | shortstring | Atom type as used in the Sybyl mol2 format | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_sybyl2_type.xpd | ||||
| A_SYBYL_TYPE | byte | Atom type as used in the Sybyl mol format (version 1, not mol2) | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_sybyl_type.xpd | ||||
| A_SYMBOL | shortstring | Atomic symbol | querysymbol: { value: ? datatype: string}
|
(builtin) | A_ISOTOPE A_ELEMENT A_QUERY | never | ||||
| A_SYMVISIBLE | boolean | Flag for atoms typically plotted with symbol | (builtin) | A_HSPECIAL A_CSPECIAL A_TYPE A_ELEMENT A_FLAGS | atomchange bondchange | |||||
| A_TAUTOMER_SYSTEM | int | Tautomer system ID of the atoms. Atoms outside any tautomer system receive ID 0, the rest of the systems are numbered starting with one. | Compiled C module | B_ISTAUTOMERIC | atomchange bondchange atom bond | mod_a_tautomer_system.so | ||||
| A_TERMINAL_DISTANCE | short | Number of bonds from terminal atom (0 if itself terminal) | (builtin) | B_TYPE | atomchange bondchange | |||||
| A_TEXTLABEL | compound | Arbitrary textual atom label plus alignment info for plots | {} @above:left:center:right:below |
label string align byte |
level: { value: 0 datatype: string}
|
(builtin) | never | |||
| A_TINKER_TYPE | short | Atom type as used in the Tinker xyz format | forcefield: { value: none datatype: string}
|
Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_tinker_type.xpd | |||
| A_TOPO_DISTANCE | shortvector | Topological distance matrix (minimum number of bonds between atoms) | bondclasses: { value: VB datatype: string}
|
Compiled C module | B_TYPE | bondchange | mod_a_topo_distance.so | |||
| A_TOTAL_CHARGE | float | Atomic charge on Sigma and Pi systems | (builtin) | A_TYPE A_ELEMENT B_TYPE B_ORDER A_SIGMA_CHARGE A_PI_CHARGE | atomchange bondchange | |||||
| A_TRAJECTORY | xyzvector | 3D atomic path trajectory, for example from a molecular modelling study. This property is for example used in the I/O modules for the GROMACS, XBSA, XYZ and GHEMICAL formats. | A_TYPE B_TYPE B_ORDER A_ELEMENT | atomchange | ||||||
| A_TRANSFORM_STATUS | byte | Atom status as result of SMIRKS transformation. None: not matched in transform, matched: matched, but unchanged, changed: element or attribute changed, new: fragment introduced by transform | none:matched:changed:new |
atomchange bondchange atom bond | ||||||
| A_TYPE | short | Classification, 0:Undef,1:Normal,2:Search,4:Epair,8:3DPoint,16:Super,32:Deloc,64:Polymer,128:Annotation,256:Open,512:Enzyme,1024:Unspecified | ^undef:normal,element:search,query:epair,electron,ep,lp:3dpoint,bq,du:super,superatom:anchor,delocalized,deloc,@:polymer,poly:annotation,annot:open:enzyme,e,protein:unspecified |
never | ||||||
| A_UNDEF_FLOAT1 | float | Some undefined atom property read from file formats with anonymous atom data | atomchange bondchange stereochange merge 3drelative 3dabsolute | |||||||
| A_UNSATURATION | byte | Sum of bond orders in excess of one of all non-aromatic bonds atom is participating in | aroisunsaturated: { value: 1 description: If set, aromatic bonds count as unsaturated datatype: boolean}
|
Compiled C module | A_TYPE B_TYPE B_ORDER B_ISAROMATIC | atomchange bondchange | mod_a_unsaturation.so | |||
| A_VALD | double | Molconn-Z atom value parameter | never | |||||||
| A_VALENCE | byte | Number of classical bond valences | (builtin) | B_ORDER B_TYPE | bondchange hadd | |||||
| A_VAMP_CHARGE | float | Atomic Charge as computed by the Vamp program. This is computed indireclty by requesting computation of heat for formation via Vamp (property E_HEAT_OF_FORMATION). | A_XYZ | atomchange bondchange | ||||||
| A_VB_NEIGHBOR_COUNT | byte | Number of classically bonded neighbor atoms | (builtin) | B_TYPE | bondchange hadd | |||||
| A_VDW_INTERACTION | floatvector | Atom-by-atom nonbonding interaction coefficients, dependent on the elements of an atom pair. The result s a float vector on each atom. The vector length is the number of atoms. The element value at each index is computed by formula hardness(a1)*hardness(a2).pow(VdwBumperRad(element1)+VdWBumperRad(element2),12). The atom hardness value is either the standard atom hardness (default 0.3) or a special hydrogen hardness (default 0.09). The diagonals are set to 0, and interactions to non-standrd atoms to -1. Note that is is only a helper property. it is not dependen on the actual atomic coordinates. It is used by the computation functions of properties E_NONBONDING_ENERGY and E_CONFORMER_ENERGY. |
stdhardness: { value: 0.30 datatype: double} hydrogenhardness: { value: 0.09 datatype: double} |
Compiled C module | A_TYPE A_ELEMENT | atomchange atom | mod_a_vdw_interaction.so | |||
| A_VDW_RADIUS | float | Default van-der-Waals radius | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_VECTOR | floatvector | Directional 3D vector originating from atoms, generic purpose | atomchange bondchange 3drelative 3dabsolute | |||||||
| A_VERTEX_DEGREE | byte | Number of neighbors which are real atoms and are connected by vb or complex bonds | Compiled C module | A_TYPE B_TYPE | atomchange bondchange hadd | mod_a_vertex_degree.so | ||||
| A_VIRTUAL_HCOUNT | byte | Sum of actual hydrogen count (A_HCOUNT) and hydrogens needed for full set (A_HYDROGENS_NEEDED) | Compiled C module | A_HCOUNT A_HYDROGENS_NEEDED | atomchange bondchange atom bond | mod_a_virtual_hcount.so | ||||
| A_VORONOI_COLOR | color | Color of Voronoi background cells in 2D structure plots | Tcl script | atomchange bondchange atom bond | a_voronoi_color.xpd | |||||
| A_VORONOI_POLYGON | xyvector | Voronoi polygon around 2D display of atom | polygonsonly: { value: 1 datatype: boolean} adddummies: { value: 1 datatype: boolean} extradummies: { value: 1 datatype: boolean} debug: { value: 0 datatype: boolean} |
Compiled C module | A_XY | never | mod_a_voronoi_polygon.so | |||
| A_WATERMARK_SENSITIVITY | float | Guestimated sensitivity of overall compound energy on atom movement for watermarking | datafile: { value: a_watermark_sensitivity.dat datatype: diskfile constraints: readable}
|
Tcl script | A_ELEMENT A_TYPE B_ORDER B_TYPE | atomchange bondchange atom bond ring | a_watermark_sensitivity.xpd | |||
| A_WATERMARK_XYZ | floatvector | Atomic 3D-coordinates with watermarking | x float y float z float |
key: { value: LNTSCSWW datatype: string} message: { value: CACTVS Watermark datatype: string} scale: { value: 100 datatype: double} sigma: { value: 1.0 datatype: double} spread: { value: 1 datatype: boolean} markhydrogens: { value: 0 datatype: boolean} alignpmi: { value: 1 datatype: boolean} usesensitivity: { value: 0 datatype: boolean} |
Compiled C module | A_XYZ A_TYPE A_ELEMENT A_WATERMARK_SENSITIVITY | atomchange bondchange stereochange | mod_a_watermark_xyz.so | ||
| A_WEIGHT | float | Atomic weight | allisotopes: { value: 0 datatype: string}
|
(builtin) | A_TYPE A_ISOTOPE A_ELEMENT | atomchange | ||||
| A_WILDMAN_CRIPPEN_TYPE | shortstring | Atom classification according to the Wildman-Crippen scheme (see litref) | J. Chem. Inf. Comput. Sci 1999, 39, 868-873 | Compiled C module | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE B_TYPE B_ORDER B_ISAROMATIC A_IUPAC_GROUP | atomchange bondchange atom bond | mod_a_wildman_crippen_type.so | |||
| A_XSYMBOL | string | Expanded element symbol, lists contain all elements | (builtin) | A_ISOTOPE A_SYMBOL A_ELEMENT A_QUERY | atomchange | |||||
| A_XY | floatpair | Atomic 2D display coordinates | x float y float |
fixbridgeheadstereo: { value: 1 datatype: string} align: { value: none datatype: string} optimize: { value: 1 datatype: string} ringalignment: { value: 1 datatype: string} heteroringalignment: { value: 1 datatype: string} bondlength: { value: 1.0 datatype: string} wedgepairs: { value: none datatype: string} wedgestyle: { value: default datatype: string} pseudo3d: { value: 0 datatype: string} template: { value: {} datatype: string} aspectratio: { value: 1.2 datatype: string} ignorewiggleh: { value: 0 datatype: string} ignoreatoms: { value: {} datatype: string} templatefile: { value: 2dtpl.cbin datatype: string} maxops: { value: 210000 datatype: string} usertemplatefiles: { value: {} datatype: string} hbondfactor: { value: 0.62 datatype: string} hwedgefactor: { value: 0.85 datatype: string} |
(builtin) | never | ||||
| A_XYDISTANCE | floatvector | Atomic distance in 2D plot coordinates | Tcl script | A_XY | atomchange bondchange | a_xydistance.xpd | ||||
| A_XYZ | floatvector | Atomic 3D-coordinates | J. Gasteiger, C. Rudolph, J. Sadowsky, <Automatic Generation of 3D Atomic Coordinates for Organic Molecules>, Tetrahedron Computer Methodol. (1992) | x float y float z float |
usechembiogrid: { value: 0 datatype: string} usepubchem: { value: 1 datatype: string} usecorina: { value: 1 datatype: string} usepubchemqc: { value: 0 datatype: string} maxconformers: { value: 1 datatype: string} corinaoptions: { value: preserve,stergen,r2d,ori,rc,flapn,msc=32,msi=1024,v3000 datatype: string} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS | atomchange bondchange stereochange | mod_a_xyz.so | |
| B_1ST_ATOM | int | First atom of a bond | Tcl script | A_LABEL | atomchange bondchange merge | b_1st_atom.xpd | ||||
| B_2ND_ATOM | int | Second atom of a bond | Tcl script | A_LABEL | atomchange bondchange merge | b_2nd_atom.xpd | ||||
| B_3RING | boolean | Flag indicating bond is part of 3-membered ring | Tcl script | atomchange bondchange | b_3ring.xpd | |||||
| B_4RING | boolean | Flag indicating bond is part of 4-membered ring | Tcl script | atomchange bondchange | b_4ring.xpd | |||||
| B_5RING | boolean | Flag indicating bond is part of 5-membered ring | Tcl script | atomchange bondchange | b_5ring.xpd | |||||
| B_6RING | boolean | Flag indicating bond is part of 6-membered ring | Tcl script | atomchange bondchange | b_6ring.xpd | |||||
| B_7RING | boolean | Flag indicating bond is part of 7-membered ring | Tcl script | atomchange bondchange | b_7ring.xpd | |||||
| B_ALLYLIC | boolean | A allylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to a carbon-carbon double bond, excluding bonds that lead back to the C=C double bond. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | A_ALLYLIC | atomchange bondchange atom bond | |||||
| B_ANGLE | float | Angle of atom triples, encoded as pseudo-bond | (builtin) | A_XYZ | atomchange bondchange 3drelative | |||||
| B_ANNOTATION | string | Bond annoations (stereo information etc.), primarily for 2D plots | style: { value: default datatype: string} stereo: { value: 1 datatype: string} query: { value: 1 datatype: string} label: { value: 0 datatype: string} |
(builtin) | B_FLAGS B_CISTRANS_STEREO B_CIP_STEREO B_LABEL_STEREO B_QUERY | atomchange bondchange stereochange | ||||
| B_ARORING_COUNT | short | Number of aromatic rings the bond is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | R_AROMATIC R_TYPE B_TYPE | atomchange bondchange ring | ||||
| B_ATOMS | intpair | Sequence numbers of atoms of traditional bond, with lower number listed first | property: { value: A_SEQUENCE_NUMBER datatype: string}
|
(builtin) | A_SEQUENCE_NUMBER | atomchange bondchange merge hadd | ||||
| B_BENZYLIC | boolean | A benzylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to an aromatic carbon, excluding bonds that lead back to an aromatic atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | A_BENZYLIC | atomchange bondchange atom bond | |||||
| B_BRICS_FRAGMENTATION | boolean | Bond which would be cut in the BRICS fragmentation method | ChemMedChem 2008, 3, 1503 | atomchange bondchange atom bond | ||||||
| B_BUGGY1 | int | Test case of buggy property computation to test recovery mechanisms | Compiled C module | atomchange bondchange | mod_b_buggy1.so | |||||
| B_BUGGY2 | int | Test case of buggy property computation to test recovery mechanisms | Compiled C module | atomchange bondchange | mod_b_buggy2.so | |||||
| B_BUGGY3 | int | Test case of buggy property computation to test recovery mechanisms | Compiled C module | B_BUGGY1 | atomchange bondchange | mod_b_buggy3.so | ||||
| B_CENTRALITY | double | Centrality rating of the bond (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN) | Compiled C module | A_TOPO_DISTANCE M_SPAN B_TYPE | atomchange bondchange atom bond | mod_b_centrality.so | ||||
| B_CGR_CHANGE | intpair | Bond change when interpreting a CGR-encoded structure. The value are the bond orders on the reagent and product sides. Bonds which are created have a zero value on the reagent side. Bonds which are broken have a zero value on the product side. Bonds which change during CGR interpretation are encoded as 'link' type in B_TYPE, while constant bonds retain their original bond type. This property is set as windfall when computing property X_CGR. | Hoonakker, F.; Lachiche, N.; Varnek, A. Condensed Graph of Reaction: Considas one single pseudo molecule. Int. J. Artif. Intell. Tools 2011, 20, 253–270. | reagent int product int |
atomchange bondchange 3dabsolute atom bond reaction | |||||
| B_CIP_STEREO | byte | Bond chirality descriptor based on CIP (E/Z) rules | E=-1:undef=0:Z=1 |
(builtin) | atomchange bondchange | |||||
| B_CISTRANS_STEREO | byte | Bond chirality descriptor based on cis/trans rules | cis=-1:undef=0:trans=1 |
(builtin) | atomchange bondchange | |||||
| B_CLASSIFICATION | bitset | Simple bond classification bits | ^none:ccbond:chbond:cxbond:xhbond:xxbond:single:double:triple:multiple:aromatic:xaromatic:caromatic:ring:smallring:mediumring:bigring:a-ring:a-aromatic:a-multiple:a-cxbond:b-ring:b-aromatic:b-multiple:b-cxbond |
Compiled C module | B_TYPE B_ORDER A_TYPE A_ELEMENT B_ISAROMATIC B_RINGS R_HETEROATOM_COUNT R_AROMATIC | atom bond ring | mod_b_classification.so | |||
| B_COLOR | colorvector | Bond rendering color | color: { value: white datatype: string}
|
(builtin) | never | |||||
| B_CONJUGATED | boolean | A conjugated bond according to the Lhasa definition. These are bonds which have a spanning atom alpha to a multiply bonded atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | A_CONJUGATED | atomchange bondchange atom bond | |||||
| B_DAYLIGHT_ARORING_COUNT | short | Number of aromatic rings the bond is member of, using explicit Daylight aromaticity in R_DAYLIGHT_AROMATIC instead of aromodel-configurable R_AROMATIC | Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE B_TYPE | atomchange bondchange ring | mod_b_daylight_aroring_count.so | ||||
| B_DELTA_PI_CHARGE | float | Difference of Gasteiger pi-charges of the bond atoms | Tcl script | A_PI_CHARGE B_TYPE | atomchange bondchange | b_delta_pi_charge.xpd | ||||
| B_DELTA_PI_ELECTRONEGATIVITY | float | Difference of Gasteiger pi-electronegativity of the bond atoms. The value is dependent on the order of the atoms in the bond. | Tcl script | A_PI_ELECTRONEGATIVITY B_TYPE | atomchange bondchange | b_delta_pi_electronegativity.xpd | ||||
| B_DELTA_SIGMA_CHARGE | float | Difference of Gasteiger sigma charges of the bond atoms | Tcl script | A_SIGMA_CHARGE B_TYPE | atomchange bondchange | b_delta_sigma_charge.xpd | ||||
| B_DELTA_SIGMA_ELECTRONEGATIVITY | float | Difference of Gasteiger sigma electronegativity of the bond atoms | Tcl script | A_SIGMA_ELECTRONEGATIVITY B_TYPE | atomchange bondchange | b_delta_sigma_electronegativity.xpd | ||||
| B_DELTA_TOTAL_CHARGE | float | Difference of Gasteiger charges (sum of pi and sigma parts) of the bond atoms | Tcl script | A_TOTAL_CHARGE B_TYPE | atomchange bondchange | b_delta_total_charge.xpd | ||||
| B_DELTA_TOTAL_WALK_COUNT | double | Difference in total walk count E_TOTAL_WALK_COUNT if bond is cut | J. Chem. Inf. Comput. Sci. 2000, 40, 99-106 | usexatoms: { value: 1 description: If set, use heteroatom vs. carbon for additional differentiation. By default, non-hydrogen atoms are anonymous datatype: boolean} usebo: { value: 1 description: If set, use bond order for additional walks datatype: boolean} |
Compiled C module | M_HEAVY_ATOM_COUNT B_TYPE B_ORDER B_ISAROMATIC B_RING_COUNT A_TYPE A_ELEMENT E_TOTAL_WALK_COUNT | atomchange bondchange mol atom bond | mod_b_delta_total_walk_count.so | ||
| B_FG_SUBSTITUENTS | bitvector | Functional group substituents on bonds as per the LHASA definition | ketone boolean aldehyde boolean acid boolean ester boolean amide*1 boolean amide*2 boolean amide*3 boolean carbonium boolean isocyanate boolean acid*halide boolean thioester boolean amine*3 boolean aziridine boolean amine*2 boolean amine*1 boolean nitroso boolean diazo boolean haloamine boolean hydrazone boolean oxime boolean imine boolean thiocyanate boolean isocyanide boolean nitrile boolean azo boolean hydroxylamine boolean nitro boolean enamine boolean amine*oxide boolean thiol boolean episulfide boolean sulfide boolean sulfoxide boolean sulfone boolean c*sulfonate boolean anhydride boolean lactam boolean phosphine boolean phosphonate boolean epoxide boolean ether boolean peroxide boolean alcohol boolean enol*ether boolean nitrite boolean o*sulfonate boolean fluoride boolean chloride boolean bromide boolean iodide boolean gem*dihalide boolean trihalide boolean acetylene boolean olefin boolean vic*dihalide boolean halohydrin boolean glycol boolean hydrate boolean hemiketal boolean ketal boolean hemiacetal boolean acetal boolean azide boolean disulfide boolean allene boolean vinylsilane boolean lactone boolean vinylw boolean vinyld boolean esterx boolean amidz boolean methylene boolean carbonyl boolean carboxyl boolean halide boolean amine boolean amide boolean selenide boolean trialkylsilyl boolean trialkylsiloxy boolean silylenolether boolean n*urea*h boolean n*urea*c boolean carbamate*h boolean carbamate*c boolean o*carbamate boolean n*carbamate boolean o*carbonate boolean dithioacetal boolean dithioketal boolean requested boolean withdrawing boolean expandable*withdrawing boolean nonexpandable*withdrawing boolean donating boolean leaving boolean good*leaving boolean |
Compiled C module | A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE | atomchange bondchange atom bond | mod_b_fg_substituents.so | |||
| B_FLAGS | bitset | Display attributes for bond | ^none:bold,fat:dotted:dashed:lowarrowtip,lowarrow:higharrowtip,higharrow:highwedgetip,highwedge,hightip,lowbase:lowwedgetip,lowwedge,lowtip,lowbase:slash,intersect,intersection:split,wintersect,wslash,wavyslash,wavyintersect,wavyintersection:lowparallelarrow,lowparallel,lowarrow:highparallelarrow,highparallel,higharrow:right:left:crossed:wavy,zigzag:circle,mark1:square,mark2:cross,mark3:anchor,mark4:wedgelocation,wedgehere,wedgeposition:selected:front:back:protected:colorsplit:highlight:doubleslash:hash:resonance:aromatic:invisible:secondary:edge |
bold boolean dotted boolean dashed boolean lowarrowtip boolean higharrowtip boolean highwedgetip boolean lowwedgetip boolean slash boolean split boolean lowparallelarrow boolean highparallelarrow boolean right boolean left boolean crossed boolean wavy boolean circle boolean square boolean cross boolean anchor boolean wedgelocation boolean selected boolean front boolean back boolean protected boolean colorsplit boolean highlight boolean doubleslash boolean hash boolean resonance boolean aromatic boolean invisible boolean secondary boolean edge boolean |
(builtin) | never | ||||
| B_FRAGMENT_CARBON_CHAIN_LENGTH | int | Maximum length of linked carbon atoms in the fragments containing the respective bond atoms as first path atom if the bond were cut. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_carbon_chain_length.so | ||||
| B_FRAGMENT_CARBON_COUNT | int | Number of carbon atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT(carbon). For a bond to hydrogen, one value is zero and the other the molecule carbon count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_carbon_count.so | ||||
| B_FRAGMENT_COMPLEXITY | double | The fragment complexity (M_COMPLEXITY equivalent) of the fragment containing the first and second atom after cutting the bond | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | ||||||
| B_FRAGMENT_DIRECTION | short | Indicator whether the bond, as seen from its first atom to its second atom, is the principal substituent connection (i.e. if the bond is cut, the second atom is in the smaller substituent, and the first atom in the core). | magic=-1:none:asstored:symmetrical:reversed:ringbond |
criteria: { value: B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH description: Properties used as criteria to determine the core-side and substituent atoms of the bond, in order of decreasing significance datatype: string constraints: propertylist}
|
Compiled C module | B_TYPE B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH B_RING_COUNT | atomchange bondchange atom bond | mod_b_fragment_direction.so | ||
| B_FRAGMENT_ELEMENT_COUNT | shortvector | Element counts in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_element_count.so | ||||
| B_FRAGMENT_FORMULA | string | Hill formula of the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_FORMULA. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | format: { value: ascii enumeration: ascii:html datatype: string} usequeryatoms: { value: 0 datatype: string} |
Compiled C module | B_FRAGMENT_ELEMENT_COUNT | atomchange bondchange mol atom bond ring | mod_b_fragment_formula.so | |||
| B_FRAGMENT_HASH | uint64 | The hashcode (M_HASHY equivalent) of the fragment containing the first and second atom after cutting the bond | Compiled C module | B_TYPE B_ORDER B_ISAROMATIC B_HASHGROUP A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_hash.so | ||||
| B_FRAGMENT_HEAVY_ATOM_COUNT | int | Number of heavy atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HEAVY_ATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heavy atom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_heavy_atom_count.so | ||||
| B_FRAGMENT_HETEROATOM_COUNT | int | Number of heteroatoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HETEROATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heteroatom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_heteroatom_count.so | ||||
| B_FRAGMENT_STEREO_HASH | uint64 | The hashcode (M_HASHSY equivalent) of the fragment containing the first and second atom after cutting the bond | Compiled C module | B_TYPE A_TYPE B_ISAROMATIC B_STEREO_HASHGROUP A_ELEMENT A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange mol atom bond ring | mod_b_fragment_stereo_hash.so | ||||
| B_FRAMEWORK | byte | Framework classification 0=ring, 1=sidechain, 2=linker | ring:sidechain,chain:linker,bridge |
(builtin) | A_FRAMEWORK | atomchange bondchange | ||||
| B_HASH | uint64 | Bond hashcode | pathlength: { value: 30 datatype: string}
|
(builtin) | A_FRAMEWORK A_HASH B_TYPE B_FRAMEWORK | atomchange bondchange | ||||
| B_HASHGROUP | index | Hash group id index for bond hash code | (builtin) | B_MOL_NUMBER B_HASH | atomchange bondchange merge | |||||
| B_HASH_STEREO | byte | Hashcode-based bond chirality descriptor | M=-1:undef=0:P=1 |
useisotope: { value: 0 datatype: string}
|
(builtin) | A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange | |||
| B_HETERO_AROMAT_COUNT | short | Count for the number of heteroaromatic rings the bond participates in | Tcl script | B_ISAROMATIC R_HETEROATOM_COUNT R_AROMATIC | atomchange bondchange ring | b_hetero_aromat_count.xpd | ||||
| B_ISALPHAARO | boolean | Flag for bonds which are not aromatic themselves but linked to aromatic atom | (builtin) | A_ARORING_COUNT B_TYPE B_ARORING_COUNT | atomchange bondchange ring | |||||
| B_ISAROMATIC | boolean | Flag whether bond is aromatic or not | (builtin) | R_AROMATIC R_TYPE B_TYPE | atomchange bondchange ring | |||||
| B_ISAROTAUTOMERIC | short | Tautosytem-number for bonds which are in a potentially tautomeric system, including those which would destroy an aromatic system | useimplicith: { value: 0 datatype: string} maxpathlen: { value: 18 datatype: string} arotautomers: { value: 1 datatype: boolean} |
Compiled C module | A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT | atomchange bondchange hadd | mod_b_isarotautomeric.so | |||
| B_ISTAUTOMERIC | short | Tautosystem number for bonds which are in a potentially tautomeric system | useimplicith: { value: 0 datatype: string} maxpathlen: { value: 18 datatype: string} arotautomers: { value: 0 datatype: string} |
(builtin) | A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT | atomchange bondchange hadd | ||||
| B_LABEL | int | Arbitrary bond label | (builtin) | never | ||||||
| B_LABELCOLOR | string | X11 style color name of bond labels | color: { value: black datatype: color}
|
Tcl script | never | b_labelcolor.xpd | ||||
| B_LABEL_STEREO | byte | Label-based bond chirality descriptor | M,MI,-=-1:undef=0:P,PL,+=1 |
(builtin) | never | |||||
| B_LENGTH | float | Bond length (taken from 3D-coordinates) | (builtin) | A_XYZ | atomchange bondchange stereochange 3drelative | |||||
| B_MAPPING | int | Bond map computed from A_MAPPING. The compute ensemble must be part of a reaction, with corresponding A_MAPPING for reagent and product ensemble. Unmapped bonds (those not having mapped atoms on both sides) have value 0. | Tcl script | atomchange bondchange atom bond reaction | b_mapping.xpd | |||||
| B_MAP_STEREO | byte | Bond stereo descriptor based on reaction mapping | M,MI,-=-1:undef=0:P,PL,+=1 |
(builtin) | A_MAPPING | never | ||||
| B_MOL_LABEL | int | Label of molecule bond belongs to | (builtin) | A_MOL_LABEL | atomchange bondchange merge shuffle hadd mol | |||||
| B_MOL_NUMBER | short | Number of molecule bond belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge shuffle hadd mol | |||||
| B_MOVED_SIGMA_CHARGE | float | Charge moved during PEOE equilibration during Gasteiger sigma charge/eneg iternation | A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 | atomchange bondchange | ||||||
| B_NCICADD_RESONANCE_CROSSED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| B_NCICADD_TAUTO_CROSSED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| B_ORDER | byte | Bond order | never | |||||||
| B_ORDER_ESTIMATE | float | Estimation of fractional bond order from 3D coordinates via element pair plus base length/exponent table. Uses external data file b_order_estimate.dat (usually located in ${data_directory}/propdata/b_order_estimate directory) for the atom pair parameters. Bonds perceived from close atom distances are created as type "link" if not yet present, and their frational bond order is larger than the threshold parameter. | threshold: { value: 0.25 description: Minimal found bond order to act upon datatype: double} patternfile: { value: b_order_estimate.dat datatype: diskfile constraints: readable} |
Tcl script | A_XYZ A_ELEMENT | never | b_order_estimate.xpd | |||
| B_POLARIZABILITY | float | Average of atom polarizabilities involved in bond | Compiled C module | A_TYPE A_POLARIZABILITY | atomchange bondchange | mod_b_polarizability.so | ||||
| B_QUERY | compound | Bond attributes for structure queries | ^none:stereo:aromatic,aro:aliphatic,ali,nonaromatic,inaromatic,unaromatic:ringsystem,ringcount:doublearo,doubleoraro,da,d/a:singlearo,singleoraro,sa,s/a:mustmap:nostereook:symmetric,symmetry:asymmetric,asymmetry:nooverlap:implicitbondorder,implicit,implicitbo:kekulecmp:any:multiaro,multioraro,ma,m/a:multiple,m:offpath:daylightaromatic,daylightaro:singledouble,s/d:singledoublearo,s/d/a |
flags bitset order bitset ringsize bitset ringcount bitset aroringcount bitset tclproc string query querytree varbo double pyfunction string |
never | |||||
| B_RACEMATE | byte | Racemate distribution of stereobond | undefined,undef:rac,racemat:pure |
atomchange bondchange | ||||||
| B_REACTION_CENTER | int | Reaction Center information from MDL rxn/rdf file, can also be computed from a reaction with atom mapping information | nocenter=-1:unmarked=0:center=1:nochange=2:madebroken=4:madebrokencenter=5:orderchange=8:orderchangecenter=9:madebrokenorderchange=12:madebrokenorderchangecenter=13 |
(builtin) | B_TYPE A_MAPPING B_ORDER B_ISAROMATIC | atomchange bondchange reaction | ||||
| B_RECAP_FRAGMENTATION | boolean | Bond which would be cut in the RECAP fragmentation method | J. Chem. Inf. Comput. Sci. 38, 1998, 511-522 | atomchange bondchange atom bond | ||||||
| B_RINGS | intvector | Labels of the rings the bond is member in | (builtin) | R_LABEL R_TYPE B_TYPE | atomchange bondchange merge ring | |||||
| B_RINGSIZE | uint64 | Bits indicate membership in ring of size N | ringset: { value: esssr datatype: string}
|
(builtin) | R_TYPE B_TYPE | atomchange bondchange ring | ||||
| B_RING_COUNT | short | Number of simple (non-enevelope) rings a bond is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | B_TYPE R_TYPE | atomchange bondchange ring | ||||
| B_RING_HETEROATOM_COUNT_BITS | bitset | A bit is set at bit position n for any ESSSR ring the bond is a member of which has n hetero atoms. Chain and bridge bonds have value 0. If the bond is a member of a carbocyclic ESSSR ring, bit position 0 is set. | Compiled C module | R_HETEROATOM_COUNT R_TYPE B_TYPE | atomchange bondchange atom bond | mod_b_ring_heteroatom_count_bits.so | ||||
| B_RING_SIZE_BITS | bitset | Bit mask for ring sizes the bond participates in | Compiled C module | R_SIZE R_TYPE B_TYPE | bondchange ring | mod_b_ring_size_bits.so | ||||
| B_RING_SUBSTITUENT_PATTERN | compound | Compute relative alignment of ring atom substituents in cases where the ring plane is the stereo-defining anchor, This is done both for ring substituents which are on directly connected ring atoms and those which are distant (for example, 1.4 cis/trans relationships in six-membered rings) and where the ring acts as a pseudo-doublebond. In the first case, the property is set on the ring bond between the substituted ring atoms. In the second case, all bonds which are on one of the shortest paths between two same-ring atoms where the A_STEREOGENIC value is "ringct" get the descriptor. For a simple 1.4 cyclohexane, these are all ring atoms. Note that a 1.3-substituted cyclohexane gets no descriptors in this property: Neither share the substituted ring atoms a bond, nor is the ring acting as a pseudo doublebond. Across-ring stereodescriptors are not set if other ring substituents impress normal atom stereogenicity on the substituted ring atoms, which is for example the case in any 1.x.4 substituent pattern. Field descriptor is the label-based stereo decriptor for the bond(s). Value 1/P: low-label off-ring substituents on different sides of ring plane, 1.2-substituents Value -1/M: Low-label off-ring substituents on same side of ring plane, 1.2-substituents Value 2/p: low-label off-ring substituents on different sides of ring plane, distant substituents Value -2/m: Low-label off-ring substituents on same side of ring plane, distant substituents Value 0: no ring substituent stereo Fields ligatom1a/ligatom2a are the low-label off-ring substitituent atoms. Fields ligatom1b/ligatom2b are the secondary off-ring substituent atoms. |
@m:M:none:P:p |
descriptor byte ligatom1a int ligatom1b int ligatom2a int ligatom2b int |
Compiled C module | A_LABEL_STEREO R_TYPE A_LABEL B_TYPE A_STEREOGENIC | atomchange bondchange stereochange ring | mod_b_ring_substituent_pattern.so | ||
| B_ROTATABILITY | byte | Classification of bond rotatability. Ring bond flag must have precedence over multi-bond flag for E_EFFECTIVE_ROTOR_COUNT | undef:terminal:ring:multiple:spheric,round,roundligand:linear,linearligand:yes:locked:forced |
Compiled C module | B_TYPE B_ORDER A_TYPE A_ELEMENT A_INAMIDE A_TERMINAL_DISTANCE | atomchange bondchange hadd | mod_b_rotatability.so | |||
| B_SEQUENCE_NUMBER | int | Sequential bond number for CTX output | (builtin) | B_MOL_NUMBER A_SEQUENCE_NUMBER A_TYPE | atomchange bondchange merge shuffle hadd mol | |||||
| B_SSMATCH | int | Ensemble is structure, property data encodes labels of matching substructure bonds, 0 for unmatched parts | sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
|
Tcl script | never | b_ssmatch.xpd | ||||
| B_SSMATCH_ENVIRONMENT | datatree | Classigied unmatched structure environment of the substructure bonds, i.e. data on the characteristics of the unmatched structure bonds sprouting from the structure bond matched by this substructure bond. Set by a substructure hit option, not directly computable. | atomchange bondchange atom bond | |||||||
| B_STEREOGENIC | byte | Can this bond be a stereocenter ? | no:maybe:checkno:yes,checkyes:ringct |
simple: { value: 0 datatype: string} ringsizecheck: { value: 1 datatype: string} electronegativitycheck: { value: 1 datatype: string} |
(builtin) | atomchange bondchange hadd | ||||
| B_STEREOINFO | byte | Stereo descriptor availability info: 1:Label,2:E/Z,4:cis/trans,8:hash,16:map | ^none:label:cip:cistrans:hash:map |
(builtin) | B_CISTRANS_STEREO B_LABEL_STEREO B_HASH_STEREO B_CIP_STEREO B_MAP_STEREO | atomchange bondchange stereochange | ||||
| B_STEREO_HASH | uint64 | Stereospecific bond hashcode | (builtin) | A_FRAMEWORK A_STEREO_HASH B_FRAMEWORK B_TYPE | atomchange bondchange | |||||
| B_STEREO_HASHGROUP | index | Hash group id index for stereospecific bond hash code | (builtin) | B_MOL_NUMBER B_HASH A_HASH_STEREO B_HASH_STEREO | atomchange bondchange merge | |||||
| B_STMATCH | int | Ensemble is substructure, property data encodes labels of matching structure bonds, 0 for unmatched parts | sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
|
Tcl script | never | b_stmatch.xpd | ||||
| B_STRAINED | boolean | Flags for strained bonds according to the Lhasa definition. These are: endocylic 3/4-membered ring bonds endocyclic 5-membered ring bonds which are part of a [2.1.1], [2.2.1] or [3.2.1] bicyclic system trans C=C double bonds in rings smaller than size 10 C=C double bonds exocyclic to 3/4-membered rings |
Compiled C module | R_TYPE B_TYPE B_ORDER A_TYPE A_LABEL A_ELEMENT B_LABEL_STEREO A_RING_COUNT | bondchange ring | mod_b_strained.so | ||||
| B_TEXTLABEL | compound | Arbitrary textual bond label plus alignment info for plots | left=-1:center=0:right=1 |
label string align byte |
never | |||||
| B_TORSION_ANGLE | float | Torsion angle of atom quartets, encoded as pseudo bond | (builtin) | A_XYZ | atomchange bondchange 3drelative | |||||
| B_TRANSFORM_STATUS | byte | Bond status as result of SMIRKS transformation. Possible values are none: not matched in transform, matched: matched, but unchanged, changed: bond order or attribute changed, new: bond introduced by transform | none:matched:changed:new |
atomchange bondchange atom bond | ||||||
| B_TYPE | int | Bond type | ^none:link:normal,valence,vb:hbond,hydrogen:dative:3center:angle,dihedral,3atom:torsion,torsional,4atom:rgroup,rg:nobond,searchnot,not:deloc,delocalized:complex:ionic |
never | ||||||
| C_COMMENT | string | Connection (edge) comment in free format | never | |||||||
| C_DIRECTED | boolean | Flag indicating whether connection/edge is directed. Global default is given in N_DIRECTED. | Compiled C module | atomchange bondchange atom bond | mod_c_directed.so | |||||
| C_GRAPHICS | compound | Connection (edge) graphics | none:arc:bitmap:image:line:oval,ellipse,ellipsis:polygon:rectangle,rect:text:box:circle:rhombus,diamond:ver_ellipsis:hor_ellipsis:triangle:pentagon:hexagon:octagon:roundedrectangle,roundrectangle,roundrect,roundedrect |
type int attributes dictionary |
usehtml: { value: 0 description: Whether to use HTML encoding of the text annotation datatype: boolean} fontsize: { value: -1 description: Font size (negative value: unset) datatype: int} font: { value: Verdana description: Font name datatype: string} fontcolor: { value: black description: Font color (empty is unset) datatype: color constraints: emptycolor} color: { value: black description: Connection line color (empty is unset) datatype: color constraints: emptycolor} |
Tcl script | C_NAME | never | c_graphics.xpd | |
| C_IDENT | string | Connection (edge) ident string | Compiled C module | never | mod_c_ident.so | |||||
| C_LABEL | int | Connection (edge) label of connections in network objects | Compiled C module | never | mod_c_label.so | |||||
| C_LABEL_GRAPHICS | compound | Connection (edge) label graphics | none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon |
type int attributes dictionary |
never | |||||
| C_NAME | string | Connection (edge) name in free format | never | |||||||
| C_ONTOLOGY_LINK | int | Ontology link type | none:is_a:has_part:is_conjugate_base_of:is_conjugate_acid_of:is_tautomer_of:is_enantiomer_of:has_functional_parent:has_parent_hydride:is_substituent_group_from:has_role |
never | ||||||
| C_PARTITION | int | Partition code for connections (edges). If a symbolic name is available, I/O modules modify the enumeration field of the property. | atomchange bondchange atom bond | |||||||
| C_TEXT | string | Connection (edge) text label | never | |||||||
| C_TYPE | string | Connection (edge) type in free format | never | |||||||
| C_URL | url | Connection reference URL | atomchange bondchange atom bond | |||||||
| C_WEIGHT | double | Graph connection (edge) weight | Compiled C module | never | mod_c_weight.so | |||||
| D_AUTHOR | compound | Dataset author data, computation copies these from the internal object author fields | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
Tcl script | never | d_author.xpd | ||||
| D_CHEMDRAW_PAGE | diskfile (switchable between blob diskfile) |
Tabular display of structure collection in ChemDraw page | ncols: { value: 3 minvalue: 1 maxvalue: 20 datatype: int} nrows: { value: 4 minvalue: 1 maxvalue: 20 datatype: int} offset: { value: 0 minvalue: 0 datatype: int} filename: { value: {} datatype: string constraints: writeable} format: { value: cdx enumeration: cdx:cdxml datatype: int} grid: { value: 1 datatype: boolean} gridcolor: { value: black datatype: color} gridselectcolor: { value: orange datatype: color} papersize: { value: a4 enumeration: a3:a4:a5:a6:a7:b3:b4:b5:b6:letter:legal:executive datatype: int} border: { value: 12.0 minvalue: 0 maxvalue: 99 datatype: double} boxspacing: { value: 6.0 minvalue: 0 maxvalue: 99 datatype: double} bonds: { value: 8 minvalue: 1 maxvalue: 25 datatype: int} boxborder: { value: 3.0 minvalue: 0 maxvalue: 99 datatype: double} orientation: { value: portrait enumeration: portrait:landscape datatype: int} cdxversion: { value: 8.0 datatype: double} journalstyle: { value: acs enumeration: default:acs,jacs datatype: int} multipage: { value: 0 datatype: boolean} headerproperty: { value: {} datatype: string constraints: propertylist} headerformat: { value: {} datatype: string} headerfont: { value: Arial datatype: string} headercolor: { value: black datatype: color} headerhighlightcolor: { value: red datatype: color} headerhighlightfilter: { value: {} datatype: string constraints: filtername} headerfontstyle: { value: none datatype: string} headerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} header2property: { value: {} datatype: string constraints: propertylist} header2format: { value: {} datatype: string} header2font: { value: Arial datatype: string} header2color: { value: black datatype: color} header2highlightcolor: { value: red datatype: color} header2highlightfilter: { value: {} datatype: string constraints: filtername} header2fontstyle: { value: none datatype: string} header2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} footerproperty: { value: E_NAME datatype: string constraints: propertylist} footerformat: { value: {} datatype: string} footerfont: { value: Arial datatype: string} footerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} footercolor: { value: black datatype: color} footerhighlightcolor: { value: red datatype: color} footerhighlightfilter: { value: {} datatype: string constraints: filtername} footerfontstyle: { value: none datatype: string} footer2property: { value: {} datatype: string constraints: propertylist} footer2format: { value: {} datatype: string} footer2font: { value: Arial datatype: string} footer2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} footer2color: { value: black datatype: color} footer2highlightcolor: { value: red datatype: color} footer2highlightfilter: { value: {} datatype: string constraints: filtername} footer2fontstyle: { value: none datatype: string} headercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int} footercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int} |
Tcl script | atomchange bondchange stereochange groupchange dataset | d_chemdraw_page.xpd | ||||
| D_COPYRIGHT | string | Copyright information | never | |||||||
| D_CREATION_TIME | datetime | Date of dataset generation | Tcl script | never | d_creation_time.xpd | |||||
| D_DATE | date | Dataset creation date | atomchange bondchange atom bond | |||||||
| D_DESCRIPTION | string | Free-form description of dataset | never | |||||||
| D_DIVERSITY_SET | dataset | Select a diverse subset from the source dataset. | property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property} query: { value: all description: Structure filter query expression datatype: string} size: { value: 50 description: Target size minvalue: 1 datatype: int} startindex: { value: -1 description: First structure source index, -1 is random datatype: int} minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int} |
Tcl script | atomchange bondchange atom bond | d_diversity_set.xpd | ||||
| D_EMF_IMAGE | diskfile | Dataset rendered as WMF/EMF image, from assembled E_EMF_IMAGE structure renderings | ncols: { value: 3 minvalue: 1 datatype: int} nrows: { value: 4 minvalue: 1 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} framewidth: { value: 1 datatype: int} boxwidth: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int} boxheight: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerheight: { value: 0 minvalue: 0 datatype: int} footerheight: { value: 0 minvalue: 0 datatype: int} comment: { value: {} datatype: string} commenttype: { value: text enumeration: none:text:property,prop datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} format: { value: pwmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} font: { value: arialn datatype: string} annotationfontsize: { value: -1 datatype: double} offset: { value: 0 datatype: int} imgproperty: { value: E_EMF_IMAGE datatype: string constraints: property} padding: { value: 1 datatype: int} boxbgcolor: { value: transparent datatype: color} boxhighlightcolor: { value: red datatype: string} selectlist: { value: {} datatype: intvector} colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,grayscale,greyscale:color,colour datatype: int} downloadfilename: { value: {} datatype: string} |
Compiled C module | E_EMF_IMAGE | dataset | mod_d_emf_image.so | |||
| D_FRAGMENT_NETWORK | network | Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies. | trace: { value: 0 description: If set, print trace information on the progress of the process datatype: boolean} mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int} maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int} minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int} bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list} |
Tcl script | dataset | d_fragment_network.xpd | ||||
| D_FRAGMENT_TABLE | table | Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies. | mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int} maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int} minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} columns: { value: E_SMILES E_HASHY count frequency source destination description: Result table columns datatype: string constraints: list} maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int} bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list} |
Tcl script | dataset | d_fragment_table.xpd | ||||
| D_FUZZY_MCSS | structure | Maximum common substructure of dataset, determined by non-deterministic fuzzy matching | maxfuzz: { value: 5 datatype: string}
|
Compiled C module | atomchange bondchange stereochange dataset | mod_d_fuzzy_mcss.so | ||||
| D_GIF | diskfile (switchable between string blob diskfile url) |
GIF image table of the contents of a dataset, assembled by tiles of E_GIF structure images | ncols: { value: 3 datatype: int} nrows: { value: 4 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} framewidth: { value: 1 datatype: int} boxwidth: { value: 200 datatype: int} boxheight: { value: 200 datatype: int} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerheight: { value: 0 datatype: int} footerheight: { value: 0 datatype: int} comment: { value: {} datatype: string} commenttype: { value: text enumeration: none:text:property datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} format: { value: gif enumeration: gif:png,png24:png8 datatype: string} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} headercolor: { value: black datatype: string} footercolor: { value: black datatype: string} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: string} font: { value: arialn datatype: string} annotationfontsize: { value: -1 datatype: double} interlace: { value: 0 datatype: boolean} offset: { value: 0 description: First dataset object to use datatype: int} imgproperty: { value: E_GIF datatype: string constraints: property} padding: { value: 1 datatype: int} boxbgcolor: { value: transparent datatype: color} boxhighlightcolor: { value: red datatype: color} selectlist: { value: {} description: Indices of dataset objects to draw with highlight background datatype: intvector} downloadfilename: { value: {} description: Save file name if http header is used datatype: string} fixiepngsize: { value: 1 description: Circumvent Windows bug in older releases datatype: boolean} checkimgsize: { value: 1 datatype: boolean} |
Compiled C module | E_GIF | dataset | mod_d_gif.so | |||
| D_HASHISY | uint64 | Stereospecific and isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHISY | dataset | mod_d_hashisy.so | ||||
| D_HASHIY | uint64 | Non-stereospecific but isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHIY | dataset | mod_d_hashiy.so | ||||
| D_HASHSY | uint64 | Stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHSY | dataset | mod_d_hashsy.so | ||||
| D_HASHY | uint64 | Non-stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHY | dataset | mod_d_hashy.so | ||||
| D_HTML_PAGE | blob (switchable between blob diskfile) |
filename: { value: {} description: Output file name, empty for tmp file datatype: string} htmlpage: { value: 0 description: If set, write complete HTML page, otherwise write only ExtJS generator statements. datatype: boolean} title: { value: {} description: Graph title datatype: string} |
Tcl script | atomchange bondchange atom bond dataset | d_html_page.xpd | |||||
| D_IDENT | string | Ident string of dataset | Tcl script | atomchange bondchange atom bond | d_ident.xpd | |||||
| D_MATCHED_PAIRS | compoundvector | Identify matched pair molecules, or matched series molecules, in a dataset. | id int datasetindex int bond int centrality double size int setindex int structure structure |
mode: { value: pairs description: In pairs mode, always find molecule pairs under any ID. In series mode, if there are more than 2 structures linked, group them all under a common ID. Example: F/Cl/Br-benzene, In pairs mode, find 3 structure pairs, in series mode, find one series with 3 members enumeration: pairs:series datatype: string} copystructures: { value: 0 description: If set, duplicate the matched pair/set structures with highlighted bonds in B_FLAGS into the "structure" field of this property. If it is not set, only the id/dataset index/bond fields are filled and the structure field is set to NULL datatype: boolean} cutxhbonds: { value: 1 description: If set, allow bonds between hydrogen and heteroatom to be part of a pair or set definition datatype: boolean} cutchbonds: { value: 1 description: If set, allow bonds between hydrogen and carbon to be part of a pair or set definition datatype: boolean} cutcxbonds: { value: 1 description: If set, allow bonds between carbon and heteroatom to be part of a pair or set definition datatype: boolean} cutccbonds: { value: 1 description: If set, allow bonds between carbon to be part of a pair or set definition datatype: boolean} cutxxbonds: { value: 1 description: If set, allow bonds between heteroatoms to be part of a pair or set definition datatype: boolean} cutchainchainbonds: { value: 1 description: If set, allow bonds between two chain atoms to be part of a pair or set definition datatype: boolean} cutringchainbonds: { value: 1 description: If set, allow bonds between a ring and a chain atom to be part of a pair or set definition datatype: boolean} cutringringbonds: { value: 1 description: If set, allow non-ring bonds between ring atoms to be part of a pair or set definition datatype: boolean} cutpreference: { value: first description: Define which bonds should be preferred if there a multiple possibilities to define a pair or set. All: report all possibilities, first: report first possibility found, core: report most central cut, peripheral: report most peripheral cut for any given set or series enumeration: all:first:core,central:peripheral datatype: string} minheavyatoms: { value: 0 description: Minimum number of heavy atoms which must be present in the R-group part datatype: int} maxheavyatoms: { value: 999 description: Maximum number of heavy atoms which must be present in the R-group part datatype: int} formulafilter: { value: {} description: A formula match expression which possible R-groups must match datatype: formulamatch} removesubsets: { value: 0 description: If set, remove (in series mode) sets which are a subset of a larger set datatype: boolean} |
Compiled C module | B_FRAGMENT_HASH B_FRAGMENT_DIRECTION B_FRAGMENT_ELEMENT_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_CENTRALITY B_STEREO_HASHGROUP A_RING_COUNT A_TYPE A_ELEMENT | atomchange bondchange atom bond dataset | mod_d_matched_pairs.so | ||
| D_MCSS | structure | Maximum common substructure of dataset | cmpflags: { value: bondorder datatype: string} hitflags: { value: {} datatype: string} exclflags: { value: st_h|ss_h datatype: string} |
Compiled C module | atomchange bondchange stereochange dataset | mod_d_mcss.so | ||||
| D_METADATA | dictionary | Dublin Core metadata for dataset | never | |||||||
| D_NAME | string | Free-form user-defined dataset name | never | |||||||
| D_NEW_FLAG | boolean | Dataset flag for new compounds. THis is primarily used in the CHAI file format. | never | |||||||
| D_PROGRAM | string | Program source of dataset | never | |||||||
| D_PS_PAGES | diskfile | Postscript dataset rendering | filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 datatype: boolean} ncols: { value: 2 datatype: int} nrows: { value: 3 datatype: int} papersize: { value: A4 enumeration: none:a3:a4:a5:a6:a7:b3:b4:b5:b6:letter,usletter:legal,uslegal:executive,exec,usexecutive,usexec datatype: string} border: { value: 10 datatype: int} title: { value: {} datatype: string} comment: { value: {} datatype: string} space: { value: 5 datatype: int} frame: { value: line enumeration: none:line:shadow datatype: string} boxproperty: { value: E_NAME datatype: string constraints: property} orientation: { value: portrait enumeration: none:landscape,wide,quer,querformat:portrait,tall,hoch,hochformat datatype: string} colormode: { value: bow enumeration: bow,bw:wob:cow,color:cob datatype: string} headerfontsize: { value: 12 datatype: double} footerfontsize: { value: 12 datatype: double} labelfontsize: { value: 10 datatype: double} pagelimit: { value: 100 minvalue: 1 maxvalue: 9999 datatype: int} pageoffset: { value: 0 minvalue: 0 maxvalue: 9999 datatype: int} psheader: { value: all enumeration: all:none:prolog:trailer datatype: string} pagecount: { value: 0 minvalue: -1 maxvalue: 9999 datatype: int} shadow: { value: 3 datatype: int} eps: { value: 0 datatype: boolean} binder: { value: none enumeration: none:left:top:right:bottom datatype: string} binderwidth: { value: 30 datatype: int} logotext: { value: {} datatype: string} printpagecount: { value: -1 datatype: int} headerheight: { value: 14 datatype: int} footerheight: { value: 14 datatype: int} labelheight: { value: 12 datatype: int} nameheight: { value: 12 datatype: int} namefontsize: { value: 10 datatype: int} atomcolor: { value: {} description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string constraints: emptycolor} downloadfilename: { value: {} datatype: string} |
Compiled C module | E_EPS_IMAGE | atomchange bondchange stereochange groupchange dataset | mod_d_ps_pages.so | |||
| D_SCAFFOLD_TABLE | table | A list of Ertl-type scaffolds extracted from a file. The table contains the counts and SMILES strings as columns, plus row-attached structures. | maxrecs: { value: -1 description: The maximum number of records to process, -1 is infinite datatype: int} maxscaffolds: { value: -1 description: The maximum number of scaffolds to record, -1 is infinite datatype: int} maxsimplification: { value: 1 description: The maximum number of scaffolds simplification steps to perform, -1 is infinite datatype: int} compoundfilter: { value: all description: A compound filter expression (see 'ens scan' command) scaffolds must match datatype: string} |
Tcl script | E_SMILES E_SCAFFOLD_TREE_STRUCTURE | atomchange bondchange stereochange atom bond | d_scaffold_table.xpd | |||
| D_SCAFFOLD_TREE | datatree | The scaffolds of the structures in the dataset in sorted, hierarchical order. The first node a an empty root node, and its children are the irreducible scaffolds. The individual scaffold nodes of the tree contain SMILES strings as value and the (non-stereo/non-isotope) ensemble hashcode as name, followed by all more complex scaffolds which are reduced to the current scaffold by one simplification step. | J. Chem. Inf. Model. 2007, 47, 47-58 | maxlevel: { value: -1 description: Maximum tree depth to generate, -1 for unlimited datatype: int} includeoriginals: { value: 0 description: If set, include the base structures. By default, only the scaffolds are included datatype: boolean} hashcode: { value: E_HASHY description: The hashcode property to be used to check structure identity datatype: string constraints: property} nodenameproperty: { value: E_HASHY description: Instance values of this property are stored as node names. datatype: string constraints: property} auxproperties: { value: {} description: Instance data of these properties is appended to the right of the SMILES data in the nodes datatype: string constraints: propertylist} |
Tcl script | atomchange bondchange atom bond dataset | d_scaffold_tree.xpd | |||
| D_SIMILARITY_MATRIX | intmatrix | Similarity matrix between structures in dataset, with dataset element indices as matrix indices | property: { value: E_SCREEN datatype: string constraints: property} method: { value: tanimoto datatype: string} |
Tcl script | E_SCREEN | atomchange bondchange merge atom bond dataset | d_similarity_matrix.xpd | |||
| D_SIZE | int | Dataset size | Tcl script | dataset | d_size.xpd | |||||
| D_SMALLWORLD_NETWORK | network | Sample implementation of R. Sayles SmallWorld network for accelerated MCSS searching | useelements: { value: 1 datatype: boolean} usebondorders: { value: 1 datatype: boolean} addsingleatomfragments: { value: 0 datatype: boolean} |
Compiled C module | E_HASHY B_HASHGROUP A_ELEMENT A_LABEL B_LABEL A_TYPE B_TYPE B_ISAROMATIC B_RING_COUNT A_SUBSTITUENT_COUNT E_NMOLECULES E_HEAVY_ATOM_COUNT | atomchange bondchange atom bond dataset | mod_d_smallworld_network.so | |||
| D_SOURCE | string | Free-form dataset source description | never | |||||||
| D_SUBSTRUCTURE_HIERARCHY | network | A tree-style network of substructure hierarchies of the structures in the dataset. | storestructures: { value: 0 description: If set, store the structures in the nodes in property V_STRUCTURE datatype: boolean} storeimages: { value: 0 description: If set, store an image of the structures in the nodes in property V_GRAPHICS datatype: boolean} directory: { value: img description: Image directory datatype: string constraints: directory} imgparameters: { value: width 100 height 100 bgcolor black atomcolor element bondcolor white format png frame 0 bonds 6 description: Image parameters datatype: dictionary} ssmatchflags: { value: -excludeh all description: Extra flags to pass to the substructure matcher datatype: string} auxlinks: { value: 0 description: if set, create additional links to alternative matches in the same level datatype: boolean} |
Tcl script | atomchange bondchange atom bond dataset | d_substructure_hierarchy.xpd | ||||
| D_SVG_IMAGE | diskfile (switchable between string blob diskfile url xmlstring) |
SVG image table of the contents of a dataset, assembled by tiles of E_SVG_IMAGE structure images | ncols: { value: 3 datatype: int} nrows: { value: 4 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} framewidth: { value: 1 datatype: int} boxwidth: { value: 200 datatype: int} boxheight: { value: 200 datatype: int} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerheight: { value: 0 datatype: int} footerheight: { value: 0 datatype: int} comment: { value: {} datatype: string} commenttype: { value: text enumeration: none:text:property datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} headercolor: { value: black datatype: string} footercolor: { value: black datatype: string} font: { value: arialn datatype: string} usewebfont: { value: 0 datatype: boolean} annotationfontsize: { value: -1 datatype: double} offset: { value: 0 description: First dataset object to use datatype: int} imgproperty: { value: E_SVG_IMAGE datatype: string constraints: property} padding: { value: 1 datatype: int} boxbgcolor: { value: transparent datatype: color} boxhighlightcolor: { value: red datatype: color} selectlist: { value: {} description: Indices of dataset objects to include, if empty, use all datatype: intvector} downloadfilename: { value: {} description: Save file name if http header is used datatype: string} id: { value: {} datatype: string} title: { value: {} datatype: string} standalone: { value: 1 datatype: boolean} xmlheader: { value: 1 datatype: boolean} metadata: { value: 1 datatype: boolean} footerproperty: { value: {} datatype: string constraints: property} headerproperty: { value: {} datatype: string constraints: property} checkimgsize: { value: 1 datatype: boolean} |
Compiled C module | E_SVG_IMAGE | dataset | mod_d_svg_image.so | |||
| D_TREE_DATA_GIF | diskfile (switchable between string blob diskfile url) |
Rendering of tree-style property data (must be of property datatype "datatree") as a GIF/PNG image using a modified Reingold-Tilford tree layout algorithm. | property: { value: D_SCAFFOLD_TREE description: Property to read rendered data from datatype: string constraints: property} treeindex: { value: 0 datatype: string} maxlevel: { value: -1 datatype: int} boxwidth: { value: 100 datatype: int} boxheight: { value: 100 datatype: int} treedistance: { value: 10 description: Minimum horizontal distance between boxes on a level which do not have the same parent datatype: int} siblingdistance: { value: 5 description: Minimum horizontal distance between boxes on a level which do have the same parent datatype: int} leveldistance: { value: 25 description: Distance between lower box Y of parent level and upper box Y of child level datatype: int} border: { value: 5 description: Unused pixels around tree datatype: int} decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean} showname: { value: 0 description: If set, include the node name in rendering datatype: boolean} showcount: { value: 0 description: If set, include non-negative count node fields in rendering datatype: boolean} interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean} alignstructures: { value: 1 description: If structures are rendered, align them hierarchically datatype: boolean} excluderoot: { value: 0 description: If set, do not render root node datatype: boolean} framewidth: { value: 0 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} linecolor: { value: red datatype: color} boxframecolor: { value: blue datatype: color} boxbgcolor: { value: grey90 datatype: color} format: { value: png enumeration: gif:png,png24:png8 datatype: string} font: { value: arialn datatype: string} fontsize: { value: 8.0 datatype: double} filename: { value: {} description: Output file name, if data type is diskfile. If empty, generate /tmp file datatype: diskfile constraints: writeable} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} |
Compiled C module | atomchange bondchange atom bond dataset | mod_d_tree_data_gif.so | ||||
| D_WATERMARK | double | Watermark detection in a set of structures with 3D coordinates | key: { value: LNTSCSWW description: Message encoder key datatype: string} message: { value: CACTVS Watermark description: Encoded message datatype: string} scale: { value: 100 datatype: double} sigma: { value: 1.0 datatype: double} spread: { value: 1 datatype: int} markhydrogens: { value: 0 description: Include hydrogens in atoms encoding the message datatype: boolean} alignpmi: { value: 1 description: Align 3D atomic coordinates to PMI datatype: boolean} usesensitivity: { value: 0 description: If set, use A_WATERMARK_SENSITITIVY data to tune coordiante shifts to minimize energy distortions datatype: boolean} |
Compiled C module | A_XYZ A_ELEMENT A_TYPE A_SMILES_RANK A_WATERMARK_SENSITIVITY E_HASHY | dataset | mod_d_watermark.so | |||
| D_XYPLOTENERGY | double | Plot pseudo energy - debug property, not intended for production use | maximprove: { value: 100 datatype: int} maxcycle: { value: 100 datatype: int} uselast: { value: 0 datatype: boolean} |
Compiled C module | A_XY A_ELEMENT A_TYPE B_TYPE | dataset | mod_d_xyplotenergy.so | |||
| E_ACROS_URL | url | Catalog URL of structure for Acros Organics/Fisher Scientific | Tcl script | atomchange bondchange atom bond | e_acros_url.xpd | |||||
| E_ACTIVE_AIDSET | intvector | Set of PubChem assay IDs testing this compound as active | Tcl script | E_CID | atomchange bondchange stereochange | e_active_aidset.xpd | ||||
| E_ADJACENCY_MATRIX | intmatrix | Standard non-canonical adjacency matrix for the representation of compounds, with bond orders in i/j elements and free electrons in i/i elements. If there is no bond, the matrix element value is zero. | Tcl script | A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS | atomchange bondchange atom bond | e_adjacency_matrix.xpd | ||||
| E_AIDSET | intvector | Set of PubChem assay IDs where this compoundwas tested | Tcl script | E_CID | atomchange bondchange stereochange | e_aidset.xpd | ||||
| E_AIDSET_URL | url | PubChem assay database URL | Tcl script | E_AIDSET | atomchange bondchange stereochange merge | e_aidset_url.xpd | ||||
| E_ALFA_AESAR_ID | string | Structure ID in the AlfaAesar catalog(www.alfa.com) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_alfa_aesar_id.xpd | ||||
| E_ALFA_AESAR_URL | url | Data page in the AlfaAesar catalog (www.alfa.com) | Tcl script | E_ALFA_AESAR_ID | atomchange bondchange atom bond | e_alfa_aesar_url.xpd | ||||
| E_ALIRING_COUNT | short | Number of aliphatic rings the ensemble contains | ringtypes: { value: esssr description: Ringset to perform count on enumeration: ^none:sssr:esssr,triple:k:envelope datatype: int}
|
Compiled C module | R_AROMATIC R_TYPE | atomchange bondchange atom bond ring | mod_e_aliring_count.so | |||
| E_AMINO_ACID_SEQUENCE | string | Amino acid sequence in 1- or 3-letter letter code. Can be computed from molecular structure with standard amino acid set. | nomenclature: { value: a description: Whether to use single-letter amino acid codes (a) or 3-letter codes (aaa) enumeration: a,letter1=1:aaa,letter3=3 datatype: int} encodeterminals: { value: 0 description: If set, include H- and -OH terminal encodings datatype: boolean} encodebridges: { value: 0 description: If set, encode SS disulfide bridges in (x) format datatype: boolean} separator: { value: {} description: Separator character between AA encodings (can be empty) datatype: string} |
Compiled C module | M_AMINO_ACID_SEQUENCE | atomchange bondchange mol atom bond | mod_e_amino_acid_sequence.so | |||
| E_ANNOTATION | choicevector | Graphical annotation objects of an ensemble. Thre various graphicsl objects supported by this property are described as separate proerties referred as choice variant fields. | text compound rectangle compound ellipse compound roundedrectangle compound polyline compound bracket compound |
A_XY | never | |||||
| E_AOPWIKI_URL | url | Display URL in the AOP Wiki (Adverse Outcome Pathway, https://aopwiki.org) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_aopwiki_url.xpd | ||||
| E_ARORING_COUNT | short | Count of aromatic rings in ESSSR | ringtypes: { value: esssr description: Ringset to perform count on enumeration: ^none:sssr:esssr,triple:k:envelope datatype: int}
|
Compiled C module | R_AROMATIC R_TYPE | atomchange bondchange atom bond ring | mod_e_aroring_count.so | |||
| E_ASCII_IMAGE | string (switchable between string unicode) |
ASCII (or Unicode) rendering of a chemical structure. Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the last line. |
width: { value: 40 minvalue: 25 maxvalue: 256 datatype: int} height: { value: 30 minvalue: 25 maxvalue: 256 datatype: int} showcharge: { value: 0 datatype: boolean} useunicode: { value: 1 datatype: boolean} bonds: { value: 10 minvalue: 3 maxvalue: 25 datatype: double} usecolor: { value: 0 datatype: boolean} usefontstyle: { value: 0 datatype: boolean} showradical: { value: 0 datatype: boolean} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,exten ded,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,y es datatype: int} csymbol: { value: all enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: white datatype: color} highlightcolor: { value: red datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} frame: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} crop: { value: left|right|top|bottom enumeration: ^none:left:right:top:bottom datatype: bitset} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} usealtcharset: { value: 0 datatype: boolean} leadnewline: { value: 0 datatype: boolean} tailnewline: { value: 0 datatype: boolean} framecolor: { value: black datatype: color} hcolor: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} unicodeforringbonds: { value: macrocycles enumeration: no,never:macrocycles,largerings:yes,always datatype: int} badunicodechars: { value: 0x2571 0x2572 0x2573 0x2afd description: Codes of Unicode chars which should not be used, for example because they are missing in the terminal font comment: 0x2afd: double slash, 0x244a: double backslash, 0x2500: horizontal single line, 0x2501: horizontal bold single line, 0x2502: vertical single line, 0x2504: vertical bold single line, 0x2504: horizontal dotted line, 0x2506: vertical dotted line, 0x250c: corner lower right, 0x2510: corner lower left, 0x2514: corner upper right, 0x2518: corner upper left, 0x2550: horizontal double line, 0x2551: vertical double line, 0x2554: double corner lower right, 0x2557: double corner lower left, 0x255A: double corner upper right, 0x255D: double corner upper left, 0x2571: diagonal lower left to upper right, 0x2572: diagonal upper left to lower right, 0x2573: cross, 0x2630: horizontal triple line datatype: string constraints: list} lineprefix: { value: {} description: Characters to add to the 2nd and later lines, for example to compensate for database table formatting datatype: string} |
Compiled C module | A_TYPE A_ELEMENT A_FLAGS B_FLAGS A_QUERY B_QUERY A_FORMAL_CHARGE A_RESIDUE A_SYMBOL A_XSYMBOL A_XY A_HSPECIAL A_CSPECIAL A_COLOR A_ANNOTATION B_TYPE B_LABEL B_ORDER B_COLOR R_TYPE | atomchange bondchange stereochange merge mol atom bond | mod_e_ascii_image.so | |||
| E_ASTATECH_ID | string | Catalog ID from AstaTech (astatechinc.om) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_astatech_id.xpd | ||||
| E_ASTATECH_URL | url | Catalog display URL for AstaTech catalog (astatechinc.om) | Tcl script | E_ASTATECH_ID | atomchange bondchange stereochange atom bond | e_astatech_url.xpd | ||||
| E_ASYNCSERVER | string | Dummy property to test asynchronous client/server property computation/communication | never | |||||||
| E_ATOMHASH_COUNT | int | Number of different basic atom hash codes | (builtin) | E_HASHGROUP_COUNT_A | atomchange bondchange merge | |||||
| E_AUTHOR | compound | Information about the original author of a structure or related document | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
never | ||||||
| E_AUTODOCK4_TORSIONAL_FREEDOM | byte | Torsional freedom parameter for Audock 4. Used in the I/O modules for the Autodoc4 PDBQT file format. | atomchange bondchange stereochange 3drelative | |||||||
| E_AUXILIARY_SCREEN | bitvector | Auxiliary custom structure search screens, configurable via pattern parameter or file | patternfile: { value: {} datatype: diskfile constraints: readable} patterns: { value: N=[N+]=[N-] datatype: string} aromode: { value: strict enumeration: strict:lenient:default datatype: int} |
Tcl script | atomchange bondchange stereochange hadd | e_auxiliary_screen.xpd | ||||
| E_BARCODE | blob (switchable between string blob diskfile) |
Barcodes in various formats as image data, returned either as a blob or disk file | code: { value: qrcode description: barcode encoding standard enumeration: code39,39:code39x,39x:code128,128:ucc,ean,ucc/ean,ean/ucc:qrcode,qr,qrc datatype: int} format: { value: png description: image format enumeration: gif:png,png24:png8 datatype: string} mode: { value: property description: encode either property data or directly specified data value enumeration: property:value datatype: int} value: { value: E_IDENT datatype: string} filename: { value: {} datatype: string constraints: writeable} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} width: { value: -1 minvalue: -1 maxvalue: 512 datatype: int} height: { value: 15 minvalue: 8 maxvalue: 50 datatype: int} checksum: { value: 1 datatype: boolean} bgcolor: { value: white datatype: color} fgcolor: { value: black datatype: color} showtext: { value: default description: Whether to also print ASCII text on the label enumeration: no:default:yes datatype: int} font: { value: arialn datatype: string} fontsize: { value: 8 minvalue: 7 maxvalue: 24 datatype: int} antialias: { value: 1 datatype: boolean} widebarfactor: { value: 3 description: Multiplier for 'wide' bars for codes which support that minvalue: 2 maxvalue: 5 datatype: int} linewidth: { value: 1 description: Minimum line width minvalue: 1 maxvalue: 3 datatype: int} downloadfilename: { value: {} description: If http header is generated, default download filename at client side datatype: string} eclevel: { value: Q description: error correction level for qr encoding enumeration: L:M:Q:H datatype: int} |
Compiled C module | never | mod_e_barcode.so | ||||
| E_BARCODE_ID | string | Barcode tracking ID | never | |||||||
| E_BEILSTEIN_NUMBER | int | Beilstein registry number for structure ensemble | Tcl script | atomchange bondchange stereochange merge | ||||||
| E_BENZENOID_INDEX | double | The count of benzene ESSSR rings divided by the total number of aromatic ESSSR rings. Zero in case there are no aromatic rings. | Roughley and Jordan, J. Med. Chem. 2011, 54, 3451-3479 | Compiled C module | R_TYPE R_AROMATIC R_HETEROATOM_COUNT | atomchange bondchange atom bond | mod_e_benzenoid_index.so | |||
| E_BINDINGDB_URL | url | Structure display URL for BindingDB database (www.bindingdb.org) | Tcl script | atomchange bondchange atom bond | e_bindingdb_url.xpd | |||||
| E_BINDING_AFFINITY | qualifiedfloat | General binding affinity descriptor | atomchange bondchange stereochange atom bond | |||||||
| E_BIOCYC_ID | string | Database identifier in the BioCyc database (biocyc.org) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_biocyc_id.xpd | ||||
| E_BIOCYC_URL | url | Display URL for a compound in the BioCyc database (biocyc.org) | Tcl script | E_BIOCYC_ID | atomchange bondchange stereochange atom bond | e_biocyc_url.xpd | ||||
| E_BOND_ORDER_COUNT | intvector | Count of bond orders (index 5==aromatic, other bond orders are index to count vector, bond order 0 for non-standard bonds) | special int single int double int triple int quadruple int aromatic int |
excludeh: { value: 0 datatype: boolean}
|
Compiled C module | B_TYPE B_ORDER A_TYPE A_ELEMENT | atomchange bondchange | mod_e_bond_order_count.so | ||
| E_BP | floatpair | Boiling point in Kelvin, with optional temperature range | value float range float |
pressure: { value: 760 datatype: double} pressureunit: { value: Torr datatype: string} |
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE | atomchange bondchange | ||||
| E_BRACKET_ANNOTATION | compound | Bracket as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION. | {} {} {} ROUND:SQUARE:BRACES:CHEVRONS SINGLE:DOUBLE |
coords floatvector linecolor color linewidth float type int orientation int |
A_XY | never | ||||
| E_BRENDA_ID | int | Ligand ID in the BRENDA database (www.brenda-enzymes.org) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_brenda_id.xpd | ||||
| E_BRENDA_URL | url | Ligand display URL in the BRENDA database (www.brenda-enzymes.org) | Tcl script | E_BRENDA_ID | atomchange bondchange stereochange atom bond | e_brenda_url.xpd | ||||
| E_BRENK_ALERTS | stringvector | Structural alerts as per Brenk et al. (see literature reference) | Brenk, R. et al., ChemMedChem 3, 435 (2008) | Tcl script | A_FORMAL_CHARGE A_ELEMENT B_ORDER B_ARORING_COUNT A_ARORING_COUNT | atomchange bondchange atom bond | e_brenk_alerts.xpd | |||
| E_BRICS_FRAGMENTS | structure | Fragmentation of the structure according to the Raray BRICS rules. | ChemMedChem 2008, 3, 1503 | shredderpatternfile: { value: brics_shred.smarts datatype: diskfile constraints: readable} excludepatternfile: { value: brics_exclude.smarts datatype: diskfile constraints: readable} trace: { value: 0 datatype: boolean} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER B_FRAGMENT_CARBON_COUNT B_FRAGMENT_CARBON_CHAIN_LENGTH | atomchange bondchange atom bond | e_brics_fragments.xpd | ||
| E_BRUNS_WATSON_DEMERIT | compound | An implementaton of the Bruns/Watson structural MedChem filters as published in J. Med. Chem. 2012, 55, 9763-9772. The return value is a score between 0 (nothing found) up to an integer >= 100. 100 is the threshold where a comoiund should be rejected, values inbetween are scaled demerits. By default the check stops after the threshold has been reached - it can happen that the sum of demerits at that time has reached exactly 100 or a higher value. It is possible to force the use of the complete rule set by a parameter to tally up the complete set of disagreeable features. The rule set is editable and can be user-expanded. The query files are located at $DATADIR/propdata/e_bruns_watson_demerit. | J. Med. Chem. 2012, 55, 9763-9772 | demerit int features dictionary |
useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold has been reached, the evaluation stops. datatype: boolean} reportallrules: { value: 0 description: If set, report on the match scores of all applied rules, not just the ones which change the demerit score datatype: boolean} threshold: { value: 100 description: The threshold after which to stop further computation datatype: int} |
Compiled C module | E_BRUNS_WATSON_INITIAL_DEMERIT | atomchange bondchange atom bond | mod_e_bruns_watson_demerit.so | |
| E_BRUNS_WATSON_INITIAL_DEMERIT | compound | Bruns/Watson non-substructural filters as published in J. Med. Chem. 2012, 55, 9763-9772. The return value is a value between 0 and 100, where 100 is outright rejection, 0 no problems found, and values inbetween for demerit points. |
J. Med. Chem. 2012, 55, 9763-9772 | demerit int features dictionary |
heavy_atom_lower_cutoff: { value: 7 description: Reject compound if fewer heavy atoms found datatype: int} heavy_atom_upper_cutoff: { value: 40 description: Reject compound if more heavy atoms found datatype: int} heavy_atom_demerit_threshold: { value: 25 description: Demerit compound if more heavy atoms found datatype: string} use_formal_charge: { value: 0 description: If set, use A_FORMAL_CHARGE for plus(minus rules. By default, use E_CHARGED_GROUP_COUNTS datatype: boolean} useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold of 100 has been reached, the evaluation stops. datatype: boolean} threshold: { value: 100 description: The threshold after which to stop further computation datatype: int} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT A_MOL_NUMBER A_HEAVY_SUBSTITUENT_COUNT A_RING_COUNT A_FORMAL_CHARGE A_ISOTOPE R_TYPE A_UNSATURATION A_CH2_CHAIN_LENGTH E_NSSSR | atomchange bondchange atom bond | mod_e_bruns_watson_initial_demerit.so | |
| E_CAMEO_ID | int | Registration ID in Cameo Chemicals safety database (https://cameochemicals.noaa.gov). | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_cameo_id.xpd | ||||
| E_CAMEO_URL | url | Data display URL in Cameo Chemicals safety database (https://cameochemicals.noaa.gov). | Tcl script | E_CAMEO_ID | atomchange bondchange stereochange atom bond | e_cameo_url.xpd | ||||
| E_CANONIC_TAUTOMER | structure | Canonic tautomer form of ensemble, selected from a rated collection of generated tautomers. | maxtautomers: { value: 500 description: Maximum number of tautomers to generate and rate datatype: int} maxtransforms: { value: -1 description: Maximum number of tautomer transforms to apply datatype: int} useneutralform: { value: 0 description: If set, compute on E_NEUTRALIZED_STRUCTURE instead of current structure datatype: boolean} preservegroups: { value: 0 datatype: boolean} |
Compiled C module | A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange merge mol atom bond | mod_e_canonic_tautomer.so | |||
| E_CARBON_COUNT | int | Number of carbon atoms in ensemble - the same as E_ELEMENT_COUNT(6) | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_carbon_count.so | ||||
| E_CAS | string | Chemical Abstracts registry number for structure ensemble | useresolver: { value: 1 datatype: string} usepubchem: { value: 1 datatype: string} uselookchem: { value: 0 datatype: string} |
Tcl script | atomchange bondchange stereochange merge | |||||
| E_CAS_URL | url | CommonChemistry URL linked via CAS number. By default the validity of the target is not verified - set parameter to perform this check. | verify: { value: 0 datatype: boolean}
|
Tcl script | E_CAS | atomchange bondchange stereochange merge | e_cas_url.xpd | |||
| E_CATALOG | compound | Catalog data | producer stringvector catnum stringvector country stringvector packsize intvector purity shortvector price intvector |
atomchange bondchange stereochange merge | ||||||
| E_CATALOG_CAS | stringvector | CAS numbers of compound in catalog | never | |||||||
| E_CATALOG_NAMES | stringvector | Names of compound in a catalog | never | |||||||
| E_CCRIS_URL | url | Display URL in EPA CCRIS (Chemical Carcinogenesis Research Information System, https://toxnet.nlm.nih.gov/newtoxnet/ccris.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_ccris_url.xpd | ||||
| E_CDXML_IMAGE | diskfile (switchable between blob diskfile xmlstring) |
A standard structure rendering in the ChemDraw XML format. This is not a complete file which could be loaded into ChemDraw, but a building block to assemble CDXML files. | width: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int} height: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int} bonds: { value: 8 minvalue: 2 maxvalue: 32 datatype: int} filename: { value: {} datatype: string constraints: writeable} border: { value: 12 minvalue: 0 maxvalue: 256 datatype: int} idstart: { value: -1 minvalue: -1 datatype: int} frame: { value: 0 datatype: boolean} xoffset: { value: 8 datatype: double} yoffset: { value: 8 datatype: double} framecolor: { value: black datatype: color} markcolor: { value: blue datatype: color} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT B_FLAGS A_FLAGS | atomchange bondchange stereochange merge mol atom bond | mod_e_cdxml_image.so | |||
| E_CDXML_STRING | xmlstring | Structure encoded in CDXML (CambridgeSoft) | Tcl script | atomchange bondchange stereochange merge hadd atom bond | e_cdxml_string.xpd | |||||
| E_CENTER | compound | Box, geometric and mass-weighted ensemble center | box floatvector geo floatvector mass floatvector |
coordinateproperty: { value: A_XYZ datatype: string} useh: { value: 1 datatype: string} |
(builtin) | E_XYZEXTENT A_WEIGHT A_XYZ | atomchange bondchange 3drelative 3dabsolute | |||
| E_CHANGEDATE | date | Change data time stamp for molecule | Tcl script | never | e_changedate.xpd | |||||
| E_CHARGE | short | Sum of charges in ensemble | (builtin) | A_FORMAL_CHARGE | atomchange | |||||
| E_CHARGED_ATOM_COUNT | int | Number of atoms which are formally charged and not direclty adjacent to an atom of opposite formal charge (such as in ionic nitro groups). | Compiled C module | A_TYPE A_FORMAL_CHARGE B_TYPE | atomchange bondchange atom bond | mod_e_charged_atom_count.so | ||||
| E_CHARGED_GROUP_COUNTS | intpair | Counts of groups charged positively or negatively under neutral conditions in protic solvents. This is a simple guestimate from A_HYDROGEN_BONDING, using acidic and basic groups as starting points and combining close centers (i.e. a P(=O)(OH)2 group with 2 acidic protons only gets a single positive charge count). | positive int negative int |
Compiled C module | M_CHARGED_GROUP_COUNTS | atomchange bondchange atom bond | mod_e_charged_group_counts.so | |||
| E_CHEBI_ID | string | ChEBI ID (www.ebi.ac.uk/chebi) | Tcl script | E_STDINCHI | atomchange bondchange stereochange merge | e_chebi_id.xpd | ||||
| E_CHEBI_URL | url | ChEBI structure data display URL | urlencoding: { value: 1 datatype: boolean}
|
Tcl script | E_CHEBI_ID | atomchange bondchange stereochange merge | e_chebi_url.xpd | |||
| E_CHECKDATE | date | Check data time stamp for molecule | Tcl script | never | e_checkdate.xpd | |||||
| E_CHEMAGORA_URL | url | Display link for ChemAogra (chemagora.jrc.ec.europa.eu) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_chemagora_url.xpd | ||||
| E_CHEMBASE_ID | int | Record ID in Chembase (en.chembase.cn) | matchatomstereo: { value: 1 datatype: boolean} matchbondstereo: { value: 1 datatype: boolean} matchisotopes: { value: 1 datatype: boolean} matchcharges: { value: 1 datatype: boolean} matchradicals: { value: 1 datatype: boolean} |
Tcl script | atomchange bondchange atom bond | e_chembase_id.xpd | ||||
| E_CHEMBASE_URL | url | Display URL in ChemBase database (en.chembase.cn) | Tcl script | E_CHEMBASE_ID | atomchange bondchange atom bond | e_chembase_url.xpd | ||||
| E_CHEMBL_ASSAY_IDS | stringvector | ChEMBL assay IDs which test the substance | limit: { value: 5000 description: Maximum number of assay IDs to retrieve minvalue: 1 datatype: int}
|
Tcl script | atomchange bondchange atom bond | e_chembl_assay_ids.xpd | ||||
| E_CHEMBL_ID | string | ChEMBL ID (https://www.ebi.ac.uk/chembl/) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange merge | e_chembl_id.xpd | ||||
| E_CHEMBL_MEDCHEM_FRIENDLY | boolean | Implementation of the simple CHEMBL MedChemFriendly filter, a simple substructure-based exclusion list. | Tcl script | atomchange bondchange atom bond | e_chembl_medchem_friendly.xpd | |||||
| E_CHEMBL_URL | url | ChEMBL compound data display URL (https://www.ebi.ac.uk/chembl) | Tcl script | E_CHEMBL_ID | atomchange bondchange stereochange merge | e_chembl_url.xpd | ||||
| E_CHEMBUYERSGUIDE_IDS | compoundvector | Get company name and their catalog number by querying chembuyersguide.com via full-structure search. | name string catalogno string |
Tcl script | atomchange bondchange atom bond | e_chembuyersguide_ids.xpd | ||||
| E_CHEMDB_ID | string | Structure ID in the NIH NIAID ChemDB database (https://chemdb.niaid.nih.gov) | Tcl script | E_CAS | atomchange bondchange atom bond | e_chemdb_id.xpd | ||||
| E_CHEMDB_URL | url | Data display URL for the NIH NIAID ChemDB database | Tcl script | E_CHEMDB_ID | atomchange bondchange stereochange atom bond | e_chemdb_url.xpd | ||||
| E_CHEMDIV_ID | string | ID of structure in ChemDiv (chemistryondemand.com) database | Tcl script | E_SMILES | atomchange bondchange atom bond | e_chemdiv_id.xpd | ||||
| E_CHEMDIV_URL | url | Data display URL for structure in catalog of chemdiv.com/chemistryondemand.com | atomchange bondchange stereochange atom bond | |||||||
| E_CHEMEO_ID | string | ID in the Chemeo properties database (www.chemeo.com) | Tcl script | atomchange bondchange atom bond | e_chemeo_id.xpd | |||||
| E_CHEMEO_URL | url | Display URL for the Chemeo properties database (www.chemeo.com) | Tcl script | atomchange bondchange atom bond | e_chemeo_url.xpd | |||||
| E_CHEMEXPER_URL | url | ChemExper data display URL (chemexper.com) | querytype: { value: fs enumeration: fs:ss datatype: int}
|
Tcl script | E_CHEMEXPER_URL | mol atom bond | e_chemexper_url.xpd | |||
| E_CHEMICALBOOK_ID | string | Database ID for the chemicalbook.com site | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_chemicalbook_id.xpd | ||||
| E_CHEMICALBOOK_URL | url | Data display URL for the chemicalbook.com site | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_chemicalbook_url.xpd | ||||
| E_CHEMICALIZE_URL | url | URL to submit compound to chemicalize.org computational service by ChemAxon | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_chemicalize_url.xpd | ||||
| E_CHEMICAL_BEAUTY | double | Chemical beauty score (aka QED, quantitative estimate of drug likeness). Because we are using different logP and HA/HD algorithms, the results are not exactly identical to those from the publication, but close. | Bickerton et al., Nature Chemistry, 4, 90 (2012) | weightingscheme: { value: max enumeration: max:mo:u datatype: int}
|
Tcl script | E_BRENK_ALERTS E_WEIGHT E_XLOGP2 E_NHDONORS E_NHACCEPTORS E_NROTBONDS E_TPSA E_ARORING_COUNT | atomchange bondchange stereochange atom bond | e_chemical_beauty.xpd | ||
| E_CHEMIDPLUS_ID | string | ChemIDPlus structure id (from http://chem.sis.nlm.nih.gov) | Tcl script | E_STDINCHIKEY | mol atom bond | e_chemidplus_id.xpd | ||||
| E_CHEMIDPLUS_URL | url | ChemIDPlus URL | Tcl script | E_CHEMIDPLUS_ID | mol atom bond | e_chemidplus_url.xpd | ||||
| E_CHEMSPIDER_ID | string | chemspider.com structure record ID | Tcl script | E_STDINCHI | atomchange bondchange stereochange merge | e_chemspider_id.xpd | ||||
| E_CHEMSPIDER_URL | url | chemspider.com structure data display URL | Tcl script | E_CHEMSPIDER_ID | atomchange bondchange stereochange merge | e_chemspider_url.xpd | ||||
| E_CHEMSYNTHESIS_ID | int | ID of structure in ChemSynthesis database (www.chemsynthesis.com) | Tcl script | atomchange bondchange merge mol | e_chemsynthesis_id.xpd | |||||
| E_CHEMSYNTHESIS_URL | url | Data sccess URL of structure in ChemSynthesis database (www.chemsynthesis.com) | Tcl script | E_CHEMSYNTHESIS_ID | atomchange bondchange merge mol | e_chemsynthesis_url.xpd | ||||
| E_CHIRALITY | byte | Stereo status and potential of ensemble | none:meso:unspecified:chiral:contradictory |
Compiled C module | M_CHIRALITY | atomchange bondchange stereochange mol atom bond | mod_e_chirality.so | |||
| E_CHIRAL_POTENTIAL | intpair | Number of possible chiral atom and bond centers | Tcl script | A_STEREOGENIC B_STEREOGENIC A_TYPE | atomchange merge atom bond | e_chiral_potential.xpd | ||||
| E_CID | int | PubChem CID structure identifier | trace: { value: 0 datatype: boolean}
|
Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange merge hadd | e_cid.xpd | |||
| E_CIF_BLOCK | table | _loop dataset of a CIF file | never | |||||||
| E_CLASSIFIED_BOND_COUNT | intvector | Counts of used-defined classes of bonds | bondtypes: { value: C-C C=C C*C C-X C=X C*X X-X X=X X*X C-H X-H description: The bond types to look for, in element/bondordersymbol/element notation datatype: string constraints: list}
|
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange merge | mod_e_classfied_bond_count.so | |||
| E_CLASSIFIED_SURFACE_AREA | doublevector | Estimated surface area classified by atom type | P. Labute, Methods in Molecular Biology, 275, 261ff | total_double double carbon double hydrogen double hetero double aromatic double aliphatic double ring double chain double |
Compiled C module | A_SURFACE_AREA A_ISAROMATIC A_ELEMENT A_TYPE A_RING_COUNT | atomchange bondchange 3dabsolute hadd atom bond | mod_e_classified_surface_area.so | ||
| E_CLASSYFIRE_CLASSIFICATION | jsonstring | ClassyFire classification (http://classyfire.wishartlab.com) | Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61. | Tcl script | atomchange bondchange stereochange merge | e_classyfire_classification.xpd | ||||
| E_CLASSYFIRE_URL | url | ClassyFire display URL (http://classyfire.wishartlab.com) | Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61. | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange merge | e_classyfire_url.xpd | |||
| E_CLEANNAME | string | Name cleaned from purity info and miscellaneous remarks | keeppurity: { value: 1 datatype: boolean} keepstereo: { value: 1 datatype: boolean} keepisotope: { value: 1 datatype: boolean} keepsalt: { value: 1 datatype: boolean} trace: { value: 0 datatype: boolean} watch: { value: {} description: String to watch out for, output notification if found datatype: string} |
Tcl script | E_NAME | never | e_cleanname.xpd | |||
| E_CML_STRING | string | CML structure record as string | pedantic: { value: 1 datatype: boolean}
|
Tcl script | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond | e_cml_string.xpd | ||||
| E_CMSSPECTRUM | compound | Continuous mass spectrum. Filled by reading JCAMP spectrum file of CMS type. | experimental boolean origin string author string date int spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum floatvector |
atomchange bondchange | ||||||
| E_COCONUT_ID | string | Structure key for the Coconut natural products database (http://coconut.naturalproducts.net) | Tcl script | E_STDINCHI | atomchange bondchange stereochange atom bond | e_coconut_id.xpd | ||||
| E_COCONUT_URL | url | Display URL for a natural product entry in the COCNUT database (coconut.naturalproducts.net) | Tcl script | atomchange bondchange atom bond | e_coconut_url.xpd | |||||
| E_COD_ID | int | ID of structure in the Crystallography Open Database (www.crystallography.net) | Tcl script | atomchange bondchange atom bond | e_cod_id.xpd | |||||
| E_COD_URL | url | URL to the Crystallography Open Database (www.crystallography.net) | Tcl script | E_COD_ID | atomchange bondchange atom bond | e_cod_url.xpd | ||||
| E_COLOR | color | Background color to use in plots | never | |||||||
| E_COMMENT | stringvector | Free form comment for ensemble | never | |||||||
| E_COMMONCHEMISTRY_URL | url | Display URL in the ACS CommonChemistry database (commonchemistryy.org) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_commonchemistry_url.xpd | ||||
| E_COMPLEXITY | float | Ensemble complexity according to modified Bertz/Hendrickson algorithm | W. D. Ihlenfeldt, Ph.D. Thesis, TU Munich 1991 | Compiled C module | M_COMPLEXITY M_HASH | atomchange bondchange merge mol | mod_e_complexity.so | |||
| E_COMPOSITION | string | Elemental composition | useimplicith: { value: 1 datatype: boolean}
|
Tcl script | A_WEIGHT A_SYMBOL A_HYDROGENS_NEEDED | atomchange | e_composition.xpd | |||
| E_CONFORMER_ENERGY | floatvector | Estimation of energy of conformer | Compiled C module | A_CONFORMER A_TYPE A_TOPO_DISTANCE A_VDW_INTERACTION | atomchange bondchange stereochange merge 3drelative hadd | mod_e_conformer_energy.so | ||||
| E_CONNECTIVITY | boolean | Pseudo property for connectivity reconstruction | (builtin) | never | ||||||
| E_CONNECTIVITY_MATRIX | floatmatrix | Connectivity matrix, configurable in several variants | usefe: { value: 0 description: If set, the diagonal contains the atom free electron count datatype: boolean} usebo: { value: 0 description: If set, atom pair matrix elements contain the VB bond order, not just 1 for an existing bond datatype: boolean} usearo: { value: 0 description: If set, and bond orders are use, the bond order for aromatic bonds is 1.5 (Kekule VB otherwise) datatype: boolean} |
Compiled C module | B_ORDER B_TYPE B_ISAROMATIC A_FREE_ELECTRONS | atomchange bondchange atom bond | mod_e_connectivity_matrix.so | |||
| E_CONSENSUSPATHDB_URL | url | Display URL in MPG ConsensusPathDB (http://consensuspathdb.org/) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_consensuspathdb_url.xpd | ||||
| E_CONVENTION | string | Free-form description of structure encoding convention | never | |||||||
| E_COSMO_DATA | dictionary | COSMO runtime information | atomchange bondchange stereochange merge 3drelative | |||||||
| E_CREST_URL | url | Display URL in the CREST (Chemical attributes, Regulatory approaches and Experimental STudies, http://www.rmeonline.net/CREST/r1/start.php) database | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_crest_url.xpd | ||||
| E_CTDBASE_ID | string | CTD database ID (ctdbase.org) | Tcl script | E_CAS | atomchange bondchange atom bond | e_ctdbase_id.xpd | ||||
| E_CTDBASE_URL | url | CTD database (ctdbase.org) data display URL | Tcl script | E_CTDBASE_ID | atomchange bondchange atom bond | e_ctdbase_url.xpd | ||||
| E_DATABASE | compound | Info about the database the molecule was read from | dbtype string database string host string port int table string id int time date |
atomchange bondchange stereochange merge | ||||||
| E_DAYLIGHT_ARORING_COUNT | short | Count of aromatic rings in ESSSR, always using Daylight aromaticity definition | Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE | atomchange bondchange atom bond ring | mod_e_daylight_aroring_count.so | ||||
| E_DBREFERENCE | stringvector | Generic free-form database references associated with ensemble | never | |||||||
| E_DECORATED_STRUCTURES | dataset | Exhaustive set of structures generated by decorating a core with any combination of user-supplied substituents. | substituents: { value: {} description: Substituent fragments in line notation. The first atom of these is their attachment point datatype: string constraints: list} coreatomfilters: { value: hydrogen chbond description: These atoms on the core will be replaced by combinations of fragments datatype: string constraints: filterlist} duphash: { value: E_HASHY description: Hash code used to remove duplicates datatype: string constraints: property} |
Tcl script | atomchange bondchange atom bond | e_decorated_structures.xpd | ||||
| E_DEGLYCOSILATED_STRUCTURE | structure | Structure with glycolisation fragments removed | spinach1: { value: C1-2O0-1H3- datatype: string} spinach2: { value: O0-2N0-1C0-2H+ datatype: string} |
Tcl script | atomchange bondchange stereochange shuffle atom bond | e_deglycosilated_structure.xpd | ||||
| E_DENSITY | float | Density of compound at room temperature in kg/L | Tcl script | A_ELEMENT A_ISOTOPE | atomchange bondchange | e_density.xpd | ||||
| E_DICTIONARY_OF_NATURAL_PRODUCTS_ID | string | Entry ID in dictionary of natural products (dnp.chemnetbase.com) | Tcl script | E_MRV_STRING | atomchange bondchange stereochange atom bond | e_dictionary_of_natural_products_id.xpd | ||||
| E_DICTIONARY_OF_NATURAL_PRODUCTS_URL | url | Display URL in dictionary of natrual products (dnp.chemnetbase.com) | Tcl script | E_DICTIONARY_OF_NATURAL_PRODUCTS_ID | atomchange bondchange atom bond | e_dictionary_of_natural_products_url.xpd | ||||
| E_DIPOLEMOMENT | compound | Dipole Moment. The computation links indirectly vie E_HEAT_OF_FORMATION to a VAMP run. | pointcharge floatvector hybrid floatvector sum floatvector |
A_XYZ | atomchange bondchange stereochange 3drelative | |||||
| E_DOTSURFACE | xyzvector | Coordinates of points on dot-surface | distance: { value: 0 description: dot distance to VDW surface (nm) datatype: double} density: { value: 30 description: average number of dots per atom datatype: int} |
A_XYZ A_ELEMENT | atomchange bondchange stereochange 3drelative 3dabsolute | |||||
| E_DRUGBANK_ID | string | Drugbank ID, looked up over the Internet | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_drugbank_id.xpd | ||||
| E_DRUGBANK_URL | url | Drugbank data display URL | Tcl script | E_DRUGBANK_ID | atomchange bondchange stereochange merge | e_drugbank_url.xpd | ||||
| E_DRUGINFO_URL | url | Display URL for the NIH DrugInfo prtal (druginfo.nlm.nih.gov) | Tcl script | E_UNII | atomchange bondchange atom bond | e_druginfo_url.xpd | ||||
| E_EC50 | compound | EC50 aids screen data | concentration float concunit shortstring flag shortstring ecconc float nexperiments short |
atomchange bondchange merge | ||||||
| E_ECHA_URL | url | Display number for a structure in the EU ECHA (European Chemicals Agency) registration system. | E_CAS | atomchange bondchange stereochange atom bond | ||||||
| E_ECHEMPORTAL_URL | url | Link into the OECD echemportal.org site | Tcl script | E_CAS | atomchange bondchange atom bond | e_echemportal_url.xpd | ||||
| E_EC_FINGERPRINT | bitvector (switchable between bitvector bytevector shortvector intvector) |
An ECFP-style fingerprint implementation. This property merges atomic enviroment hash codes from property A_EC_HASH for different numbers of spheres into a fingerprint or count vector. The number of enviroment spheres used is controlled by the settings of A_EC_HASH - this is a vector, and each element is the hashed atom enviroment including an additional sphere. If changed from default data type bitvector to bytevector, shortvector or intvector, the number of found atom environments in A_EC_HASH is counted. |
diameter: { value: -1 description: Maximum neighbor distance to consider. Must be <= length of A_EC_HASH vector, use -1 to use vector length minvalue: -1 maxvalue: 15 datatype: int} length: { value: 1024 description: Folded bitvector length minvalue: 16 maxvalue: 32768 datatype: int} counts: { value: 0 description: Whether to use counts enumeration: no:linear:exponential datatype: int} debug: { value: 0 description: If set, print debug info datatype: boolean} |
Compiled C module | A_EC_HASH | atomchange bondchange atom bond | mod_e_ec_fingerprint.so | |||
| E_EC_NUMBER | string | The European Community registration number for a compound with the European Chemicals Agency (ECHA, echa.europa.eu). This replaces the EINECS system (property E_EINECS_ID). Note that this identifier is very different from the enzyme commission EC number for proteins. | usepubchem: { value: 0 datatype: boolean} useecha: { value: 1 datatype: boolean} |
Tcl script | E_CID E_CAS | atomchange bondchange stereochange atom bond | e_ec_number.xpd | |||
| E_EEROS_URL | url | Data display URL for compound in Wiley Electronic Encyclopedia of Reagents for Organic Synthesis (https://onlinelibrary.wiley.com/doi/book/10.1002/047084289X) | Tcl script | E_STDINCHIKEY | atomchange bondchange atom bond | e_eeros_url.xpd | ||||
| E_EFFECTIVE_ROTOR_COUNT | double | Effective rotor count, computed from rotatable bonds (B_ROTATABILITY) and fractional values for ring flexibility. | usecanonictautomer: { value: 0 description: If set, compute on standard tautomer instead of current structure datatype: boolean}
|
Tcl script | B_ROTATABILITY | atomchange bondchange | e_effective_rotor_count.xpd | |||
| E_EGAN_BIOAVAILABILITY_FLAG | boolean | Veber bioavailability flag (E_XLOGP2<=5.88 && E_TPSA<=131.6) | Journal of Medicinal Chemistry, Vol. 43, pp. 3867-3877, 2000 | Compiled C module | E_XLOGP2 E_TPSA | atomchange bondchange atom bond | mod_e_egan_bioavailability_flag.so | |||
| E_EIGENVALUES | floatvector | MO Eigenvalues | A_XYZ | atomchange bondchange | ||||||
| E_EINECS_ID | string | EINECS ID. Note that this is now an outdated identifier with the launch of the EU REACH system. It should be replaced by the ECHA (https://echa.europa.eu) European Commission EC number (property E_EC_NUMBER, this is not the same as the Enzyme Commission protein EC number). | Tcl script | E_SDF_STRING | atomchange bondchange stereochange merge | e_einecs_id.xpd | ||||
| E_ELECTRONIC_ENERGY | float | Measured or computed electronic energy, as returned by, for example, a QM program. This property currently is used for reading VAMP data. | atomchange bondchange | |||||||
| E_ELEMENT_COUNT | shortvector | Count of element types of atoms of ensemble | ? short h short he short li short be short b short c short n short o short f short ne short na short mg short al short si short p short s short cl short ar short k short ca short sc short ti short v short cr short mn short fe short co short ni short cu short zn short ga short ge short as short se short br short kr short rb short sr short y short zr short nb short mo short tc short ru short rh short pd short ag short cd short in short sn short sb short te short i short xe short cs short ba short la short ce short pr short nd short pm short sm short eu short gd short tb short dy short ho short er short tm short yb short lu short hf short ta short w short re short os short ir short pt short au short hg short tl short pb short bi short po short at short rn short fr short ra short ac short th short pa short u short np short pu short am short cm short bk short cf short es short fm short md short no short lr short rf short db short sg short bh short hs short mt short ds short |
(builtin) | A_ELEMENT A_TYPE | atomchange merge hadd | ||||
| E_ELLIPSE_ANNOTATION | compound | Ellipse as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float bgcolor color style bitset |
A_XY | never | ||||
| E_EMBL_SIDER_URL | url | Data display link in the EMBL Sider database (http://sideeffects.embl.de) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_embl_sider_url.xpd | ||||
| E_EMBL_STITCH_URL | url | Data display URL in the STITCH database (http://stitch.embl.de) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_embl_stitch_url.xpd | ||||
| E_EMF_IMAGE | diskfile (switchable between blob diskfile url) |
Metafile WIN32 structure drawing | width: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int} height: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue" datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: string} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: smiles datatype: string} metadata: { value: 1 datatype: boolean constraints: writeable} filename: { value: {} datatype: diskfile} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.4 datatype: double} colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} symbolfontsize: { value: -1 datatype: double} annotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} usehatch: { value: 0 datatype: boolean} format: { value: wmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int} frame: { value: 1 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: int} linespacing: { value: 2.0 datatype: double} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 6 datatype: int} wiggleamplitude: { value: 1.5 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} crop: { value: -1 datatype: int} showstereogroups: { value: 0 datatype: boolean} font: { value: Arial datatype: string} usesubscripts: { value: 1 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR A_ANNOTATION B_FLAGS A_FLAGS | atomchange bondchange stereochange merge hadd mol | mod_e_emf_image.so | |||
| E_EMOLECULES_ID | string | EMolecules Web database ID (www.emolecules.com) | catalog: { value: all enumeration: SC:BB:all datatype: string}
|
Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_emolecules_id.xpd | |||
| E_EMOLECULES_URL | url | EMolecules (www.emolecules.com) Web database display URL | Tcl script | E_EMOLECULES_ID | atomchange bondchange stereochange merge | e_emolecules_url.xpd | ||||
| E_ENAMINE_ID | string | Catalog ID for the Enamine catalog (enaminestore.com) | Tcl script | atomchange bondchange stereochange atom bond | e_enamine_id.xpd | |||||
| E_ENAMINE_URL | url | Data display URL for the Enamine catalog (enaminestore.com) | Tcl script | E_ENAMINE_ID | atomchange bondchange stereochange atom bond | e_enamine_url.xpd | ||||
| E_ENANTIOMER | structure | Enantiomer of ensemble (i.e. all tetrahedral stereochemistry is reversed) | Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange merge | e_enantiomer.xpd | ||||
| E_ENERGY | float | Ensemble energy | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange stereochange merge 3drelative | ||||||
| E_ENS_COUNT | int | Pseudo-property: Number of ens in ensemble - always 1, needed for generality in processing bind sets in "scan" queries | Compiled C module | atomchange bondchange atom bond | mod_e_ens_count.so | |||||
| E_EPA_ACTOR_URL | url | EPA Actor data access | Tcl script | E_CAS | atomchange bondchange stereochange | e_epa_actor_url.xpd | ||||
| E_EPA_COMPTOX_URL | url | Data display URL for the new EPA CompTox portal | Tcl script | E_STDINCHIKEY | atomchange bondchange atom bond | e_epa_comptox_url.xpd | ||||
| E_EPA_HPVIS_URL | url | Data display URL in US EPA High Production Volume Information System (HPVIS), https://www.epa.gov/hpvis | Tcl script | E_CAS | atomchange bondchange atom bond | e_epa_hpvis_url.xpd | ||||
| E_EPRSPECTRUM | compound | EPR spectrum, usually read from JCAMP file | experimental boolean origin string author string date int spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum floatvector |
atomchange bondchange stereochange | ||||||
| E_EPS_IMAGE | diskfile (switchable between blob diskfile) |
A 2D-plot of the structure as EPS image file | width: { value: 180 datatype: int} height: { value: 180 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: string} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: string} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: string} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: string} comment: { value: E_NAME datatype: string} structure: { value: none enumeration: none:smiles:stdinchi:cactvs:molfile datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} httpheader: { value: 0 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3,tetrahedral:sp2,planar:all datatype: string} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.3 datatype: double} colormode: { value: mono datatype: string} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} symbolfontsize: { value: -1 datatype: double} annotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: string} frame: { value: 0 datatype: boolean} linespacing: { value: 2.5 datatype: double} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filterlist} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filterlist} wigglecount: { value: 10 datatype: int} wiggleamplitude: { value: 3.0 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} showstereogroups: { value: 0 datatype: boolean} font: { value: Helvetica datatype: string} contractgroups: { value: 0 datatype: boolean} framecolor: { value: black datatype: color} downloadfilename: { value: {} datatype: string constraints: writeable} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION | atomchange bondchange stereochange merge hadd | mod_e_eps_image.so | |||
| E_EXACT_MASS | floatpair | Exact mass of most abundant compound isotope combination, assuming natural abundance | weight double abundance double |
useimplicith: { value: 1 description: Whether to include implicit hydrogens in the computation datatype: boolean}
|
Compiled C module | atomchange merge atom | mod_e_exact_mass.so | |||
| E_EXPANDED_QUERY_STRUCTURES | dataset | Tcl script | atomchange bondchange stereochange atom bond | e_expanded_query_structures.xpd | ||||||
| E_EXPERIMENT | string | Experimental setup used to obtain structure data | never | |||||||
| E_EXP_CONNECTIVITY_MATRIX | floatmatrix | Exponent of the connectivity matrix, as per the work of Alexey Lagunin | Molecular Informatics 30, 2011, 241-250 | multiplier: { value: -0.5 description: multiplier for all matrix elements applied before exponent computation datatype: double}
|
Compiled C module | E_CONNECTIVITY_MATRIX | atomchange bondchange atom bond | mod_e_exp_connectivity_matrix.so | ||
| E_FDA_OBJECT_CODE | compound | FDA data code triple from SPL file, identiying for example the type of structure extracted | code string codesystem string displayname string |
atomchange bondchange atom bond | ||||||
| E_FDA_SPL_URL | url | Tcl script | E_UNII | atomchange bondchange atom bond | e_fda_spl_url.xpd | |||||
| E_FDA_SRS_URL | url | Link into FDA SRS (structure registration system) database | Tcl script | E_UNII | atomchange bondchange atom bond | e_fda_srs_url.xpd | ||||
| E_FEATURES | bytevector | Count of structural features defined as parameters by SMARTS expressions | carboxylic_acid byte acid_halogenide byte aldehyde byte ketone byte amine byte primary_amine byte secondary_amine byte tertiary_amine byte quarternary_amine byte hydrazine byte urea byte 12diamine byte pyridine byte thp byte piperidine byte piperazine byte morpholine byte thiomorpholine byte amide byte ester byte alpha_aminoacid byte betaaminoacid byte alpha_ketoacid byte betaketoacid byte alcohol byte phenol byte thiol byte thiophenol byte ether byte thioether byte epoxide byte acetal byte enol byte lactone byte oxime byte nitro byte isocyanate byte thioisocyanate byte anhydride byte cyanide byte sulfonic_acid byte sulfonic_acid_halogenide byte sulfonamide byte phosphoric_acid byte boronic_ester byte silyl_hydride byte siloxyl byte aliphatic_halogen byte aromatic_halogen byte trifluoromethyl byte 11_diphenyl_methyl byte alpha_haloketone byte chalcone byte aromatic_nitrogen byte aromatic_oxygen byte aromatic_sulphur byte cc_doublebond byte cc_triplebond byte phenyl byte |
patterns: { value: {{carboxylic acid} C(=O)O[#1]} {{acid halogenide} C(=O)[Cl,Br,I,F]} {aldehyde CC(=O)[#1]} {ketone CC(=O)C} {amine N([Cx1,cx1,#1])([Cx1,cx1,#1])[Cx1,cx1,#1]} {{primary amine} [Cx1,cx1][NH2;v3]} {{secondary amine} [NH;v3]([Cx1,cx1])([Cx1,cx1])} {{tertiary amine} [N;v3]([Cx1,cx1])([Cx1,cx1])[Cx1,cx1]} {{quarternary amine} [N;v4](C)(C)(C)C} {hydrazine [N;R0][N;R0]} {urea [N;x0]C(=O)[N;x0]} {{1.2-diamine} [NH2]CC[NH2]} {pyridine n1ccccc1} {tetrahydropyrrole N1CCCC1} {piperidine [N;A]1CCCCC1} {piperazine N1CCNCC1} {morpholine N1CCOCC1} {thiomorpholine S1CCOCC1} {amide CC(=O)N([C,c,#1])[C,c,#1]} {ester CC(=O)[O;R0]C} {{alpha-aminoacid} NCC(=O)O} {{beta-aminoacid} NCCC(=O)O} {{alpha-ketoacid} O=CC(=O)O} {{beta-ketoacid} O=CCC(=O)O} {alcohol [C;X4;A]O[#1]} {phenol [c]O[#1]} {thiol [C;X4;A]S[#1]} {thiophenol [c]S[#1]} {ether [Cx1,cx1][O;!r3][Cx1,cx1]} {thioether [Cx1,cx1][S;!r3][Cx1,cx1]} {epoxide C1OC1} {acetal [Cx1,cx1]O[Cx2]O[Cx1,cx1]} {enol C=CO} {lactone [C;R](=O)[O;R]} {oxime C=NO} {nitro N(=O)O} {isocyanate N=C=O} {thioisocyanate N=C=S} {anhydride {C(=O)OC(=O)C}} {cyanide C#N} {{sulfonic acid} S(=O)(=O)O[#1]} {{sulfonic acid halogenide} S(=O)(=O)[F,Cl,Br,I]} {sulfonamide S(=O)(=O)N} {{phosphoric acid derivative} P(=[O,S,N])[N,O,S,F,Cl,Br,I]} {{boronic ester} C[B](O[C,#1])O[C,#1]} {{silyl hydride} [SiH]} {{siloxyl} [Si]O} {{aliphatic halogen} [C;A][F,Cl,Br,I]} {{aromatic halogen} [c][F,Cl,Br,I]} {trifluoromethyl C(F)(F)F} {{1.1-diphenyl-methyl} c1ccccc1C(c1ccccc1)[!C;!c;!#1]} {{alpha-haloketone} CC(=O)C[F,Cl,Br,I]} {chalcone CC(=O)[C;A]=[C;A]} {{aromatic nitrogen} [n]} {{aromatic oxygen} [o]} {{aromatic sulphur} [s]} {{C-C double bond} [C;A]=[C;A]} {{C-C triple bond} C#C} {{phenyl ring} c1ccccc1} datatype: string}
|
Tcl script | A_ELEMENT B_ORDER B_TYPE | atomchange bondchange merge hadd atom bond ring | e_features.xpd | ||
| E_FELDMAN_FINGERPRINT | bitvector | Feldman and Hodes, JCICS 1975 15(3) 147-152 | Python script | atomchange bondchange atom bond | e_feldman_fingerprint.xpd | |||||
| E_FG_COUNT | shortvector | Count of functional groups in ensemble, summed up from molecular FG counts in M_FG_COUNT | Compiled C module | M_FG_COUNT | atomchange bondchange | mod_e_fg_count.so | ||||
| E_FICTS_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICTS datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICTS_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHISY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficts_id.xpd | |||
| E_FICTS_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FICTU_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICTu datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICTU_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHIY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_fictu_id.xpd | |||
| E_FICTU_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FICUS_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICuS datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICUS_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHISY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficus_id.xpd | |||
| E_FICUS_STRUCTURE | structure | Standardized structure for FICUS computations. | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | |||||
| E_FICUU_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICuu datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICUU_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHIY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficuu_id.xpd | |||
| E_FICUU_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FICXX_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICxx datatype: string} scope: { value: private datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICXX_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHIY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficxx_id.xpd | |||
| E_FICXX_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FILE | compound | Info about the file the molecule was read from | filename string startrecord int endrecord int line int format string offset int64 length int |
atomchange bondchange merge | ||||||
| E_FLEXNOVO_FILTER | boolean | Test whether structure passes the FlexNovo smarts pattern filter (which removes reactive or non-druglike componds) | patternfile: { value: flexnovo_exclude.sma datatype: diskfile constraints: readable} trace: { value: 0 datatype: boolean} |
Tcl script | atomchange bondchange atom bond | e_flexnovo_filter.xpd | ||||
| E_FLG_FICTS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_FICTU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_FICUS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_FICUU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUTS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUTU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUUS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUUU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FORMAT | string | Original format in data file (I/O module name) | never | |||||||
| E_FORMULA | string | Molecular formula of ensemble | usecharges: { value: 0 datatype: string} format: { value: ascii datatype: string} useimplicith: { value: 1 datatype: string} usequeryatoms: { value: 0 datatype: string} |
(builtin) | A_ISOTOPE | atomchange merge | ||||
| E_FRAGMENT_COMPOSITION | intvector | Get composition of structure using a user-defined hierarchical fragment database with SMILES/SMARTS fragment definition. Larger fragments, and fragments with more specialized attributes have precedence. Multiple solutions may be found and are attached as E_FRAGMENT_COMPOSITION/n. The result is an int vector with the counts for each fragment in their definition file order. The default fragment set is for the UNIFAC method. Various other fragment files for Joback, Lyderson, Sedlbaur methods are also supplied in the data directory. |
fragfile: { value: unifac.sma datatype: diskfile constraints: readable} explicith: { value: 0 datatype: boolean} debug: { value: 0 datatype: boolean} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange merge hadd | e_fragment_composition.xpd | |||
| E_FRAGMENT_COUNT | dictionary | Counts of all (filtered) fragments the structure, The result is a dictionary with SMARTS keys, and occurence count values. | minsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int} maxsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int} hydrogen: { value: 0 datatype: boolean} mode: { value: absolute description: In relative mode, scale to total count 1 enumeration: absolute:relative datatype: int} keeparo: { value: 0 description: If set, lock A_ISAROMATIC datatype: boolean} aroquery: { value: 0 description: If set, rewrite SMARTS to match only aromatic fragments where applicable datatype: boolean} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange merge atom bond | e_fragment_count.xpd | |||
| E_FRAGMENT_TREE_CUTS | datatree | Topological fragment hierarchy tree - cut bond classification | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| E_FRAGMENT_TREE_HASH | datatree | Topological fragment hierarchy tree - hashcodes | maxcuts: { value: 3 datatype: int} minsize: { value: 2 datatype: int} cutphenyl: { value: 0 datatype: boolean} queryhash: { value: 0 datatype: boolean} dupcheck: { value: hierarchical enumeration: hierarchical:global datatype: string} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | mod_e_fragment_tree_hash.so | |||
| E_FRAGMENT_TREE_LABELS | datatree | Topological fragment hierarchy tree - atom labels of fragments | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| E_FRAGMENT_TREE_SMARTS | datatree | Topological fragment hierarchy tree - SMARTS of fragments | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| E_FRAGMENT_TREE_TABLE | table | Summary of fragmentation routes | Tcl script | E_FRAGMENT_TREE_HASH E_FRAGMENT_TREE_CUTS E_FRAGMENT_TREE_LABELS | atomchange bondchange | e_fragment_tree_table.xpd | ||||
| E_FREQUENCY | string | Generic computed frequencies. Used in Gaussian Archive I/O module | atomchange bondchange merge 3drelative hadd | |||||||
| E_FSP3 | double | Carbon flatness score - the ratio of SP3 hybridized carbon atoms to total carbon atom count | Lovering, F. et al., J.Med.Chem. 2009, 52, 6752-6756 | Compiled C module | A_TYPE A_ELEMENT A_HYBRIDIZATION | atomchange bondchange atom bond | mod_e_fsp3.so | |||
| E_GC | compound | Measured gas-chromatograph spectrum. Used for example in JCAMP I/O module | experimental boolean origin string author string date int spectrometer string parameters string reference string purity float source string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int spectrum floatvector |
atomchange bondchange | ||||||
| E_GDL_ID | int | Substance ID in German hazardous chemicals database (http://www.gefahrstoff-info.de) | Tcl script | E_CAS | atomchange bondchange atom bond | e_gdl_id.xpd | ||||
| E_GDL_URL | url | Data display URL in German hazardous chemicals database (http://www.gefahrstoff-info.de) | Tcl script | E_GDL_ID | atomchange bondchange atom bond | e_gdl_url.xpd | ||||
| E_GENETOX_URL | url | Display URL in EPA GENE-TOX (Genetic Toxicology Data Bank, https://toxnet.nlm.nih.gov/newtoxnet/genetox.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_genetox_url.xpd | ||||
| E_GENOTOXIC_ALERTS | shortvector | Check for problematic potentially genotoxic groups | CE&N Sep 27, 2010 p16ff | patternfile: { value: genotoxic.sma datatype: diskfile constraints: readable}
|
Tcl script | atomchange bondchange merge hadd mol atom bond ring | e_genotoxic_alerts.xpd | |||
| E_GEOOPT_METHOD | string | Geometry optimization method description string. Used for example in the Gaussian Input, Gaussian Archive and Sharc file forms. | atomchange bondchange 3drelative 3dabsolute | |||||||
| E_GI50 | compound | GI50 tumor screen data | concunit shortstring lcconc float panel shortstring cell string panelnumber short cellnumber short nlog_gi50 float ntest_this short ntest_max short |
atomchange bondchange merge | ||||||
| E_GIF | diskfile (switchable between string blob diskfile url) |
A 2D-plot of the structure as a GIF or PNG file | width: { value: 180 datatype: int} height: { value: 180 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} interlace: { value: 1 datatype: boolean} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} secondarycolor: { value: #00D000 datatype: color} highlightbonds: { value: {} datatype: intvector} highlightatoms: { value: {} datatype: intvector} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} crop: { value: -1 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} format: { value: gif enumeration: gif:png:png8:bmp datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string} footerproperty: { value: {} datatype: string} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} font: { value: arialn datatype: string} symbolfontsize: { value: -1 datatype: int} annotationfontsize: { value: -1 datatype: int} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} showisotope: { value: 1 datatype: boolean} isotopemapping: { value: none datatype: string} showstereoh: { value: 1 datatype: boolean} suppressedmols: { value: {} datatype: intvector} linewidth: { value: 1.4 datatype: double} showempty: { value: 0 datatype: boolean} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} showmapping: { value: 0 datatype: boolean} showstereogroups: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color} showchirality: { value: none enumeration: none:simple:extended datatype: int} frame: { value: 0 datatype: boolean} framecolor: { value: black datatype: diskfile} linespacing: { value: 2.0 datatype: double} headerfontsize: { value: -1 datatype: int} footerfontsize: { value: -1 datatype: int} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circlefilter: { value: {} datatype: string} circleatoms: { value: {} datatype: intvector} atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int} wigglecount: { value: 6 datatype: int} wiggleamplitude: { value: 2.0 datatype: double} fixiepngsize: { value: 1 datatype: string} rawcoordinates: { value: 0 datatype: boolean} checkintersection: { value: 0 datatype: boolean} usegrouplabels: { value: 0 datatype: boolean} usesubscripts: { value: 1 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} colormode: { value: color datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} saverendercoordinates: { value: 0 datatype: boolean} labelproperty: { value: {} datatype: string} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION | atomchange bondchange stereochange groupchange merge hadd | mod_e_gif.so | |||
| E_GOLM_URL | url | Data display link into the GOLM metabolome database (http://gmd.mpimp-golm.mpg.de) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_golm_url.xpd | ||||
| E_GOOGLE_SCHOLAR_URL | url | URL for data in the Google Scholar search engine | Tcl script | E_STDINCHI E_STDINCHIKEY E_CAS | atomchange bondchange stereochange atom bond | e_google_scholar_url.xpd | ||||
| E_GPCR_LIGAND_LIKENESS | compound | GPCR ligand structural likeness, computed as maximum similarity score with standard similarity property E_SCREEN on a diverse 1K cpds subset of the GLL database. | Gatica, Cavasotto, J. Chem. Inf. Model. 2011, 52, 1 | similarity byte structure structure |
Tcl script | E_SCREEN | atomchange bondchange atom bond | e_gpcr_ligand_likeness.xpd | ||
| E_GRAPHICS_TEXT | stringvector | Head- and footline for graphics plots | never | |||||||
| E_GRID_VOLUME | floatvolume | Generic floating-point volume grid data. Used for exmapl ein the STF and Gausscube file I/O modules. | atomchange bondchange stereochange merge 3drelative hadd atom bond ring | |||||||
| E_GROUP_COUNT | int | Number of groups defined for the ensemble | Compiled C module | atomchange bondchange groupchange atom bond | mod_e_group_count.so | |||||
| E_GUIDETOPHARMACOLOGY_ID | int | Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org) | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_guidetopharmacology_id.xpd | ||||
| E_GUIDETOPHARMACOLOGY_URL | url | Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org) | Tcl script | E_GUIDETOPHARMACOLOGY_ID | atomchange bondchange stereochange merge | e_guidetopharmacology_url.xpd | ||||
| E_HALIDE_FRACTION | double | Fraction of molecular weight contributed by halogen atoms | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_halide_fraction.so | ||||
| E_HASH | uint64 | Basic ensemble hashcode | (builtin) | M_HASHGROUP M_HASH | atomchange bondchange merge | |||||
| E_HASH128 | uint128 | Perturbed ensemble hashcode, extended to 128 bits | Compiled C module | M_HASHGROUP128 M_HASH128 | atomchange bondchange merge hadd | mod_e_hash128.so | ||||
| E_HASHGROUP_COUNT_A | intvector | Population of basic atom hash groups | (builtin) | A_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_AI | intvector | Population of isotope atom hash groups | (builtin) | A_ISOTOPE_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_AIS | intvector | Population of isotopic stereospecific basic atom hash groups | (builtin) | A_ISOTOPE_STEREO_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_AS | intvector | Population of stereospecific basic atom hash groups | (builtin) | A_STEREO_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_B | intvector | Population of bond hash groups | (builtin) | B_HASH | atomchange bondchange merge | |||||
| E_HASHGROUP_COUNT_BS | intvector | Population of stereospecific bond hash groups | (builtin) | B_STEREO_HASH | atomchange bondchange merge | |||||
| E_HASHGROUP_COUNT_M | intvector | Population of perturbed molecule hash groups | (builtin) | M_HASHY | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_MI | intvector | Population of isotopic perturbed molecule hash groups | (builtin) | M_HASHIY | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_MIS | intvector | Population of isotopic stereospecific perturbed molecule hash groups | (builtin) | M_HASHISY | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_MS | intvector | Population of stereospecifc perturbed molecule hash groups | (builtin) | M_HASHSY | atomchange bondchange merge hadd | |||||
| E_HASHISY | uint64 | Perturbed isotope stereo ensemble hashcode | (builtin) | M_ISOTOPE_STEREO_HASHGROUP_Y M_HASHISY | atomchange bondchange merge hadd | |||||
| E_HASHIY | uint64 | Perturbed isotope ensemble hashcode | (builtin) | M_ISOTOPE_HASHGROUP_Y M_HASHIY | atomchange bondchange merge hadd | |||||
| E_HASHS | uint64 | Stereospecific basic ensemble hashcode | (builtin) | M_STEREO_HASHGROUP M_HASHS | atomchange bondchange merge | |||||
| E_HASHSY | uint64 | Perturbed stereospecific ensemble hashcode | useisotope: { value: 0 datatype: string}
|
(builtin) | M_STEREO_HASHGROUP_Y M_HASHSY | atomchange bondchange merge hadd | ||||
| E_HASHY | uint64 | Perturbed ensemble hashcode | useisotope: { value: 0 datatype: string}
|
(builtin) | M_HASHGROUP_Y M_HASHY | atomchange bondchange merge hadd | ||||
| E_HEAT_OF_FORMATION | float | Measured or computed Heat of Formation. The computation procedure tries to run a simple VAMP job. This proeprties acts as the cornerstone for a standard set of QM-related properties via windfall/indirect property definition relationships. | filename: { value: {} datatype: string} prgpath: { value: /usr/local/bin/vamp datatype: string} method: { value: AM1 datatype: string} |
Tcl script | A_XYZ | atomchange bondchange | e_heat_of_formation.xpd | |||
| E_HEAVY_ATOM_COUNT | int | Number of non-hydrogen atoms in the ensemble | Compiled C module | A_ELEMENT A_TYPE | atomchange bondchange mol atom bond | mod_e_heavy_atom_count.so | ||||
| E_HEAVY_BOND_COUNT | int | Count of VB bonds which do not contain hydrogen | Compiled C module | A_TYPE A_ELEMENT B_TYPE | atomchange | mod_e_heavy_bond_count.so | ||||
| E_HETEROATOM_CARBON_RATIO | double | Number of hetero atoms devided by number of carbon atoms | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_heteroatom_carbon_ratio.so | ||||
| E_HETEROATOM_COUNT | int | Number of hetero (not C or H) atoms in the ensemble | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_heteroatom_count.so | ||||
| E_HISTORY | compoundvector | Record history | program string version string patchlevel string pgmdate date user string date date machine string |
never | ||||||
| E_HIT2LEAD_ID | int | Catalog number from www.hit2lead.com (aka ChemBridge) | database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
|
Tcl script | E_SDF_STRING | atomchange bondchange atom bond | e_hit2lead_id.xpd | |||
| E_HIT2LEAD_URL | url | Display URL for a hit2lead (www.hit2lead.com, aka ChemBridge) database entry | database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
|
Tcl script | E_HIT2LEAD_ID | atomchange bondchange atom bond | e_hit2lead_url.xpd | |||
| E_HMDB_ID | string | ID of structure in the HMDB database (www.hmdb.ca) | Tcl script | E_SMILES | atomchange bondchange atom bond | e_hmdb_id.xpd | ||||
| E_HMDB_URL | url | Display URL of structure in the HMDB database (www.hmdb.ca) | Tcl script | E_HMDB_ID | atomchange bondchange atom bond | e_hmdb_url.xpd | ||||
| E_HSDB_URL | url | Display URL for the HSDB (http://toxnet.nlm.nih.gov/newtoxnet/hsdb.htm) database | Tcl script | E_CAS | atomchange bondchange atom bond | e_hsdb_url.xpd | ||||
| E_HYDROGEN_BOND_CENTER_COUNT | int | Number of heavy atoms that can act as hydrogen donor or acceptor | Tcl script | A_HYDROGEN_BONDING | never | e_hydrogen_bond_center_count.xpd | ||||
| E_HYDROGEN_COMPLETE | boolean | Boolean flag indicating whether there are no open hydrogen sites | Compiled C module | A_HYDROGENS_NEEDED | atomchange bondchange hadd atom bond | mod_e_hydrogen_complete.so | ||||
| E_IC50 | compound | IC50 aids screen data | concentration float concunit shortstring flag shortstring icconc float nexperiments short |
atomchange bondchange merge | ||||||
| E_ICSC_CARD_ID | shortstring | International Chemical Safety Cards ID (from www.ilo.org) | Tcl script | E_CAS | atomchange bondchange atom bond | e_icsc_card_id.xpd | ||||
| E_ICSC_CARD_URL | url | International Chemical Safety Cards display URL (from www.ilo.org) | Tcl script | E_ICSC_CARD_ID | atomchange bondchange atom bond | e_icsc_card_url.xpd | ||||
| E_IDENT | string | Short ensemble identification string | (builtin) | never | ||||||
| E_IDENTIFIER_NORM_DATASET | dataset | Debug property for FICUS suite | atomchange bondchange atom bond | |||||||
| E_IDENTIFIER_NORM_EXEMPTION_LIST | stringvector | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_IDTF_MODEL | blob (switchable between blob diskfile mapfile) |
3D structure model in Intel IDTF format | style: { value: spacefill enumeration: ballstick:capped:spacefill:wireframe:all datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} bondradius: { value: 15 datatype: double} ignoreh: { value: 0 datatype: boolean} vdwscaling: { value: 25 datatype: double} atomhighlightcolor: { value: red datatype: color} highlightatoms: { value: {} datatype: intvector} bondhighlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} showbondorder: { value: 0 datatype: boolean} bondcolor: { value: atomsplit datatype: string} structure: { value: 0 datatype: boolean} showlabel: { value: 0 datatype: boolean} labelcolor: { value: purple datatype: color} addlights: { value: 0 datatype: boolean} addview: { value: 0 datatype: boolean} glossfactor: { value: 75 datatype: double} labelsize: { value: 15 datatype: int} tesselation: { value: octahedron 4 20 20 datatype: string} dynamictesselation: { value: 1 datatype: boolean} downloadfilename: { value: {} datatype: string} suppressedatoms: { value: {} datatype: intvector} suppressedbonds: { value: {} datatype: intvector} |
Compiled C module | A_XYZ A_ELEMENT B_TYPE B_ORDER B_FLAGS A_FLAGS A_COLOR B_COLOR | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd | mod_e_idtf_model.so | |||
| E_IMAGEMAP | string | HTML imagemap associated with a GIF/PNG image (property E_GIF) | name: { value: {} datatype: string} mode: { value: mol enumeration: atom:bond:mol datatype: int} target: { value: {} datatype: string} url: { value: {} datatype: string} title: { value: {} datatype: string} |
Tcl script | E_GIF | never | e_imagemap.xpd | |||
| E_IMAGE_SCALING | doublevector | 2D coordinate scaling information (A_XY) for rendering in an image of specified size. The fields are the coordinate scale factor, the x and y offsets (these three values place the drawing into the 0..w/h-1 pixel area), the relative scale factor for the structure needed to fit into the "bonds" size box (1.0 if it fits into the box), and suggested symbol and annotation font sizes in points. | factor double xoffset double yoffset double scale double symbolfontsize double annotationfontsize double |
width: { value: 25ß description: Image width (pixel) datatype: int} height: { value: 250 description: Image height (pixel) datatype: int} border: { value: 10 description: Image border (pixel) minvalue: 0 maxvalue: 100 datatype: int} bonds: { value: 8 description: Number of standard bonds across image minvalue: 1 maxvalue: 20 datatype: int} hidefragment: { value: {} description: Structure fragment to hide and exclude from computation datatype: structure} |
Compiled C module | A_XY | atomchange bondchange atom bond | mod_e_image_scaling.so | ||
| E_INACTIVE_AIDSET | intvector | Set of PubChem assay IDs testing this compound as inactive | Tcl script | E_CID | atomchange bondchange stereochange | e_inactive_aidset.xpd | ||||
| E_INCHI | string | First release InChI identifier (E_STDINCHI following the current standard is preferred) | options: { value: DONOTADDH FIXEDH RECMET NOWARNINGS description: Set of default option words as used in the original NIST software comment: Supported option words: MISMATCHISERROR OUTERRINCHI Key XHash1 XHash2 SNON NEWPSOFF DONOTADDH LooseTSACheck SREL ChiralFlagOFF SUU SLUUD FIXEDH RECMET KET 15T PT_22_00 PT_16_00 PT_06_00 PT_39_00 LargeMolecules Polymers Polymers105 NPZz NoWarnings FoldCRU FoldSRU FrameShift: NoFrameShift NoEdits SATZZ FNUDOFF FixSp3bugOFF FBOFF FB2OFF SPXYZOFF SASXYZOFF Polymers105+. Record processing and output options NOLABELS SAVEOPT AUXNONE NoInCXhI INPAUX START: END: RECORD: MergeHash have no effect. datatype: string constraints: list} fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean} stereoperception: { value: 1 description: If set, perceive stereochemistry, if no, use what is presently set on the structure datatype: boolean} stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int} autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean} prefix: { value: 1 description: If set, include InChI= prefix in output datatype: boolean} stripstereolayer: { value: 0 datatype: boolean} stripisotopelayer: { value: 0 datatype: boolean} stripfixedhlayer: { value: 0 description: If set, the /f layer *and* the following /h and /q layers are stripped datatype: boolean} stripreconnectlayer: { value: 0 datatype: boolean} stripchargelayer: { value: 0 datatype: boolean} |
Compiled C module | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE B_STEREOGENIC B_ISAROMATIC A_ALLENE | atomchange bondchange stereochange merge atom bond | mod_e_inchi.so | |||
| E_INCHIKEY | string | Hash of InChI string | prefix: { value: 1 datatype: boolean}
|
Compiled C module | E_INCHI | atomchange bondchange stereochange atom bond | mod_e_inchikey.so | |||
| E_INCHI_AUXINFO | string | InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting E_INCHI | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange hadd atom bond | ||||||
| E_INPUTDATE | date | Time stamp for molecule | Tcl script | never | e_inputdate.xpd | |||||
| E_IONIZATION_POTENTIAL | float | Measured or computed Ionization potential. This can be computed indirectly via E_HEAT_OF_FORMATION by a VAMP run. | A_XYZ | atomchange bondchange | ||||||
| E_IRIS_URL | url | Display URL in EPA IRIS (Integrated Risk Information System, https://toxnet.nlm.nih.gov/newtoxnet/iris.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_iris_url.xpd | ||||
| E_IRSPECTRUM | compound | Measured or computed IR spectrum. The compuation function attempts to get an IR spectrum from the NIST WebBook, or run a simple VAMP job depending on the "source" parameter, which should be set to "NIST" or "VAMP". | experimental boolean origin string author string date datetime spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum xyvector peaks floatvector peakshape stringvector peakintensity floatvector peakname stringvector |
filename: { value: {} description: temporary job file datatype: diskfile constraints: writeable} prgpath: { value: /usr/local/bin/vamp datatype: diskfile constraints: existing} method: { value: AM1 datatype: string} freqfactor: { value: 0.98 datatype: string} cofreqfactor: { value: 0.90 datatype: string} source: { value: NIST enumeration: NIST:VAMP datatype: int} |
Tcl script | A_XYZ | atomchange bondchange 3drelative | e_irspectrum.xpd | ||
| E_IRSPECTRUM_IMAGE | diskfile (switchable between string blob diskfile url) |
IR spectrum rendering | height: { value: 250 datatype: int} width: { value: 500 datatype: int} bgcolor: { value: white datatype: color} title: { value: {} datatype: string} filename: { value: {} datatype: string constraints: writeable} format: { value: gif enumeration: png,png24:gif:png8 datatype: string} titlecolor: { value: black datatype: color} framecolor: { value: black datatype: color} signalcolor: { value: #DD0000 datatype: color} ystyle: { value: transmittance enumeration: transmittance:absorbance datatype: int} xdirection: { value: reverse enumeration: normal:reverse datatype: int} xstyle: { value: 1/cm enumeration: 1/cm:um datatype: int} |
Tcl script | E_IRSPECTRUM | atomchange bondchange merge mol | e_irspectrum_image.xpd | |||
| E_ISOTOPE_ATOMHASH_COUNT | int | Number of different isotopic basic atom hash codes | (builtin) | E_HASHGROUP_COUNT_AI | atomchange bondchange merge | |||||
| E_ISOTOPE_COUNT | int | Number of isotopically labelled atoms | Compiled C module | A_TYPE A_ISOTOPE | atomchange merge atom bond | mod_e_isotope_count.so | ||||
| E_ISOTOPE_HASH128 | uint128 | Perturbed isotope-sensitive ensemble hashcode, extended to 128 bits | Compiled C module | M_ISOTOPE_HASHGROUP128 M_ISOTOPE_HASH128 | atomchange bondchange merge hadd | mod_e_isotope_hash128.so | ||||
| E_ISOTOPE_MOLHASH_COUNT | int | Number of different isotopic perturbed molecule hash codes | (builtin) | E_HASHGROUP_COUNT_MI | atomchange bondchange merge hadd | |||||
| E_ISOTOPE_STEREO_ATOMHASH_COUNT | int | Number of different isotopic stereospecific basic atom hash codes | (builtin) | E_HASHGROUP_COUNT_AIS | atomchange bondchange merge | |||||
| E_ISOTOPE_STEREO_HASH128 | uint128 | Perturbed isotope-sensitive and stereo-sensitive ensemble hashcode, extended to 128 bits | Compiled C module | M_ISOTOPE_STEREO_HASHGROUP128 M_ISOTOPE_STEREO_HASH128 | atomchange bondchange merge hadd | mod_e_isotope_stereo_hash128.so | ||||
| E_ISOTOPE_STEREO_MOLHASH_COUNT | int | Number of different isotopic stereospecific perturbed molecule hash codes | (builtin) | E_HASHGROUP_COUNT_MIS | atomchange bondchange merge hadd | |||||
| E_ISOTOPE_STEREO_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant ensemble isotope stereo hashcode | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_HASHISY | atomchange bondchange stereochange merge | mod_e_isotope_stereo_tauto_hash.so | |||
| E_ISOTOPE_STEREO_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant ensemble isotope stereo hashcode, 128 bit version | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_ISOTOPE_STEREO_HASH128 | atomchange bondchange stereochange merge | mod_e_isotope_stereo_tauto_hash128.so | |||
| E_ISOTOPE_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant ensemble stereo hashcode, with isotope labels but without stereochemistry | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} setcount: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} stereobondmalus: { value: 0 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_HASHIY | atomchange bondchange merge | mod_e_isotope_tauto_hash.so | |||
| E_ISOTOPE_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant ensemble isotope hashcode, 128 bit version | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_ISOTOPE_HASH128 | atomchange bondchange stereochange merge | mod_e_isotope_tauto_hash128.so | |||
| E_ITER_URL | url | Display URL in EPA ITER (International Toxicity Estimates for Risk, https://toxnet.nlm.nih.gov/newtoxnet/iter.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_iter_url.xpd | ||||
| E_IUPAC_ALLOWED_NAME | string | Allowed IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_allowed_name.xpd | |||||
| E_IUPAC_OECAS_NAME | string | IUPAC name (OEChem CAS-like Style). This is a field in PubChem and used by the ASN I/O module. | atomchange bondchange stereochange | |||||||
| E_IUPAC_PREFERRED_NAME | string | Preferred IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_preferred_name.xpd | |||||
| E_IUPAC_SYSTEMATIC_NAME | string | Systematic IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_systematic_name.xpd | |||||
| E_IUPAC_TRADITIONAL_NAME | string | Traditional IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_traditional_name.xpd | |||||
| E_IUPHAR_ID | int | Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org) | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_iuphar_id.xpd | ||||
| E_IUPHAR_URL | url | Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org) | Tcl script | E_GUIDETOPHARMACOLOGY_ID | atomchange bondchange stereochange merge | e_iuphar_url.xpd | ||||
| E_JCAMP_SPECTRA_BLOCK | compound | Embedded JCAMP spectral data block. Currently only used in E_NMRSPECTRUM to support the newer NTUPLES data table JCAMP style, with real/imaginary spectrum and real/imaginary FID possibly stored all in one file. | name string symbol string {#points} int firstx double lastx double firsty double lasty double xfactor double yfactor double xunit string yunit string data floatvector |
atomchange bondchange atom bond | ||||||
| E_JCHECK_URL | url | Data display URL in Japanese JCHECK databases (www.safe.nite.go.jp) | Tcl script | E_CAS E_MITI_ID | atomchange bondchange atom bond | e_jcheck_url.xpd | ||||
| E_JGLOBAL_ID | string | Database ID for the J-GLOBAL registry (https://jglobal.jst.go.jp) | Tcl script | atomchange bondchange atom bond | e_jglobal_id.xpd | |||||
| E_JGLOBAL_URL | url | Display URL for the J-GLOBAL registry (https://jglobal.jst.go.jp) | Tcl script | atomchange bondchange atom bond | e_jglobal_url.xpd | |||||
| E_JHOTI_FRAGMENTLIKENESS_VIOLATIONS | byte | Congreve, Carr, Murray, Jhoti, Drug. Discov. Today 2003, 8, 876 | Tcl script | E_WEIGHT E_NHDONORS E_NHACCEPTORS E_XLOGP2 | atomchange bondchange atom bond | e_jhoti_fragmentlikeness_violations.xpd | ||||
| E_JME_STRING | string | JME editor structure encoding | Compiled C module | A_ELEMENT B_ORDER B_TYPE A_TYPE A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange stereochange hadd mol atom bond ring | mod_e_jme_string.so | ||||
| E_JSTDATA | stringvector | JST extended molfile data in skip section | atomchange bondchange stereochange merge | |||||||
| E_KEGG_BRITE_CLASSIFICATION | stringvector | Compound classification codes as per the KEGG BRITE database (http://www.genome.jp/kegg/brite.html). Compounds must be present in KEGG database, i.e. have a KEGG ID. | Tcl script | atomchange bondchange atom bond | e_kegg_brite_classification.xpd | |||||
| E_KEGG_COMPOUND_ID | string | KEGG ID (www.genome.jp) | Tcl script | atomchange bondchange stereochange merge | e_kegg_compound_id.xpd | |||||
| E_KEGG_COMPOUND_URL | url | KEGG compound display URL (www.genome.jp) | Tcl script | E_KEGG_COMPOUND_ID | atomchange bondchange stereochange merge | e_kegg_compound_url.xpd | ||||
| E_KEGG_DRUG_ID | string | KEGG drug ID (www.genome.jp) | Tcl script | atomchange bondchange stereochange merge | e_kegg_drug_id.xpd | |||||
| E_KEGG_DRUG_URL | url | KEGG drug display URL (www.genome.jp) | Tcl script | E_KEGG_DRUG_ID | atomchange bondchange stereochange merge | e_kegg_drug_url.xpd | ||||
| E_KEKULESET | dataset | Generated set of alternative Kekule forms of the structure- The generated forms are duplicate-filtered by symmetry hashcodes - that means there is only a single Kekule form for benzene, pyridine, pyrimidine (1.3-diazine) or pyrazine (1.4-diazine) - but two for pyridazine (1.2-diazine, with a double or single bond between the adjacent nitrogens). | maxkekuleforms: { value: 512 datatype: int}
|
Compiled C module | A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange merge atom bond | mod_e_kekuleset.so | |||
| E_KEYWORDS | stringvector | Keywords associated with ensemble | never | |||||||
| E_KLIFS_ID | int | Database ID for the KLIFS database (http://klifs.vu-compmedchem.nl) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_klifs_id.xpd | ||||
| E_KLIFS_URL | url | Data display URL for the KLIFS database (http://klifs.vu-compmedchem.nl) | Tcl script | E_KLIFS_ID | atomchange bondchange stereochange atom bond | e_klifs_url.xpd | ||||
| E_KNAPSACK_ID | string | Database ID of compund in KNAPSACK database (http://www.knapsackfamily.com) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_knapsack_id.xpd | ||||
| E_KNAPSACK_URL | url | Data display URL for the Knapsack database (www.knapsackfamily.com) | Tcl script | E_KNAPSACK_ID | atomchange bondchange stereochange atom bond | e_knapsack_url.xpd | ||||
| E_LC50 | compound | LC50 tumor screen data | concunit shortstring lcconc float panel shortstring cell string panelnumber short cellnumber short nlog_lc50 float ntest_this short ntest_max short |
atomchange bondchange merge | ||||||
| E_LEVEL | int | Ensemble level | never | |||||||
| E_LHASA_REAGENT_SCAN_VERIFICATION | compound | Test conditions for Lhasa transform reagent scan verification. The value consists of a transform ID this test applies to, and a bit set indicating which starting material reagent condition this structure should match (0 if none) | {} {none:intramolecular:intermolecular1:intermolecular2:intermolecular3:intermolecular4} |
transformid int reagentmatches bitset |
atomchange bondchange stereochange atom bond | |||||
| E_LINCS_ID | string | Dabase ID of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_lincs_id.xpd | ||||
| E_LINCS_URL | url | Display URL of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu) | Tcl script | E_LINCS_ID | atomchange bondchange stereochange atom bond | e_lincs_url.xpd | ||||
| E_LINKTEXTS | stringvector | Toplevel link texts of HTML URLs leading to this molecule | never | |||||||
| E_LIPIDMAPS_ID | string | Structure ID for the Lipidmaps database | Tcl script | atomchange bondchange stereochange atom bond | e_lipidmaps_id.xpd | |||||
| E_LIPIDMAPS_URL | url | Tcl script | atomchange bondchange atom bond | e_lipidmaps_url.xpd | ||||||
| E_LIPINSKI_ACCEPTOR_COUNT | int | Number of hydrogens on N and O atoms - H-bond acceptors according to simple Lipinski definition. For a more refined definition, use property E_NHACCEPTORS. |
Compiled C module | A_TYPE A_ELEMENT A_FREE_ELECTRONS | atomchange bondchange atom bond | mod_e_lipinski_acceptor_count.so | ||||
| E_LIPINSKI_DONOR_COUNT | int | Number of oxygen and nitrogen atoms according to really simple Lipinski definition. For a more refined definition, use E_NHDONORS. | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_lipinski_donor_count.so | ||||
| E_LITERATURE_REFERENCE | stringvector | Auxiliary literature references | never | |||||||
| E_LOOKCHEM_URL | url | PubChem compound database URL | Tcl script | atomchange bondchange stereochange merge | e_lookchem_url.xpd | |||||
| E_MACCS_KEYS | bitvector | MDL MACCS fingerprint (166 bits) | Tcl script | atom bond | e_maccs_keys.xpd | |||||
| E_MANUFACTURERS | compoundvector | Data about manufactorers of a chemical | catno string manufacturer string catalog string price float currency string amount float unit string info string purity string |
atomchange bondchange stereochange merge | ||||||
| E_MAP_ANNOTATION | compoundvector | Map markers to be used in conjuction with D_ANNOTATED_MAP | {} {none:circle:triangle:invtriangle:square:diamond:pentagon:hexagon} |
tag string object string size int outlinecolor color fillcolor color textcolor color header string footer string |
atomchange bondchange stereochange 3drelative atom bond | |||||
| E_MARKED | boolean | Flag for marked structures | never | |||||||
| E_MASSBANK_URL | url | Display URL for MassBank (https://massbank.eu) entry | Tcl script | atomchange bondchange atom bond | e_massbank_url.xpd | |||||
| E_MASS_PATTERN | xyvector | Mass distribution pattern | cutoff: { value: 0.01 description: Minimum abundancy to include in output vector minvalue: 0.00 maxvalue: 1.00 datatype: double} useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean} |
Compiled C module | A_ELEMENT A_TYPE A_ISOTOPE | atomchange | mod_e_mass_pattern.so | |||
| E_MATRIX_SCIENTIFIC_IDS | stringvector | ID of the compound Matrix Scientific catalog | Tcl script | atomchange bondchange stereochange atom bond | e_matrix_scientific_ids.xpd | |||||
| E_MATRIX_SCIENTIFIC_URLS | urlvector | URL Matrix Scientific catalog entry | Tcl script | E_MATRIX_SCIENTIFIC_IDS | atomchange bondchange atom bond | e_matrix_scientific_urls.xpd | ||||
| E_MAX_CHAIN_FRAGMENT_SIZE | int | The maximum value of A_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-hydrogen atoms. | Compiled C module | A_CHAIN_LENGTH | atomchange bondchange atom bond | mod_e_max_chain_fragment_size.so | ||||
| E_MAX_CONJUGATED_SYSTEM_SIZE | int | The maximum size of a conjugated system in the ensemble according to the Shoichet definition (see literature reference). | J. Med. Chem. 2003, 46, 4477-4486 | Compiled C module | A_CONJUGATED_SYSTEM_SIZE | atomchange bondchange atom bond | mod_e_max_conjugated_system_size.so | |||
| E_MAX_LINEAR_CHAIN_FRAGMENT_SIZE | int | The maximum value of A_LINEAR_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-branching non-hydrogen atoms. | Compiled C module | A_LINEAR_CHAIN_LENGTH | atomchange bondchange atom bond | mod_e_max_linear_chain_fragment_size.so | ||||
| E_MCULE_ID | string | Get database ID of structure in MCULE (mcule.com) database | Tcl script | E_SMILES | atomchange bondchange atom bond | e_mcule_id.xpd | ||||
| E_MCULE_URL | url | Display URL for MCULE (mcule.com) database | Tcl script | E_MCULE_ID | atomchange bondchange atom bond | e_mcule_url.xpd | ||||
| E_MDL_NAME | string | Name as extracted from MDL Molfile header | never | |||||||
| E_MDL_NUMBER | string | MDL substance number | Tcl script | atomchange bondchange atom bond | e_mdl_number.xpd | |||||
| E_MEREG | string | MDL external registry number | never | |||||||
| E_MESH_ID | string | MESH ID, extracted from E_MESH_TERMS at the toplevel | Tcl script | E_MESH_TERMS | atomchange bondchange atom bond | e_mesh_id.xpd | ||||
| E_MESH_TERMS | compoundvector | Mesh terms associated with structure retrieved from PubChem | id int terms stringvector url url ontotree datatree |
Tcl script | E_CID | atomchange bondchange stereochange merge atom bond | e_mesh_terms.xpd | |||
| E_MESH_URL | url | MESH display URL, extracted from E_MESH_TERMS at the toplevel | Tcl script | E_MESH_TERMS | atomchange bondchange atom bond | e_mesh_url.xpd | ||||
| E_MESO | boolean | Check whether at least one molecule is a meso compound, and all other molecules are either also meso, or not stereogenic | Tcl script | M_MESO M_STEREO_STATUS | atomchange bondchange stereochange merge mol atom bond | e_meso.xpd | ||||
| E_MESOMER_SET | dataset | A generator for all duplicate-filtered mesomers accessible by moving existing charges along pi systems. Does not create new charges. | Tcl script | atomchange bondchange atom bond | e_mesomer_set.xpd | |||||
| E_METABOLIGHTS_ID | string | Structure access key for MetaboLights database (https://www.ebi.ac.uk/metabolights) | Tcl script | E_INCHI | atomchange bondchange stereochange atom bond | e_metabolights_id.xpd | ||||
| E_METABOLIGHTS_URL | url | Structure data display URL for MetaboLights database (https://www.ebi.ac.uk/metabolights) | Tcl script | E_METABOLIGHTS_ID | atomchange bondchange atom bond | e_metabolights_url.xpd | ||||
| E_METABOLOMICSWORKBENCH_CLASSIFICATION | dictionary | Compund description in the Metabolomics Workbench (www.metabolomicsworkbench.org) | Tcl script | E_METABOLOMICSWORKBENCH_ID | atomchange bondchange stereochange atom bond | e_metabolomicsworkbench_classification.xpd | ||||
| E_METABOLOMICSWORKBENCH_ID | int | Compund registration ID in the Metabolomics Workbench (www.metabolomicsworkbench.org) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_metabolomicsworkbench_id.xpd | ||||
| E_METACYC_URL | url | Link into the MetaCyc database (metacyc.org) | Tcl script | atomchange bondchange atom bond | e_metacyc_url.xpd | |||||
| E_METADATA | dictionary | Dublin Core metadata for structure | never | |||||||
| E_METHOD | string | QM method description string | atomchange bondchange | |||||||
| E_MIF_IMAGE | diskfile (switchable between string blob diskfile xmlstring) |
Ensemble image in MIF FrameMaker format | width: { value: 180 datatype: int} height: { value: 180 datatype: boolean} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.2 datatype: double} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: string} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} annotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} frame: { value: 1 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: int} linespacing: { value: 1.5 datatype: double} unit: { value: {} datatype: string} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: color constraints: emptycolor} voronoifilter: { value: {} datatype: string constraints: filtername} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 10 datatype: int} wiggleamplitude: { value: 3.0 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} showstereogroups: { value: 0 datatype: boolean} font: { value: Arial datatype: string} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | atomchange bondchange stereochange merge atom bond | mod_e_mif_image.so | ||||
| E_MINIMOL | blob | Ultracompact structure representation for structure database applications, with precomputed data for most common substructure attributes. Queries with extended attributes are still possible by converting the Minimol into a standard ensemble. The format is designed to be expanded into a simple memory blob for matching, minimizing malloc/free oberhead. In scripting interpreters, "ens create" auto-detects and decodes binary and hex-encoded Minimols. | version: { value: 3 datatype: int}
|
Compiled C module | A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO B_ORDER B_TYPE A_TYPE A_STEREO_GROUP | atomchange bondchange stereochange hadd mol atom bond | mod_e_minimol.so | |||
| E_MIREG | string | MDL internal registry number. This is a standard field in RD files. | never | |||||||
| E_MITI_ID | string | Japanese hazardous substance registration number (www.safe.nite.go.jp) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_miti_id.xpd | ||||
| E_MNA | dictionary | MNA (multilevel neighborhood of atoms) fragment set, as defined by Poroikov et al. | J. Chem. Inf. Comput. Sci. 1999, 39, 666-670 | levels: { value: 1 2 description: Neighbor sphere radii to include in the result set datatype: intvector}
|
Tcl script | A_SYMBOL | atomchange bondchange atom bond | e_mna.xpd | ||
| E_MOL2_STRING | string | Sybyl MOL2 structure encoding as string | Tcl script | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond | e_mol2_string.xpd | |||||
| E_MOLAR_REFRACTIVITY | double | Molar refractivity computed by the Wildman-Crippen method (see litref) | J. Chem. Inf. Comput. Sci. 1999, 39, 868-873 | Compiled C module | A_WILDMAN_CRIPPEN_TYPE | atomchange bondchange atom bond | mod_e_molar_refractivity.so | |||
| E_MOLBASE_URL | url | Supplier data display page from molbase.com | Tcl script | atomchange bondchange atom bond | e_molbase_url.xpd | |||||
| E_MOLD2_DESCRIPTORS | floatvector | MOLD2 descriptor collection, computed with original source encapsulated as a Cactvs module. The MOLD2 code unfortunately uses statically allocated data structures, and thus has a limit on 150 atoms, 400 paths and 9 ligands per atom. Larger structures fail. | J. Chem. Inf. Model., 2008, 48 (7), pp 1337-1344 | d001 float d002 float d003 float d004 float d005 float d006 float d007 float d008 float d009 float d010 float d011 float d012 float d013 float d014 float d015 float d016 float d017 float d018 float d019 float d020 float d021 float d022 float d023 float d024 float d025 float d026 float d027 float d028 float d029 float d030 float d031 float d032 float d033 float d034 float d035 float d036 float d037 float d038 float d039 float d040 float d041 float d042 float d043 float d044 float d045 float d046 float d047 float d048 float d049 float d050 float d051 float d052 float d053 float d054 float d055 float d056 float d057 float d058 float d059 float d060 float d061 float d062 float d063 float d064 float d065 float d066 float d067 float d068 float d069 float d070 float d071 float d072 float d073 float d074 float d075 float d076 float d077 float d078 float d079 float d080 float d081 float d082 float d083 float d084 float d085 float d086 float d087 float d088 float d089 float d090 float d091 float d092 float d093 float d094 float d095 float d096 float d097 float d098 float d099 float d100 float d101 float d102 float d103 float d104 float d105 float d106 float d107 float d108 float d109 float d110 float d111 float d112 float d113 float d114 float d115 float d116 float d117 float d118 float d119 float d120 float d121 float d122 float d123 float d124 float d125 float d126 float d127 float d128 float d129 float d130 float d131 float d132 float d133 float d134 float d135 float d136 float d137 float d138 float d139 float d140 float d141 float d142 float d143 float d144 float d145 float d146 float d147 float d148 float d149 float d150 float d151 float d152 float d153 float d154 float d155 float d156 float d157 float d158 float d159 float d160 float d161 float d162 float d163 float d164 float d165 float d166 float d167 float d168 float d169 float d170 float d171 float d172 float d173 float d174 float d175 float d176 float d177 float d178 float d179 float d180 float d181 float d182 float d183 float d184 float d185 float d186 float d187 float d188 float d189 float d190 float d191 float d192 float d193 float d194 float d195 float d196 float d197 float d198 float d199 float d200 float d201 float d202 float d203 float d204 float d205 float d206 float d207 float d208 float d209 float d210 float d211 float d212 float d213 float d214 float d215 float d216 float d217 float d218 float d219 float d220 float d221 float d222 float d223 float d224 float d225 float d226 float d227 float d228 float d229 float d230 float d231 float d232 float d233 float d234 float d235 float d236 float d237 float d238 float d239 float d240 float d241 float d242 float d243 float d244 float d245 float d246 float d247 float d248 float d249 float d250 float d251 float d252 float d253 float d254 float d255 float d256 float d257 float d258 float d259 float d260 float d261 float d262 float d263 float d264 float d265 float d266 float d267 float d268 float d269 float d270 float d271 float d272 float d273 float d274 float d275 float d276 float d277 float d278 float d279 float d280 float d281 float d282 float d283 float d284 float d285 float d286 float d287 float d288 float d289 float d290 float d291 float d292 float d293 float d294 float d295 float d296 float d297 float d298 float d299 float d300 float d301 float d302 float d303 float d304 float d305 float d306 float d307 float d308 float d309 float d310 float d311 float d312 float d313 float d314 float d315 float d316 float d317 float d318 float d319 float d320 float d321 float d322 float d323 float d324 float d325 float d326 float d327 float d328 float d329 float d330 float d331 float d332 float d333 float d334 float d335 float d336 float d337 float d338 float d339 float d340 float d341 float d342 float d343 float d344 float d345 float d346 float d347 float d348 float d349 float d350 float d351 float d352 float d353 float d354 float d355 float d356 float d357 float d358 float d359 float d360 float d361 float d362 float d363 float d364 float d365 float d366 float d367 float d368 float d369 float d370 float d371 float d372 float d373 float d374 float d375 float d376 float d377 float d378 float d379 float d380 float d381 float d382 float d383 float d384 float d385 float d386 float d387 float d388 float d389 float d390 float d391 float d392 float d393 float d394 float d395 float d396 float d397 float d398 float d399 float d400 float d401 float d402 float d403 float d404 float d405 float d406 float d407 float d408 float d409 float d410 float d411 float d412 float d413 float d414 float d415 float d416 float d417 float d418 float d419 float d420 float d421 float d422 float d423 float d424 float d425 float d426 float d427 float d428 float d429 float d430 float d431 float d432 float d433 float d434 float d435 float d436 float d437 float d438 float d439 float d440 float d441 float d442 float d443 float d444 float d445 float d446 float d447 float d448 float d449 float d450 float d451 float d452 float d453 float d454 float d455 float d456 float d457 float d458 float d459 float d460 float d461 float d462 float d463 float d464 float d465 float d466 float d467 float d468 float d469 float d470 float d471 float d472 float d473 float d474 float d475 float d476 float d477 float d478 float d479 float d480 float d481 float d482 float d483 float d484 float d485 float d486 float d487 float d488 float d489 float d490 float d491 float d492 float d493 float d494 float d495 float d496 float d497 float d498 float d499 float d500 float d501 float d502 float d503 float d504 float d505 float d506 float d507 float d508 float d509 float d510 float d511 float d512 float d513 float d514 float d515 float d516 float d517 float d518 float d519 float d520 float d521 float d522 float d523 float d524 float d525 float d526 float d527 float d528 float d529 float d530 float d531 float d532 float d533 float d534 float d535 float d536 float d537 float d538 float d539 float d540 float d541 float d542 float d543 float d544 float d545 float d546 float d547 float d548 float d549 float d550 float d551 float d552 float d553 float d554 float d555 float d556 float d557 float d558 float d559 float d560 float d561 float d562 float d563 float d564 float d565 float d566 float d567 float d568 float d569 float d570 float d571 float d572 float d573 float d574 float d575 float d576 float d577 float d578 float d579 float d580 float d581 float d582 float d583 float d584 float d585 float d586 float d587 float d588 float d589 float d590 float d591 float d592 float d593 float d594 float d595 float d596 float d597 float d598 float d599 float d600 float d601 float d602 float d603 float d604 float d605 float d606 float d607 float d608 float d609 float d610 float d611 float d612 float d613 float d614 float d615 float d616 float d617 float d618 float d619 float d620 float d621 float d622 float d623 float d624 float d625 float d626 float d627 float d628 float d629 float d630 float d631 float d632 float d633 float d634 float d635 float d636 float d637 float d638 float d639 float d640 float d641 float d642 float d643 float d644 float d645 float d646 float d647 float d648 float d649 float d650 float d651 float d652 float d653 float d654 float d655 float d656 float d657 float d658 float d659 float d660 float d661 float d662 float d663 float d664 float d665 float d666 float d667 float d668 float d669 float d670 float d671 float d672 float d673 float d674 float d675 float d676 float d677 float d678 float d679 float d680 float d681 float d682 float d683 float d684 float d685 float d686 float d687 float d688 float d689 float d690 float d691 float d692 float d693 float d694 float d695 float d696 float d697 float d698 float d699 float d700 float d701 float d702 float d703 float d704 float d705 float d706 float d707 float d708 float d709 float d710 float d711 float d712 float d713 float d714 float d715 float d716 float d717 float d718 float d719 float d720 float d721 float d722 float d723 float d724 float d725 float d726 float d727 float d728 float d729 float d730 float d731 float d732 float d733 float d734 float d735 float d736 float d737 float d738 float d739 float d740 float d741 float d742 float d743 float d744 float d745 float d746 float d747 float d748 float d749 float d750 float d751 float d752 float d753 float d754 float d755 float d756 float d757 float d758 float d759 float d760 float d761 float d762 float d763 float d764 float d765 float d766 float d767 float d768 float d769 float d770 float d771 float d772 float d773 float d774 float d775 float d776 float d777 float |
Compiled C module | atomchange bondchange merge | mod_e_mold2_descriptors.so | |||
| E_MOLHASH_COUNT | int | Number of different pertured molecule hash codes | (builtin) | E_HASHGROUP_COUNT_M | atomchange bondchange merge hadd | |||||
| E_MOLINSTINCTS_ANALYSIS_URL | url | Access URL for structure analysis in the Molinstincts database (molinstincts.com) | Tcl script | E_MOLINSTINCTS_ID | atomchange bondchange atom bond | e_molinstincts_analysis_url.xpd | ||||
| E_MOLINSTINCTS_CONSTANT_PROPERTY_URL | url | Display URL for constant properties in the Molinstincts database (molinstincts.com) | Tcl script | E_MOLINSTINCTS_ID | atomchange bondchange atom bond | e_molinstincts_constant_property_url.xpd | ||||
| E_MOLINSTINCTS_DESCRIPTOR_PROPERTY_URL | url | Display URL for molecular descriptor properties in the Molinstincts database (molinstincts.com) | Tcl script | E_MOLINSTINCTS_ID | atomchange bondchange atom bond | e_molinstincts_descriptor_property_url.xpd | ||||
| E_MOLINSTINCTS_DRUG_PROPERTY_URL | url | Display URL for molecular drug properties in the Molinstincts database (molinstincts.com) | Tcl script | E_MOLINSTINCTS_ID | atomchange bondchange atom bond | e_molinstincts_drug_property_url.xpd | ||||
| E_MOLINSTINCTS_ID | string | ID in MolInstincts database (www.molinstincts.com) | Tcl script | atomchange bondchange atom bond | e_molinstincts_id.xpd | |||||
| E_MOLINSTINCTS_QUANTUM_PROPERTY_URL | url | Display URL for molecular quantum properties in the Molinstincts database (molinstincts.com) | Tcl script | E_MOLINSTINCTS_ID | atomchange bondchange atom bond | e_molinstincts_quantum_property_url.xpd | ||||
| E_MOLINSTINCTS_SPECTRA_URL | url | Display URL for structure spectra in the Molinstincts database (molinstincts.com) | Tcl script | E_MOLINSTINCTS_ID | atomchange bondchange atom bond | e_molinstincts_spectra_url.xpd | ||||
| E_MOLNAME | string | Ensemble name as free format string, no associated with any specific naming convention | atomchange bondchange merge | |||||||
| E_MOLPORT_ID | string | ID of structure in the MOLPORT database (www.molport.com) | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_molport_id.xpd | ||||
| E_MOLPORT_URL | url | Display URL in the Molport portal (www.molport.com) | E_MOLPORT_ID | atomchange bondchange stereochange merge | ||||||
| E_MONOISOTOPIC_MASS | float | Mass computed with most abundant isotope only, not natural abundance | useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean}
|
Compiled C module | A_ELEMENT A_TYPE A_ISOTOPE | atomchange | mod_e_monoisotopic_mass.so | |||
| E_MP | floatpair | Melting Point in Kelvin, with optional range | value float range float |
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE | atomchange bondchange | |||||
| E_MQN | shortvector | Reymond molecular quantum numbers | L. Ruddigkeit, L. C. Blum, J.-L. Reymond, J. Chem. Inf. Model. 2013, 53, 56-65 | c int f int cl int br int i int s int p int an int cn int ao int co int hac int asb int adb int atb int csb int cdb int ctb int rbc int hbam int hba int hdbm int hdb int neg int pos int asv int adv int atv int aqv int cdv int dtv int cqv int r3 int r4 int r5 int r6 int r7 int r8 int r9 int rg10 int afr int bfr int |
Compiled C module | A_TYPE B_TYPE A_ELEMENT B_RING_COUNT B_ORDER A_RING_COUNT B_ROTATABILITY R_TYPE R_SIZE E_CHARGED_GROUP_COUNTS | atomchange bondchange atom bond | mod_e_mqn.so | ||
| E_MRV_STRING | string | MRV structure encoding | Tcl script | A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange stereochange merge hadd atom bond | e_mrv_string.xpd | ||||
| E_MSDS_URL | url | URL of MSDS from Matrix Scientific Website | Tcl script | atomchange bondchange atom bond | e_msds_url.xpd | |||||
| E_MSSPECTRUM | compound | Mass spectrum. The computation function attempts a NIST WebBook retrieval. | experimental boolean origin string author string date int spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string mass floatvector signal floatvector label stringvector |
Tcl script | A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange stereochange | e_msspectrum.xpd | |||
| E_MSSPECTRUM_IMAGE | diskfile (switchable between string blob diskfile url) |
MS spectrum rendering | height: { value: 250 datatype: int} width: { value: 500 datatype: int} bgcolor: { value: white datatype: color} title: { value: {} datatype: string} filename: { value: {} datatype: string constraints: writeable} format: { value: gif enumeration: png,png24:gif:png8 datatype: string} titlecolor: { value: black datatype: color} framecolor: { value: black datatype: color} signalcolor: { value: #DD0000 datatype: color} |
Tcl script | E_MSSPECTRUM | atomchange bondchange merge mol | e_msspectrum_image.xpd | |||
| E_MS_ACADEMIC_URL | url | URL for data in Maicrosoft Academic Search | Tcl script | E_STDINCHI E_CAS | atomchange bondchange stereochange atom bond | e_ms_academic_url.xpd | ||||
| E_MULTIPLICITY | byte | Spin multiplicity of the whole molecular ensemble. Used in Gaussion Archive I/O module. | atomchange bondchange merge hadd | |||||||
| E_MURCKO_SCAFFOLD | structure | Compute various Murcko-Style scaffolds | J. Med. Chem. (1996), 39(15), 2887-2893 | heteroatomreplacement: { value: none description: Whether to change hetero atoms into a generic hetero atom, or into carbon enumeration: none:generic,het,x:carbon,c datatype: int} hydrogenate: { value: none description: If set, hydrogenate aliphatic or any double bonds enumeration: none:aliphatic:all datatype: int} minringsize: { value: 0 description: Minimum required un-annealed ring size for retention minvalue: 0 datatype: int} preserveexodb: { value: 0 description: If set, preserve exo-ring double bond stub datatype: boolean} |
Tcl script | atomchange bondchange atom bond | e_murcko_scaffold.xpd | |||
| E_MURRAY_DRUGLIKENESS_VIOLATIONS | byte | Number of failed tests according to the Jhoti-Murray rules. This is a stricter form of the Lipinski Rule-of-5 criterion. | Jhoti, Williams, Rees, Murray, Nat.. Rev. Drug. Discov. 2013, 12, 644 | Tcl script | E_NHDONORS E_NHACCEPTORS E_WEIGHT E_XLOGP2 E_NROTBONDS E_TPSA | atomchange bondchange atom bond | e_murray_druglikeness_violations.xpd | |||
| E_NAME | string | Long ensemble identification string | pubchemlookup: { value: 0 datatype: string} lmchlookup: { value: 0 datatype: string} useformula: { value: 1 datatype: string} |
(builtin) | never | |||||
| E_NAMEKEYSET | stringvector | List of chemical keys of alternative compound names in phonetic encoding, derived from the names in E_NAMESET | maxlen: { value: 100 description: maxiumum number of characters to include datatype: int} expand: { value: 0 description: expand common chemistry-specific spelling variants datatype: boolean} |
Compiled C module | E_NAMESET | never | mod_e_namekeyset.so | |||
| E_NAMESET | stringvector | List of alternative compound names The computation function retrieves a full set names registered in the NCI resolver. | Tcl script | E_HASHISY | atomchange bondchange stereochange | e_nameset.xpd | ||||
| E_NATOMS | int | Number of atoms in ensemble | (builtin) | atomchange merge hadd | ||||||
| E_NATURAL_PRODUCT_LIKENESS | double | Natrual product-likeness score according to the Ertl/Roggo/Schuffenhauer algorithm | Ertl, Roggo, Schuffenhauer, J. Chem. Inf. Model. 2008, 48, 68-74 | Tcl script | atomchange bondchange atom bond | e_natural_product_likeness.xpd | ||||
| E_NBHASH | int | Number of different bond hash codes | (builtin) | E_HASHGROUP_COUNT_B | atomchange bondchange merge | |||||
| E_NBHASHS | int | Number of different stereospecific bond hash codes | (builtin) | E_HASHGROUP_COUNT_BS | atomchange bondchange merge | |||||
| E_NBONDS | int | Number of bonds in ensemble | (builtin) | atomchange bondchange merge hadd | ||||||
| E_NCBI_ACTIVITY | byte | Activity summary (Outcome) | inactive=1:active=2:inconclusive=3:unspecified=4:probe=5 |
never | ||||||
| E_NCBI_BIBLIO_AFFILIATION | choice | NCBI author affiliation | str string std compound |
never | ||||||
| E_NCBI_BIBLIO_AFFILIATION_LIST | choicevector | NCBI author affiliations | str string std compound |
never | ||||||
| E_NCBI_BIBLIO_ARTICLE_FROM | choice | Article container reference | journal compound book compound proc compound |
never | ||||||
| E_NCBI_BIBLIO_ARTICLE_ID_SET | choicevector | Article reference ID set | pubmed int medline int doi string pii string pmcid int pmcpid string pmpid string other compound |
never | ||||||
| E_NCBI_BIBLIO_AUTHORS | choice | NCBI author reference | std compoundvector ml stringvector str stringvector |
never | ||||||
| E_NCBI_BIBLIO_AUTHOR_LIST | compound | NCBI author reference | names choice affil choice |
never | ||||||
| E_NCBI_BIBLIO_FULL_AUTHOR | compound | NCBI author reference | {} primary=1:secondary=2 compiler=1:editor=2:patent-assignee=3:translator=4 |
name choice level int role int affil choice is-corr boolean |
never | |||||
| E_NCBI_BIBLIO_FULL_AUTHOR_SET | compoundvector | NCBI author reference | {} primary=1:secondary=2 compiler=1:editor=2:patent-assignee=3:translator=4 |
name choice level int role int affil choice is-corr boolean |
never | |||||
| E_NCBI_BIBLIO_IMPRINT | compound | Document imprint data | {} {} {} {} {} {} {} {} {} published:submitted:in-press:other=255 {} {} none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255 |
date date volume string issue string pages string section string pub choice cprt date part-sup string language string prepub int part-supi string retract compound pubstatus int history compoundvector |
never | |||||
| E_NCBI_BIBLIO_MEETING | compound | Meeting reference | number string date date place choice |
never | ||||||
| E_NCBI_BIBLIO_PATENT_ID | choice | Patent ID reference | number string app-number string |
never | ||||||
| E_NCBI_BIBLIO_PATENT_PRIORITY | compoundvector | Patent priorities | country string number string date date |
never | ||||||
| E_NCBI_BIBLIO_PUBSTATUS_HISTORY | compoundvector | Publication status history | none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255 |
pubstatus int date date |
never | |||||
| E_NCBI_BIBLIO_RETRACTION | compound | Document retraction information | none:retracted:notice:in-error:erratum |
type int exp string |
never | |||||
| E_NCBI_BIBLIO_STD_AFFILIATION | compound | NCBI structured affiliation | affil string div string city string sub string country string street string email string fax string phone string postal-code string |
never | ||||||
| E_NCBI_BIBLIO_TITLE | choicevector | NCBI bibliographic title reference | name string tsub string trans string jta string iso-jta string ml-jta string coden string issn string abr string isdn string |
never | ||||||
| E_NCBI_DBTAG | compound | NCBI database reference | db string tag string |
never | ||||||
| E_NCBI_DBTRACKING | compound | NCBI substance db source data | name string source-id string date date description string pub choice |
never | ||||||
| E_NCBI_IMAGE | diskfile | A 2D-plot default image of the structure as a GIF or PNG file | hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} interlace: { value: 1 datatype: boolean} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: string} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} crop: { value: -1 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} format: { value: png8 datatype: string} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 0 datatype: boolean} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} showstereoh: { value: 0 datatype: boolean} symbolfontsize: { value: -1 datatype: int} annotationfontsize: { value: -1 datatype: double} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int} highlightgroups: { value: {} datatype: string} boxgroups: { value: {} datatype: string} font: { value: arialbd.ttf datatype: string} groupcolor: { value: purple datatype: color} showisotope: { value: 1 datatype: boolean} isotopemapping: { value: none datatype: string} suppressedmols: { value: {} datatype: string} linewidth: { value: 1.4 datatype: double} showempty: { value: 0 datatype: boolean} voronoicolorproperty: { value: {} datatype: color constraints: emptycolor} voronoifilter: { value: {} datatype: string constraints: filtername} showmapping: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: string constraints: emptycolor} showchirality: { value: none enumeration: none:simple:extended datatype: int} frame: { value: 0 datatype: boolean} linespacing: { value: 2.0 datatype: double} headerfontsize: { value: -1 datatype: int} footerfontsize: { value: -1 datatype: int} circlecolorproperty: { value: {} datatype: string} circlefilter: { value: {} datatype: string constraints: filtername} width: { value: 300 datatype: int} height: { value: 300 datatype: int} bgcolor: { value: grey96 datatype: color} bondcolor: { value: split datatype: string} atomcolor: { value: type datatype: string} asymbol: { value: xsymbol datatype: string} border: { value: 16 datatype: int} bonds: { value: 8 datatype: int} commenttype: { value: none enumeration: none:text:property,prop datatype: string} metadata: { value: 0 datatype: boolean} wigglecount: { value: 10 datatype: int} wiggleamplitude: { value: 2 datatype: double} fixiepngsize: { value: 1 datatype: boolean} rawcoordinates: { value: 0 datatype: boolean} checkintersection: { value: 0 datatype: boolean} showstereogroups: { value: 1 datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION A_ELEMENT | atomchange bondchange stereochange merge hadd | mod_e_ncbi_image.so | |||
| E_NCBI_MMDB | compound | MMDB source information | mmdb-id int molecule-id int molecule-name stringvector residue-id int residue-name string atom-id int atom-name string |
never | ||||||
| E_NCBI_PERSON_ID | choice | NCBI person reference | dbtag compound name compound str string consortium string |
never | ||||||
| E_NCBI_PUBLICATION | choice | Publication in PubMed style | gen compound sub compound medline compound muid int article compound journal compound book compound proc compound patent compound pat-id compound man compound equiv choicevector pmid int |
never | ||||||
| E_NCBI_PUBLICATION_ARTICLE | compound | Article reference | title choicevector authors compound from choice ids choicevector |
never | ||||||
| E_NCBI_PUBLICATION_BOOK | compound | Book reference | title choicevector coll choicevector authors compound imp compound |
never | ||||||
| E_NCBI_PUBLICATION_GENERAL | compound | General publication reference | cit string authors compound muid int journal choicevector volume string issue string pages string date date serial-number int title string pmid int |
never | ||||||
| E_NCBI_PUBLICATION_JOURNAL | compound | Journal reference | title choicevector imp compound |
never | ||||||
| E_NCBI_PUBLICATION_MANUSCRIPT | compound | Manuscript reference | {} {} unknown:manuscript:letter:thesis |
cit compound man-id string type int |
never | |||||
| E_NCBI_PUBLICATION_MEDLINE | compound | Medline reference | {} {} {} {} {} {} {} {} {} {} {} {} publisher:premedline:medline |
uid int em date cit compound abstract string mesh compoundvector substance compoundvector xref compoundvector idnum stringvector gene stringvector pmid int pub-type stringvector mlfield compoundvector status int |
never | |||||
| E_NCBI_PUBLICATION_MEDLINE_FIELD_DOCREF_SET | compoundvector | Docrefs of NCBI medline field of publication | none:medline:pubmed:ncbigi |
type int uid int |
never | |||||
| E_NCBI_PUBLICATION_MEDLINE_FIELD_SET | compoundvector | NCBI medline field of publication | other:comment:erratum |
type int str string ids compoundvector |
never | |||||
| E_NCBI_PUBLICATION_MEDLINE_MESH_QUALIFIER_SET | compoundvector | Medline mesh term qualifiers | mp boolean subh string |
never | ||||||
| E_NCBI_PUBLICATION_MEDLINE_MESH_SET | compoundvector | Medline mesh references | mp boolean term string qual compoundvector |
never | ||||||
| E_NCBI_PUBLICATION_MEDLINE_RN_SET | compoundvector | Medline substance references | nameonly:cas:rc |
type int cit string name string |
never | |||||
| E_NCBI_PUBLICATION_MEDLINE_SI_SET | compoundvector | Medline crossreferences | none:ddbj:carbbank:embl:hdb:genbank:hgml:mim:msd:pdb:pir:prfseqdb:psd:swissprot:gdb |
type int cit string |
never | |||||
| E_NCBI_PUBLICATION_PATENT | compound | Patent reference | title string authors compound country string doc-type string number string date-issue date class stringvector app-number string app-date date applicants compound assignees compound priority compoundvector abstract string |
never | ||||||
| E_NCBI_PUBLICATION_PATENT_ID | compound | Patent ID reference | country string id choice doc-type string |
never | ||||||
| E_NCBI_PUBLICATION_PROCEEDINGS | compound | Proceedings reference | book compound meeting compound |
never | ||||||
| E_NCBI_PUBLICATION_SET | choicevector | Publication in PubMed style | gen compound sub compound medline compound muid int article compound journal compound book compound proc compound patent compound pat-id compound man compound equiv string pmid int |
never | ||||||
| E_NCBI_PUBLICATION_SUBMISSION | compound | Submission reference | {} {} unknown:paper:tape:floppy:email:other=255 |
authors compound imp compound medium int date date descr string |
never | |||||
| E_NCBI_RESONANCE_SCORE | int | Score of low-energy resonance form selected for standardization | A_ELEMENT B_ORDER B_TYPE A_TYPE | atomchange bondchange merge | ||||||
| E_NCBI_STANDARDIZER_HASH | uint64 | NCBI standardization hashcode (no h, no charges, bond order) | Tcl script | A_ELEMENT B_ORDER A_TYPE B_TYPE | atomchange bondchange merge | e_ncbi_standardizer_hash.xpd | ||||
| E_NCBI_STD_NAME | compound | NCBI standardized name reference | last string first string middle string full string initials string suffix string title string |
never | ||||||
| E_NCBI_SUBSTANCE_COMMENT | stringvector | Substance comments | never | |||||||
| E_NCBI_SUBSTANCE_ID | compound | NCBI substance identifier. If set to zero, use data in E_NCBI_SUBSTANCE_SOURCE | id int version int |
never | ||||||
| E_NCBI_SUBSTANCE_ID_LIST | intvector | NCBI substance identifier list, usually for a CID/SID mapping | never | |||||||
| E_NCBI_SUBSTANCE_SOURCE | choice | NCBI substance source data | individual choice db compound mmdb compound |
never | ||||||
| E_NCBI_SUBSTANCE_SYNONYMS | stringvector | Substance synonyms | Tcl script | E_CID | never | e_ncbi_substance_synonyms.xpd | ||||
| E_NCBI_SUBSTANCE_XREF | choicevector | NCBI substance crossreference data | regid string rn string mesh string pmid int gi int mmdb int sid int cid int dburl url sburl url asurl url protein-gi int nucleotide-gi int taxonomy int aid int mim int gene int probe int biosystem int geogse int geogsm int patent string protein-accession string nucleotide-accession string doi string citation string |
never | ||||||
| E_NCBI_THUMBNAIL | diskfile (switchable between string blob diskfile url) |
A 2D-plot thumbnail of the structure as a GIF or PNG or SVG file | hsymbol: { value: special datatype: string} csymbol: { value: special datatype: string} hcolor: { value: {} datatype: string} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: string} footercolor: { value: black datatype: string} interlace: { value: 1 datatype: boolean} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} filename: { value: {} datatype: string} highlightcolor: { value: red datatype: string} highlightbonds: { value: {} datatype: string} httpheader: { value: 0 datatype: int} crop: { value: -1 datatype: string} wedges: { value: 1 datatype: string} wiggles: { value: sp2 datatype: string} format: { value: png8 description: Format svg uses E_SVG_IMAGE property computation, the others E_GIF enumeration: gif:png:png8:bmp:svg datatype: int} markcolor: { value: blue datatype: string} logofile: { value: {} datatype: string} logoscale: { value: 1 datatype: string} dashes: { value: 1 datatype: string} headerproperty: { value: {} datatype: string} footerproperty: { value: {} datatype: string} bead: { value: 0 datatype: string} showcharge: { value: 1 datatype: string} showradical: { value: 1 datatype: string} showstereo: { value: 1 datatype: string} symbolfontsize: { value: -1 datatype: string} annotationfontsize: { value: -1 datatype: string} antialiasing: { value: 3 datatype: string} highlightgroups: { value: {} datatype: string} boxgroups: { value: {} datatype: string} groupcolor: { value: purple datatype: string} showisotope: { value: 1 datatype: string} isotopemapping: { value: none datatype: string} showstereoh: { value: 0 datatype: string} suppressedmols: { value: {} datatype: string} linewidth: { value: 1.4 datatype: string} showempty: { value: 0 datatype: string} voronoicolorproperty: { value: {} datatype: string} voronoifilter: { value: {} datatype: string} showmapping: { value: 0 datatype: string} font: { value: {} datatype: string} annotationcolor: { value: {} datatype: string} showchirality: { value: none datatype: string} frame: { value: 0 datatype: string} linespacing: { value: 2.0 datatype: string} headerfontsize: { value: -1 datatype: string} footerfontsize: { value: -1 datatype: string} circlecolorproperty: { value: {} datatype: string} circlefilter: { value: {} datatype: string} width: { value: 100 datatype: string} height: { value: 100 datatype: string} bgcolor: { value: grey96 datatype: string} bondcolor: { value: black datatype: string} atomcolor: { value: type datatype: string} asymbol: { value: box datatype: string} border: { value: 6 datatype: string} bonds: { value: 8 datatype: string} commenttype: { value: none datatype: string} metadata: { value: 0 datatype: string} wigglecount: { value: 4 datatype: string} wiggleamplitude: { value: 2 datatype: string} fixiepngsize: { value: 1 datatype: string} rawcoordinates: { value: 0 datatype: string} checkintersection: { value: 0 datatype: string} showstereogroups: { value: 0 datatype: string} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION A_ELEMENT | atomchange bondchange stereochange merge hadd | mod_e_ncbi_thumbnail.so | |||
| E_NCICADD_PARENT_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: ncicad_parent datatype: string} scope: { value: private datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_NCICADD_PARENT_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 0 resonance 0 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHISY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 0 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 0 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ncicadd_parent_id.xpd | |||
| E_NCICADD_PARENT_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_NCICADD_TEST_ERROR_BITSET | bitvector | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_NCICADD_TEST_STATUS_BITSET | bitvector | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_NCOLLISIONS | int | Number of atomic close contacts | Compiled C module | A_XYZ A_ELEMENT A_TYPE | atomchange 3drelative | mod_e_ncollisions.so | ||||
| E_NCONFORMERS | int | Number of conformations in A_CONFORMER | Tcl script | A_CONFORMER | atomchange bondchange merge | e_nconformers.xpd | ||||
| E_ND20 | float | Substance refractive index (20 oC, sodium D line 589.3 nm) | atomchange bondchange atom bond | |||||||
| E_NENVELOPE | short | Total number of envelope rings in ensemble | (builtin) | R_TYPE | atomchange bondchange merge ring | |||||
| E_NESSSR | short | Total number of extended SSSR rings in ensemble, including all basic SSSR rings | (builtin) | R_TYPE | atomchange bondchange merge ring | |||||
| E_NEUTRALIZED_STRUCTURE | structure | Structure with neutralized charges and charge pairs | Compiled C module | A_FORMAL_CHARGE | atomchange bondchange stereochange | mod_e_neutralized_structure.so | ||||
| E_NHACCEPTORS | short | Number of hydrogen bond acceptors | Tcl script | A_HYDROGEN_BONDING | atomchange bondchange | e_nhacceptors.xpd | ||||
| E_NHDONORS | short | Number of atoms which are bonded to hydrogens which may act as H-bridge donors | countdonorhs: { value: 0 datatype: boolean}
|
Tcl script | A_HYDROGEN_BONDING | atomchange bondchange | e_nhdonors.xpd | |||
| E_NIKKAJI_ID | string | ID of the compound in the Japanese Nikkaji substance dictionary | atomchange bondchange stereochange atom bond | |||||||
| E_NIOSH_URL | url | NIOSH (http://www.cdc.gov/niosh-rtecs) data display URL | Tcl script | E_RTECS_NUMBER | atomchange bondchange atom bond | e_niosh_url.xpd | ||||
| E_NIST_SOLUBILITY_URL | url | Dislay URL for compound solubility in any registered solvent (https://srdata.nist.gov/solubility/) | Tcl script | E_CAS | atomchange bondchange atom bond | e_nist_solubility_url.xpd | ||||
| E_NIST_WEBBOOK_ID | string | NIST WebBook ID (webbook.nist.gov) | Tcl script | A_ELEMENT A_TYPE B_TYPE B_ORDER A_ISOTOPE | atomchange bondchange stereochange mol atom bond | e_nist_webbook_id.xpd | ||||
| E_NIST_WEBBOOK_URL | url | NIST WebBook URL (webbook.nist.gov) | Tcl script | E_NIST_WEBBOOK_ID | mol atom bond | e_nist_webbook_url.xpd | ||||
| E_NMOLECULES | int | Number of molecules in ensemble | (builtin) | atomchange bondchange merge shuffle mol | ||||||
| E_NMRDB_PREDICTOR_URL | url | nmrdb.org URL linking to a dynamic NMR spectra prediction for the structure | Tcl script | E_SMILES | mol atom bond | e_nmrdb_predictor_url.xpd | ||||
| E_NMRSHIFTDB_ID | int | NMRShiftDB URL | baseurl: { value: http://www.nmrshiftdb.org description: Base URL for Internet access datatype: url}
|
Tcl script | E_INCHI | mol atom bond | e_nmrshiftdb_id.xpd | |||
| E_NMRSHIFTDB_URL | url | NMR Shift DB display URL (http://nmrshiftdb.nmr.uni-koeln.de) | baseurl: { value: http://www.nmrshiftdb.org description: Base URL for Internet access datatype: url}
|
Tcl script | E_NMRSHIFTDB_ID | atomchange bondchange atom bond | e_nmrshiftdb_url.xpd | |||
| E_NMRSIGMA_METHOD | string | NMR shielding computation method description string. Used in SHARC/SHGI and Gaussian Input I/O modules. | atomchange bondchange 3drelative 3dabsolute | |||||||
| E_NMRSPECTRUM | compound | NMR spectrum | experimental boolean nucleus string origin string author string date date spectrometer string parameters string specificparams dictionary reference string temperature float purity float source string description string solvent string procedure string resolution double coding string spectrum compound imagspectrum compound fid compound imagfid compound shift floatvector multiplicity stringvector integral floatvector ja floatvector jb floatvector jc floatvector jadist shortvector jbdist shortvector jcdist shortvector assignment stringvector assignmentmethod string range floatvector state string standard string |
source: { value: nmrshiftdb enumeration: nmrshiftdb datatype: int} nucleus: { value: 13C description: Nucleus, with isotope mass prefixed, i.e. 13C, 1H, etc. datatype: string} tryretrieval: { value: 1 datatype: boolean} tryprediction: { value: 1 datatype: boolean} |
Tcl script | atomchange bondchange | e_nmrspectrum.xpd | |||
| E_NMRSPECTRUM_IMAGE | diskfile (switchable between string blob diskfile url) |
NMR spectrum rendering | datafield: { value: spectrum datatype: string} height: { value: 250 datatype: int} width: { value: 500 datatype: int} bgcolor: { value: white datatype: color} title: { value: {} datatype: string} filename: { value: {} datatype: string constraints: writeable} format: { value: png enumeration: png,png24:gif:png8 datatype: string} titlecolor: { value: black datatype: color} framecolor: { value: black datatype: color} signalcolor: { value: #DD0000 datatype: color} |
Tcl script | E_NMRSPECTRUM | atomchange bondchange merge mol | e_nmrspectrum_image.xpd | |||
| E_NONBONDING_ENERGY | float | Estimate of NBE computed from VdW-Sphere Interaction in A_XYZ coordinates | Compiled C module | A_XYZ A_TYPE A_TOPO_DISTANCE A_VDW_INTERACTION | atomchange bondchange stereochange merge 3drelative hadd | mod_e_nonbonding_energy.so | ||||
| E_NOTEBOOK_ID | string | Laboratory notebook registration ID | A_ELEMENT A_TYPE B_TYPE B_ORDER | never | ||||||
| E_NO_HYDROGEN_QUERY_SCREEN | bitvector | Bitvector optimized for standard superstructure queries, with focus on ring systems and ring substitutions as well as the capability to generalized heteroatoms and standard element classes (halogens, N/O/S, etc.). | size: { value: 1952 description: Vector size minvalue: 256 maxvalue: 4096 datatype: int} power: { value: 2 description: Count step escalation minvalue: 1 maxvalue: 3 datatype: int} nbitsperpath: { value: 4 description: Bit positions to ser per unique path minvalue: 1 maxvalue: 16 datatype: int} maxcount: { value: 3 description: Maximum path count to use minvalue: 1 maxvalue: 16 datatype: int} minpathlen: { value: 2 description: Minimum length of paths fo hash minvalue: 2 maxvalue: 5 datatype: int} maxpathlen: { value: 5 description: Maximum length of pathes to hash minvalue: 2 maxvalue: 10 datatype: int} maxpathsperatom: { value: -1 description: Maximum nmber of paths to find per atom, -1 is unlimited minvalue: -1 maxvalue: 9999 datatype: int} isquery: { value: 0 description: Whether structure is a query sub/superstructure, or a complete structure datatype: boolean} ignoreh: { value: 1 description: If set, do not create any codes involving hydrogen datatype: boolean} tauto: { value: 0 description: If set, do not set any bits with H, or involving bond orders in tauo systems datatype: boolean} debug: { value: 0 description: If set, print found paths datatype: boolean} useringcombos: { value: 1 description: If set, add ring combo screen bits datatype: boolean} tracebit: { value: -1 description: Trace which pattern sets this bit position minvalue: -1 maxvalue: 4096 datatype: int} cmpflags: { value: bondorder|useatomtree|usebondtree description: Comparison flags which will be used in subsequent atom-by-atom matching. Some flags can be used for increasing the filter efficiency enumeration: one:wedge,wedges:charge:stereo:bondorder,bo:terminal:nozwitterioncollapse:nosinglaonaro:nodoubleonaro:isotope:tautomer:arotautomer:matchbondringcount:lazymatchbondringcount:kekule,kekuleodd:strictnomatch:nochainonaro:lazymatchatomringcount:matchatomringcount:bondreaction:pionaro:noaliphaticonaro:relativestereo:fixedframework,fixedframe:nomultibondfg:noarobondfg:noheterofg:useatomtree,atomtree:usebondtree,bondtree:excludesmartsenvironment:openhcount:varbondglobal:varbondindividual:kekuleeven:unsetaromaticisaliphatic:implicitonsingleoraro:nullsubstructureismismatch:nochainonring:atomlistidentity:splitfragments:generalizeheteroatoms:nosuperatomonh:singleattachmentsuperatomsonly:remembercomplexmatches:matchallheavyatoms:fullringsystem:noatomstereook:nobondstereook:multibondorder,singleonany,singleisany:matchfullmolecule,matchfullmol:matchfullensemble,matchfullens:nosmallerrings:noalkyllinks:containedatomlists:chained:no3dcoordinatecomputation,no3dcoordinatescomputation datatype: bitset} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER B_ISAROMATIC A_ISAROMATIC E_ELEMENT_COUNT R_TYPE R_AROMATIC A_HASH A_RING_COUNT B_RING_COUNT | atomchange bondchange hadd atom bond ring | mod_e_no_hydrogen_query_screen.so | |||
| E_NO_HYDROGEN_SCREEN | bitvector | Screening bits for superstructure search (same as E_SCREEN, but not including any fragments which contain a hydrogen atom) | usevariants: { value: 0 datatype: boolean} maxvariants: { value: 10 datatype: int} extended: { value: 2 minvalue: 0 maxvalue: 2 datatype: int} tauto: { value: 0 datatype: boolean} ignoreh: { value: 1 datatype: boolean} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange hadd mol | mod_e_no_hydrogen_screen.so | |||
| E_NRINGS | short | Total number of rings in ensemble | (builtin) | atomchange bondchange merge ring | ||||||
| E_NROTBONDS | int | Number of bonds which are rotatable and where the rotation has a steric effect | Compiled C module | B_ROTATABILITY | atomchange bondchange hadd | mod_e_nrotbonds.so | ||||
| E_NSC | int | NCI Cancer screening database record number | atomchange bondchange | |||||||
| E_NSSSR | short | Total number of SSSR rings in ensemble | (builtin) | R_TYPE | atomchange bondchange merge ring | |||||
| E_NUCLEAR_RECEPTOR_LIGAND_LIKENESS | compound | Structural likeness to known nucleic receptor agonists or antatonists, computed as highest Tanimoto similarity (on standard similarity property E_SCREEN) to a diverse 1K cpds subset of the NRLiSt BDB (Nuclear Receptors Ligands and Structures Benchmarking Database, http://nrlist.drugdesign.fr/download.php) | Lagarde, Nasr, Jeremie, Guillemain, Laville, Labib, Zagury, Montes, J. Med. Chem.. 2014, 57, 3117 | similarity byte structure structure |
Tcl script | E_SCREEN | atomchange bondchange atom bond | e_nuclear_receptor_ligand_likeness.xpd | ||
| E_NVARIANTS | int | Estimate of number of structure variant if lists, rgroups, etc. are enumerated. No symmetry analysis! | Tcl script | A_TYPE | atomchange bondchange merge atom bond | e_nvariants.xpd | ||||
| E_OPENPHACTS_ID | int | RSC OpenPhacts ID (www.openphacts.org) | Tcl script | E_SMILES | atomchange bondchange atom bond | e_openphacts_id.xpd | ||||
| E_OPENPHACTS_URL | url | Data display link for structure data in OpenPHACTS database (openphacts.org). | Tcl script | E_OPENPHACTS_ID | atomchange bondchange hadd atom bond | e_openphacts_url.xpd | ||||
| E_OPREA_LEADLIKENESS_VIOLATIONS | byte | Teague, Davis, Leeson, Oprea, Angew. Chem. Int. Ed. 1999, 38, 3743 | Tcl script | E_WEIGHT E_XLOGP2 E_NROTBONDS | atomchange bondchange atom bond | e_oprea_leadlikeness_violations.xpd | ||||
| E_ORGANOBORONS_ID | string | Database ID in www.organoborons.com | Tcl script | atomchange bondchange atom bond | e_organoborons_id.xpd | |||||
| E_ORGANOBORONS_URL | url | Display URL for entry in www.organoborons.com | Tcl script | E_ORGANOBORONS_ID | atomchange bondchange atom bond | e_organoborons_url.xpd | ||||
| E_ORIGINAL_STRUCTURE | structure | Original structure (usually saved as backup property on modified/standardized structure) | Tcl script | never | e_original_structure.xpd | |||||
| E_OSDB_ID | string | Record ID in the OSDB database (osdb.info) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_osdb_id.xpd | ||||
| E_OSDB_URL | url | Display URL in the OSDB database (osdb.info) | Tcl script | E_OSDB_ID | atomchange bondchange stereochange atom bond | e_osdb_url.xpd | ||||
| E_OUTPUTDATE | date | Output date time stamp for molecule | Tcl script | never | e_outputdate.xpd | |||||
| E_OWNER | string | Owner or contributor of a data record | never | |||||||
| E_PAINS_FILTER | compound | Compound filtering by the PAINS filters (J. Med. Chem., 2010, 53 (7), pp 2719?2740) by Baell et al. Filtering is done by means of the original SLN filters from the paper, not the SMARTS approximation which can found on the Internet. The property has two fields: The filter status (0: no filter match, 1:filter match with pattern from table S6 in original publication with >150 hits, 2: filer match from table S7, 15..150 hits, 3: filter match from table S8, <15 hits in the test dataset used in the paper), and the name of the first matching pattern, as used in the original publication. |
J. Med. Chem., 2010, 53 (7), pp 2719–2740 | match int id string |
Tcl script | atomchange bondchange atom bond | e_pains_filter.xpd | |||
| E_PARENT_HASH128 | uint128 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_hash128.xpd | ||||
| E_PARENT_HASHY | uint64 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_hashy.xpd | ||||
| E_PARENT_ISOTOPE_HASH128 | uint128 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_isotope_hash128.xpd | ||||
| E_PARENT_ISOTOPE_HASHY | uint64 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_isotope_hashy.xpd | ||||
| E_PARENT_ISOTOPE_STEREO_HASH128 | uint128 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_isotope_stereo_hash128.xpd | ||||
| E_PARENT_ISOTOPE_STEREO_HASHY | uint64 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_isotope_stereo_hashy.xpd | ||||
| E_PARENT_STEREO_HASH128 | uint128 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_stereo_hash128.xpd | ||||
| E_PARENT_STEREO_HASHY | uint64 | Hashcode of the parent structure | Tcl script | E_PARENT_STRUCTURE | atomchange bondchange merge | e_parent_stereo_hashy.xpd | ||||
| E_PARENT_STRUCTURE | structure | Parent structure | saltfile: { value: ions.smi description: Standard counterions datatype: diskfile constraints: readable} clearisotope: { value: 0 datatype: boolean} clearatomstereo: { value: 0 datatype: boolean} clearbondstereo: { value: 0 datatype: boolean} uniquetautomer: { value: 0 datatype: boolean} maxtautomers: { value: 250 datatype: int} pgfile: { value: pg.smi description: Standard protecting group definitions datatype: diskfile constraints: readable} deprotect: { value: 0 description: If set, try to remove standard protecting groups datatype: boolean} style: { value: cactvs enumeration: cactvs:pubchem datatype: int} clearinorganic: { value: 1 datatype: boolean} clearensprops: { value: 1 datatype: boolean} cutmetalsalts: { value: 1 datatype: boolean} cutcomplexbonds: { value: 1 datatype: boolean} cutmetalbonds: { value: 0 datatype: boolean} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange | e_parent_structure.xpd | |||
| E_PASS_DATA_PA | floatvector | PASS software Pa value (probability of being an antagonist). This data is for example served by the NCI cancer screening database. | cathepsin_b_inhibitor float opioid_agonist float leukotriene_synthesis_inhibitor float estrogen_receptor_modulator float antibiotic_oxacephem-like float dopa_decarboxylase_inhibitor float bradykinin_antagonist float factor_xiiia_inhibitor float gynecological_disorders_treatment float urinary_incontinence_treatment float antibiotic_oxazolidinone-like float antimitotic float cyclooxygenase_inhibitor float purinergic_p2_agonist float cytostatic float antiallergic float cyclooxygenase_2_inhibitor float phosphodiesterase_v_inhibitor float squalene_epoxidase_inhibitor float nitric_oxide_synthase_inhibitor float teratogen float glutamate_(mglur5)_antagonist float cardiotoxic float 5_hydroxytryptamine_4_agonist float geranylgeranyltransferase_inhibitor float dermatologic float interleukin_1_antagonist float acetylcholine_nicotinic_antagonist float sulfonylureas float dopamine_antagonist float adenosine_deaminase_inhibitor float corneal_wound_healing_stimulator float non-steroidal_antiinflammatory_agent float vasopressin_1_antagonist float interferon_inducer float growth_hormone_secretion_inhibitor float hestagen_antagonist float glucocorticoid_agonist float vitamin float retinoid-like float muscle_relaxant float excitatory_amino_acid_antagonist float hiv_protease_inhibitor float endothelin_antagonist float antimycobacterial float 5_hydroxytryptamine_3_antagonist float growth_stimulant float cholinergic_agonist float immunomodulator float hypertermic float uterine_stimulant float antibiotic_anthracycline-like float antiprotozoal float antibiotic_beta_lactam-like float endothelin_a_receptor_antagonist float hiv-1_protease_inhibitor float spasmolytic float antibiotic_glycopeptide-like float spasmogenic float adenosine_a2_receptor_agonist float antipsoriatic float 5_hydroxytryptamine_1d_agonist float antitoxic float benzodiazepine_agonist float steroid-like float immunosuppressant float antineoplastic float reverse_transcriptase_inhibitor float psychotropic float factor_xa_inhibitor float histamine_h2_receptor_antagonist float thrombolytic float estrone_sulfatase_inhibitor float trypsin_inhibitor float antiviral_(hepatitis_c) float glutamate_(mglur1)_agonist float antiviral float oxytocin_agonist float growth_hormone_release_promoting float 5_hydroxytryptamine_2c_agonist float purinergic_receptor_antagonist float nmda_receptor_polyamine_site_activator float sodium_channel_blocker float progesterone_antagonist float antitrypanosomal float antiinflammatory_intestinal float antimycoplasmal float vasopressin_2_antagonist float dopamine_autoreceptor_agonist float gaba_receptor_antagonist float antimigraine float thyroid_hormone_agonist float immunosuppressant_cyclosporine-like float 5_hydroxytryptamine_antagonist float ileal_bile_acid_transport_inhibitor float kainate_receptor_antagonist float bronchodilator float microtubule_formation_inhibitor float saluretic_reabsorbtion_inhibitor float acetylcholinesterase_inhibitor float platelet_antagonist float 5_hydroxytryptamine_2a_antagonist float complement_inhibitor float prolactin_inhibitor float 5_hydroxytryptamine_4_antagonist float anti-helicobacter_pylori float mydriatic float glutamate_(mglur5a)_agonist float opioid_mu_receptor_agonist float alpha_adrenoreceptor_agonist float antiglaucomic float postcoital_contraceptive float antineoplastic_enhancer float phospholipase_a2_inhibitor float adrenaline_antagonist float atrial_natriuretic_polypeptide_agonist float histamine_release_stimulant float antidiuretic_hormone_antagonist float embryotoxic float spermicide float interleukin_1_beta_converting_enzyme_inhibitor float antibiotic_penicillin-like float antimalarial float neutral_endopeptidase_inhibitor float substance_p_antagonist float endothelin_b_receptor_antagonist float beta_adrenoreceptor_antagonist float antiischemic float adenosine_kinase_inhibitor float uterine_relaxant float antiobesity float anticerebroischemic float antibacterial float mao-a_inhibitor float hypertensive_ophthalmic float tryptase_inhibitor float luteinizing_hormone-releasing_hormone_agonist float histamine_h3_receptor_agonist float acetylcholine_release_stimulant float aldose_reductase_inhibitor float histamine_h3_receptor_antagonist float luteinizing_hormone-releasing_hormone_antagonist float antiinfective_(hiv) float urokinase_inhibitor float antidepressant_imipramin-like float antimetabolite float gastrin-releasing_peptide_antagonist float 5_hydroxytryptamine_uptake_inhibitor float antiparkinsonian_tremor_relieving float antibiotic_trimethoprim-like float acute_neurologic_disorders_treatment float 5_hydroxytryptamine_2b_antagonist float inflammatory_bowel_disease_threatment float glutamate_(mglur5)_agonist float thymidine_kinase_inhibitor float 5_hydroxytryptamine_1_agonist float antitussive float glutamate_(mglur3)_antagonist float factor_viia_inhibitor float carbonic_anhydrase_inhibitor float nmda_receptor_agonist float anabolic float photosensitizer float 5_hydroxytryptamine_1a_antagonist float calcium_regulator float acetylcholine_antagonist float antiseptic float antiinfertility_female float gaba_aminotransferase_inhibitor float aromatase_inhibitor float anesthetic_general float antiinflammatory float contraceptive float glutamate_receptor_antagonist float uridine_phosphorylase_inhibitor float diuretic float topoisomerase_inhibitor float alcohol_dehydrogenase_inhibitor float glucagon_receptor_antagonist float immunostimulant float ornithine_decarboxylase_inhibitor float antiosteoporotic float hypertensive float rhinitis_treatment float collagenase_inhibitor float adenosine_receptor_agonist float analgesic_non-opioid float angiotensin_antagonist float histamine_agonist float anticataract float 5_hydroxytryptamine_1a_agonist float antiemphysemic float tyrosine_kinase_inhibitor float cholesterol_esterase_inhibitor float purinergic_receptor_agonist float phosphodiesterase_iv_inhibitor float analeptic float antihelmintic float chemoprotective float antihypertensive float sympatholytic float beta_1_adrenoreceptor_antagonist float dihydroorotate_dehydrogenase_inhibitor float alkylator float androgen_agonist float nitric_oxide_donor float hypoglycemic float cytokine_modulator float mutagenic float 5_hydroxytryptamine_2c_antagonist float antiarthritic float antipruritic float quisqualate_antagonist float cannabinoid_receptor_agonist float corticosteroid-like float cocain_dependency_treatment float antiinflammatory_steroid float prostaglandin_agonist float 5_alpha_reductase_inhibitor float adrenergic_transmitter_uptake_inhibitor float succinic_dehydrogenase_inhibitor float s-adenosyl-l-methionine_decarboxylase_inhibitor float alpha_adrenoreceptor_antagonist float antilipidemic float glycine_receptor_agonist float hdl-cholesterol_increasing float cardiovascular_analeptic float antibiotic_penem-like float glutamate_receptor_agonist float antiinflammatory_pancreatic float 5_hydroxytryptamine_agonist float glutamate_(mglur2)_antagonist float kainate_receptor_agonist float cytosole_dipeptidase_inhibitor float nasal_decongestant float selectin_antagonist float adp_ribosyl_transferase_inhibitor float ampa_receptor_agonist float calmodulin_antagonist float o6-alkylguanine-dna_alkyltransferase_inhibitor float psychosexual_dysfunction_treatment float elastase_inhibitor float choleretic float glucocorticoid_antagonist float acetylcholine_m1_receptor_agonist float glutamate_(mglur2)_agonist float calcium_agonist float chemopreventive float sedative float cognition_disorders_treatment float antiamebic float neuropeptide_y_antagonist float antibiotic_naphthyridine-like float protein_kinase_c_inhibitor float benzodiazepine_antagonist float beta_3_adrenoreceptor_agonist float acetylcholine_neuromuscular_blocking_agent float tumour_necrosis_factor_antagonist float adenosine_receptor_antagonist float dipeptidyl_aminopeptidase_iv_inhibitor float histamine_antagonist float neurokinin_2_antagonist float cystic_fibrosis_treatment float myocardial_ischemia_treatment float leukopoiesis_inhibitor float signal_transduction_pathways_inhibitor float matrix_metalloproteinase_inhibitor float male_reproductive_disfunction_treatment float mao_inhibitor float gaba_b_receptor_agonist float acetylcholine_muscarinic_agonist float thromboxane_antagonist float vasopressor float beta_2_adrenoreceptor_agonist float 3_hydroxyanthranilate_oxygenase_inhibitor float progestin_agonist float myristoyl_transferase_inhibitor float poly(adp-ribose)synthethase_inhibitor float 23-oxidosqualene-lanosterol_cyclase_inhibitor float hematopoietic_inhibitor float antismoking float sclerosant float beta_1_adrenoreceptor_agonist float adrenaline_agonist float metabolic float thyrotropin_releasing_hormone_agonist float alpha_glucosidase_inhibitor float acetylcholine_nicotinic_agonist float phospholipase_c_inhibitor float interleukin_antagonist float thiol_protease_inhibitor float cholecystokinin_agonist float bone_formation_stimulant float cholecystokinin_a_agonist float oxytocin_antagonist float angiotensin_ii_receptor_antagonist float glutamate_(mglur1)_antagonist float skeletal_muscle_relaxant float dopamine_beta_hydroxylase_inhibitor float antibiotic_isocephem-like float adenosine_a2a_receptor_antagonist float glutamate_uptake_inhibitor float potassium_channel_antagonist float antibiotic_carbapenem-like float bisphosphonate float leukotriene_d4_antagonist float acetylcholine_m2_receptor_antagonist float psychostimulant float anticoccidial float antimitotic_taxane-like float 5_hydroxytryptamine_2_agonist float interleukin_6_antagonist float teratogen_and/or_embryotoxic float antibiotic_quinolone-like float reductant float antibiotic_rifamycin-like float adenosine_a2a_receptor_agonist float renin_inhibitor float opioid_antagonist float angiogenesis_inhibitor float insulin_secretagoues float antidepressant float neurokinin_3_antagonist float excitatory_amino_acid_agonist float analgesic_opioid float glutamate_(mglur6)_agonist float radiosensitizer float glutamate_(mglur)_agonist float antidiabetic float nmda_receptor_glycine_site_agonist float hiv_integrase_inhibitor float aminopeptidase_microsomal_inhibitor float adenosine_a1_receptor_agonist float acetylcholine_muscarinic_antagonist float anticoagulant float thrombin_inhibitor float anxiolytic float nmda_receptor_antagonist float xanthine_oxidase_inhibitor float gaba_receptor_agonist float thymidylate_synthase_inhibitor float sigma_receptor_antagonist float prostaglandin_e2_antagonist float hepatoprotectant float 5_hydroxytryptamine_1d_antagonist float antitussive_narcotic float cardioprotectant float antiviral_(hepatitis) float cholecystokinin_a_antagonist float antineoplastic_alkaloid float antiarrhythmic float dopamine_d1_agonist float protocollagen_prolyl_hydroxylase_inhibitor float antiviral_(influenza) float enkephalinase_inhibitor float alkylphospholipid float gaba_a_receptor_antagonist float prolactin_secretion_inhibitor float 5_hydroxytryptamine_1b_agonist float mucolytic float angiotensin_at1_receptor_antagonist float hestagen-like float antiviral_(hiv) float respiratory_distress_syndrome_treatment float bradykinin_b2_receptor_antagonist float hematopoietic float thyroid_hormone_antagonist float catechol_o_methyltransferase_inhibitor float adenosine_a1_receptor_antagonist float lymphocytopoiesis_inhibitor float glutamate_(mglur)_antagonist float nmda_receptor_glycine_site_antagonist float topoisomerase_ii_inhibitor float 5_hydroxytryptamine_1f_agonist float neurotensin_receptor_antagonist float prostaglandin_antagonist float antianginal float neuraminidase_(influenza)_inhibitor float opioid_kappa_receptor_agonist float purinergic_p2_antagonist float somatostatin_agonist float adenosine_a3_receptor_agonist float anesthetic_local float anaphylatoxin_receptor_antagonist float alpha_1_adrenoreceptor_antagonist float nootropic float glucose-6-phosphate_translocase_inhibitor float endothelin-converting_enzyme_inhibitor float antihypercholesterolemic float antibiotic_cephalosporin-like float antiparkinsonian_rigidity_relieving float leukotriene_antagonist float cholinergic_antagonist float acetylcholine_m3_receptor_antagonist float antiulcerative float hcv_ns3-helicase_inhibitor float antiparkinsonian float nmda_receptor_polyamine_site_blocker float bone_resorption_inhibitor float radioprotector float cathepsin_l_inhibitor float cardiodepressant float renal_disease_treatment float arrhythmogenic float glycinamide_ribonucleotide_formyltransferase_inhibitor float prostate_disorders_treatment float bombesin_antagonist float cholecystokinin_b_antagonist float vasodilator float ribonucleoside_diphosphate_reductase_inhibitor float ulcerogenic float xanthine-like float phosphodiesterase_inhibitor float insulin_promoter float dopamine_d1_antagonist float keratoses_actinic(solar)_treatment float antiacne float platelet_aggregation_inhibitor float 5_hydroxytryptamine_release_stimulant float restenosis_treatment float glutamate_(mglur3)_agonist float alpha_2_adrenoreceptor_antagonist float gaba_uptake_inhibitor float peristaltic_stimulant float phosphodiesterase_iii_inhibitor float expectorant float histamine_h2_receptor_agonist float hmg_coa_reductase_inhibitor float histidine_decarboxylase_inhibitor float antibiotic_tetracycline-like float lipoxygenase_inhibitor float aldosterone_antagonist float gaba_b_receptor_antagonist float gastric_antisecretory float antifungal float angiotensin_at2_receptor_antagonist float interleukin_8_antagonist float adenosine_a2_receptor_antagonist float miotic float cholecystokinin_antagonist float antibiotic float antibiotic_aminoglycoside-like float melatonin_antagonist float anesthetic_inhalation float phospholipase_inhibitor float antibiotic_macrolide-like float acetylcholine_agonist float gp_iib/iiia_receptor_antagonist float hcv_serine_protease_inhibitor float antiemetic float potassium_channel_activator float estrogen_agonist float respiratory_analeptic float sodium_channel_blocker_class_ib float erythropoietin float leukotriene_b4_antagonist float hmg_coa_synthase_inhibitor float liver_fibrosis_treatment float benzodiazepine_inverse_agonist float anticonvulsant float benzodiazepine_agonist_partial float 5_hydroxytryptamine_3_agonist float antispirochetal float dopamine_d2_antagonist float phosphodiesterase_i_inhibitor float antioxidant float hypolipemic float mao-b_inhibitor float tnf-alpha_release_inhibitor float vitamin_d-like float angiotensin_converting_enzyme_inhibitor float lipid_peroxidase_inhibitor float purine_nucleoside_phosphorylase_inhibitor float mineralocorticoid float neurokinin_antagonist float alpha_2_adrenoreceptor_agonist float camp_phosphodiesterase_inhibitor float keratolytic float spasmolytic_papaverin-like float androgen_antagonist float multiple_sclerosis_treatment float estrogen_antagonist float dopamine_d2_agonist float anesthetic float chymotrypsin_inhibitor float alpha_1_adrenoreceptor_agonist float antipsychotic float mannosidase_inhibitor float antidyskinetic float ampa_receptor_antagonist float antidiabetic_symptomatic float septic_shock_treatment float neuropeptide_antagonist float pancreatic_disorders_treatment float carcinogenic float alzheimer's_disease_treatment float motilin-like float adenosine_a3_receptor_antagonist float cardiotonic float leukotriene_a4_hydrolase_inhibitor float parathyroid_hormone_antagonist float 5_hydroxytryptamine_1_antagonist float antibiotic_carbacephem-like float platelet_activating_factor_antagonist float dopamine_d3_antagonist float antitrichomonal float dihydrofolate_reductase_inhibitor float purinergic_p2t_antagonist float mediator_release_inhibitor float h+/k+-transporting_atpase_inhibitor float s-adenosyl-l-homocysteine_hydrolase_inhibitor float dopamine_uptake_inhibitor float opioid_delta_receptor_agonist float interleukin_agonist float gastrin_inhibitor float camp_modulator float neurotrophic_factor float anorexic float dopamine_agonist float farnesyltransferase_inhibitor float glutamate_(mglur6)_antagonist float antiasthmatic float antimitotic_podophyllotoxin-like float glutamate_(mglur1a)_agonist float maillard_reaction_inhibitor float melatonin_agonist float antineoplastic_antibiotic float saluretic float anticholelithogenic float gaba_a_receptor_agonist float hypnotic float coagulant float opioid_partial_agonist float beta_lactamase_inhibitor float treponemicidal float ribonucleotide_reductase_inhibitor float uricosuric float hcv_ns3-4a_protease_inhibitor float dna_intercalator float squalene_synthetase_inhibitor float endothelin_receptor_antagonist float beta_adrenoreceptor_agonist float thromboxane_synthase_inhibitor float antibiotic_tribactam-like float analgesic float calpain_inhibitor float cns_active_muscle_relaxant float hcv_ns3_protease_inhibitor float 5_hydroxytryptamine_2_antagonist float protease_inhibitor float narcotic_antagonist float ophthalmic_drug float acetyl_coa_transferase_inhibitor float hypotermic float antihistaminic float dopamine_d4_antagonist float irritable_bowel_syndrome_therapy float platelet_adhesion_inhibitor float spasmolytic_urinary float atherosclerosis_treatment float nucleotide_metabolism_regulator float prolyl_endopeptidase_inhibitor float hair_growth_promoter float calcium_channel_antagonist float histamine_h1_receptor_antagonist float |
never | ||||||
| E_PASS_DATA_PI | floatvector | PASS software Pi value (probability of being an inhibitor). This data is for example served by the NCI cancer screening database. | cathepsin_b_inhibitor float opioid_agonist float leukotriene_synthesis_inhibitor float estrogen_receptor_modulator float antibiotic_oxacephem-like float dopa_decarboxylase_inhibitor float bradykinin_antagonist float factor_xiiia_inhibitor float gynecological_disorders_treatment float urinary_incontinence_treatment float antibiotic_oxazolidinone-like float antimitotic float cyclooxygenase_inhibitor float purinergic_p2_agonist float cytostatic float antiallergic float cyclooxygenase_2_inhibitor float phosphodiesterase_v_inhibitor float squalene_epoxidase_inhibitor float nitric_oxide_synthase_inhibitor float teratogen float glutamate_(mglur5)_antagonist float cardiotoxic float 5_hydroxytryptamine_4_agonist float geranylgeranyltransferase_inhibitor float dermatologic float interleukin_1_antagonist float acetylcholine_nicotinic_antagonist float sulfonylureas float dopamine_antagonist float adenosine_deaminase_inhibitor float corneal_wound_healing_stimulator float non-steroidal_antiinflammatory_agent float vasopressin_1_antagonist float interferon_inducer float growth_hormone_secretion_inhibitor float hestagen_antagonist float glucocorticoid_agonist float vitamin float retinoid-like float muscle_relaxant float excitatory_amino_acid_antagonist float hiv_protease_inhibitor float endothelin_antagonist float antimycobacterial float 5_hydroxytryptamine_3_antagonist float growth_stimulant float cholinergic_agonist float immunomodulator float hypertermic float uterine_stimulant float antibiotic_anthracycline-like float antiprotozoal float antibiotic_beta_lactam-like float endothelin_a_receptor_antagonist float hiv-1_protease_inhibitor float spasmolytic float antibiotic_glycopeptide-like float spasmogenic float adenosine_a2_receptor_agonist float antipsoriatic float 5_hydroxytryptamine_1d_agonist float antitoxic float benzodiazepine_agonist float steroid-like float immunosuppressant float antineoplastic float reverse_transcriptase_inhibitor float psychotropic float factor_xa_inhibitor float histamine_h2_receptor_antagonist float thrombolytic float estrone_sulfatase_inhibitor float trypsin_inhibitor float antiviral_(hepatitis_c) float glutamate_(mglur1)_agonist float antiviral float oxytocin_agonist float growth_hormone_release_promoting float 5_hydroxytryptamine_2c_agonist float purinergic_receptor_antagonist float nmda_receptor_polyamine_site_activator float sodium_channel_blocker float progesterone_antagonist float antitrypanosomal float antiinflammatory_intestinal float antimycoplasmal float vasopressin_2_antagonist float dopamine_autoreceptor_agonist float gaba_receptor_antagonist float antimigraine float thyroid_hormone_agonist float immunosuppressant_cyclosporine-like float 5_hydroxytryptamine_antagonist float ileal_bile_acid_transport_inhibitor float kainate_receptor_antagonist float bronchodilator float microtubule_formation_inhibitor float saluretic_reabsorbtion_inhibitor float acetylcholinesterase_inhibitor float platelet_antagonist float 5_hydroxytryptamine_2a_antagonist float complement_inhibitor float prolactin_inhibitor float 5_hydroxytryptamine_4_antagonist float anti-helicobacter_pylori float mydriatic float glutamate_(mglur5a)_agonist float opioid_mu_receptor_agonist float alpha_adrenoreceptor_agonist float antiglaucomic float postcoital_contraceptive float antineoplastic_enhancer float phospholipase_a2_inhibitor float adrenaline_antagonist float atrial_natriuretic_polypeptide_agonist float histamine_release_stimulant float antidiuretic_hormone_antagonist float embryotoxic float spermicide float interleukin_1_beta_converting_enzyme_inhibitor float antibiotic_penicillin-like float antimalarial float neutral_endopeptidase_inhibitor float substance_p_antagonist float endothelin_b_receptor_antagonist float beta_adrenoreceptor_antagonist float antiischemic float adenosine_kinase_inhibitor float uterine_relaxant float antiobesity float anticerebroischemic float antibacterial float mao-a_inhibitor float hypertensive_ophthalmic float tryptase_inhibitor float luteinizing_hormone-releasing_hormone_agonist float histamine_h3_receptor_agonist float acetylcholine_release_stimulant float aldose_reductase_inhibitor float histamine_h3_receptor_antagonist float luteinizing_hormone-releasing_hormone_antagonist float antiinfective_(hiv) float urokinase_inhibitor float antidepressant_imipramin-like float antimetabolite float gastrin-releasing_peptide_antagonist float 5_hydroxytryptamine_uptake_inhibitor float antiparkinsonian_tremor_relieving float antibiotic_trimethoprim-like float acute_neurologic_disorders_treatment float 5_hydroxytryptamine_2b_antagonist float inflammatory_bowel_disease_threatment float glutamate_(mglur5)_agonist float thymidine_kinase_inhibitor float 5_hydroxytryptamine_1_agonist float antitussive float glutamate_(mglur3)_antagonist float factor_viia_inhibitor float carbonic_anhydrase_inhibitor float nmda_receptor_agonist float anabolic float photosensitizer float 5_hydroxytryptamine_1a_antagonist float calcium_regulator float acetylcholine_antagonist float antiseptic float antiinfertility_female float gaba_aminotransferase_inhibitor float aromatase_inhibitor float anesthetic_general float antiinflammatory float contraceptive float glutamate_receptor_antagonist float uridine_phosphorylase_inhibitor float diuretic float topoisomerase_inhibitor float alcohol_dehydrogenase_inhibitor float glucagon_receptor_antagonist float immunostimulant float ornithine_decarboxylase_inhibitor float antiosteoporotic float hypertensive float rhinitis_treatment float collagenase_inhibitor float adenosine_receptor_agonist float analgesic_non-opioid float angiotensin_antagonist float histamine_agonist float anticataract float 5_hydroxytryptamine_1a_agonist float antiemphysemic float tyrosine_kinase_inhibitor float cholesterol_esterase_inhibitor float purinergic_receptor_agonist float phosphodiesterase_iv_inhibitor float analeptic float antihelmintic float chemoprotective float antihypertensive float sympatholytic float beta_1_adrenoreceptor_antagonist float dihydroorotate_dehydrogenase_inhibitor float alkylator float androgen_agonist float nitric_oxide_donor float hypoglycemic float cytokine_modulator float mutagenic float 5_hydroxytryptamine_2c_antagonist float antiarthritic float antipruritic float quisqualate_antagonist float cannabinoid_receptor_agonist float corticosteroid-like float cocain_dependency_treatment float antiinflammatory_steroid float prostaglandin_agonist float 5_alpha_reductase_inhibitor float adrenergic_transmitter_uptake_inhibitor float succinic_dehydrogenase_inhibitor float s-adenosyl-l-methionine_decarboxylase_inhibitor float alpha_adrenoreceptor_antagonist float antilipidemic float glycine_receptor_agonist float hdl-cholesterol_increasing float cardiovascular_analeptic float antibiotic_penem-like float glutamate_receptor_agonist float antiinflammatory_pancreatic float 5_hydroxytryptamine_agonist float glutamate_(mglur2)_antagonist float kainate_receptor_agonist float cytosole_dipeptidase_inhibitor float nasal_decongestant float selectin_antagonist float adp_ribosyl_transferase_inhibitor float ampa_receptor_agonist float calmodulin_antagonist float o6-alkylguanine-dna_alkyltransferase_inhibitor float psychosexual_dysfunction_treatment float elastase_inhibitor float choleretic float glucocorticoid_antagonist float acetylcholine_m1_receptor_agonist float glutamate_(mglur2)_agonist float calcium_agonist float chemopreventive float sedative float cognition_disorders_treatment float antiamebic float neuropeptide_y_antagonist float antibiotic_naphthyridine-like float protein_kinase_c_inhibitor float benzodiazepine_antagonist float beta_3_adrenoreceptor_agonist float acetylcholine_neuromuscular_blocking_agent float tumour_necrosis_factor_antagonist float adenosine_receptor_antagonist float dipeptidyl_aminopeptidase_iv_inhibitor float histamine_antagonist float neurokinin_2_antagonist float cystic_fibrosis_treatment float myocardial_ischemia_treatment float leukopoiesis_inhibitor float signal_transduction_pathways_inhibitor float matrix_metalloproteinase_inhibitor float male_reproductive_disfunction_treatment float mao_inhibitor float gaba_b_receptor_agonist float acetylcholine_muscarinic_agonist float thromboxane_antagonist float vasopressor float beta_2_adrenoreceptor_agonist float 3_hydroxyanthranilate_oxygenase_inhibitor float progestin_agonist float myristoyl_transferase_inhibitor float poly(adp-ribose)synthethase_inhibitor float 23-oxidosqualene-lanosterol_cyclase_inhibitor float hematopoietic_inhibitor float antismoking float sclerosant float beta_1_adrenoreceptor_agonist float adrenaline_agonist float metabolic float thyrotropin_releasing_hormone_agonist float alpha_glucosidase_inhibitor float acetylcholine_nicotinic_agonist float phospholipase_c_inhibitor float interleukin_antagonist float thiol_protease_inhibitor float cholecystokinin_agonist float bone_formation_stimulant float cholecystokinin_a_agonist float oxytocin_antagonist float angiotensin_ii_receptor_antagonist float glutamate_(mglur1)_antagonist float skeletal_muscle_relaxant float dopamine_beta_hydroxylase_inhibitor float antibiotic_isocephem-like float adenosine_a2a_receptor_antagonist float glutamate_uptake_inhibitor float potassium_channel_antagonist float antibiotic_carbapenem-like float bisphosphonate float leukotriene_d4_antagonist float acetylcholine_m2_receptor_antagonist float psychostimulant float anticoccidial float antimitotic_taxane-like float 5_hydroxytryptamine_2_agonist float interleukin_6_antagonist float teratogen_and/or_embryotoxic float antibiotic_quinolone-like float reductant float antibiotic_rifamycin-like float adenosine_a2a_receptor_agonist float renin_inhibitor float opioid_antagonist float angiogenesis_inhibitor float insulin_secretagoues float antidepressant float neurokinin_3_antagonist float excitatory_amino_acid_agonist float analgesic_opioid float glutamate_(mglur6)_agonist float radiosensitizer float glutamate_(mglur)_agonist float antidiabetic float nmda_receptor_glycine_site_agonist float hiv_integrase_inhibitor float aminopeptidase_microsomal_inhibitor float adenosine_a1_receptor_agonist float acetylcholine_muscarinic_antagonist float anticoagulant float thrombin_inhibitor float anxiolytic float nmda_receptor_antagonist float xanthine_oxidase_inhibitor float gaba_receptor_agonist float thymidylate_synthase_inhibitor float sigma_receptor_antagonist float prostaglandin_e2_antagonist float hepatoprotectant float 5_hydroxytryptamine_1d_antagonist float antitussive_narcotic float cardioprotectant float antiviral_(hepatitis) float cholecystokinin_a_antagonist float antineoplastic_alkaloid float antiarrhythmic float dopamine_d1_agonist float protocollagen_prolyl_hydroxylase_inhibitor float antiviral_(influenza) float enkephalinase_inhibitor float alkylphospholipid float gaba_a_receptor_antagonist float prolactin_secretion_inhibitor float 5_hydroxytryptamine_1b_agonist float mucolytic float angiotensin_at1_receptor_antagonist float hestagen-like float antiviral_(hiv) float respiratory_distress_syndrome_treatment float bradykinin_b2_receptor_antagonist float hematopoietic float thyroid_hormone_antagonist float catechol_o_methyltransferase_inhibitor float adenosine_a1_receptor_antagonist float lymphocytopoiesis_inhibitor float glutamate_(mglur)_antagonist float nmda_receptor_glycine_site_antagonist float topoisomerase_ii_inhibitor float 5_hydroxytryptamine_1f_agonist float neurotensin_receptor_antagonist float prostaglandin_antagonist float antianginal float neuraminidase_(influenza)_inhibitor float opioid_kappa_receptor_agonist float purinergic_p2_antagonist float somatostatin_agonist float adenosine_a3_receptor_agonist float anesthetic_local float anaphylatoxin_receptor_antagonist float alpha_1_adrenoreceptor_antagonist float nootropic float glucose-6-phosphate_translocase_inhibitor float endothelin-converting_enzyme_inhibitor float antihypercholesterolemic float antibiotic_cephalosporin-like float antiparkinsonian_rigidity_relieving float leukotriene_antagonist float cholinergic_antagonist float acetylcholine_m3_receptor_antagonist float antiulcerative float hcv_ns3-helicase_inhibitor float antiparkinsonian float nmda_receptor_polyamine_site_blocker float bone_resorption_inhibitor float radioprotector float cathepsin_l_inhibitor float cardiodepressant float renal_disease_treatment float arrhythmogenic float glycinamide_ribonucleotide_formyltransferase_inhibitor float prostate_disorders_treatment float bombesin_antagonist float cholecystokinin_b_antagonist float vasodilator float ribonucleoside_diphosphate_reductase_inhibitor float ulcerogenic float xanthine-like float phosphodiesterase_inhibitor float insulin_promoter float dopamine_d1_antagonist float keratoses_actinic(solar)_treatment float antiacne float platelet_aggregation_inhibitor float 5_hydroxytryptamine_release_stimulant float restenosis_treatment float glutamate_(mglur3)_agonist float alpha_2_adrenoreceptor_antagonist float gaba_uptake_inhibitor float peristaltic_stimulant float phosphodiesterase_iii_inhibitor float expectorant float histamine_h2_receptor_agonist float hmg_coa_reductase_inhibitor float histidine_decarboxylase_inhibitor float antibiotic_tetracycline-like float lipoxygenase_inhibitor float aldosterone_antagonist float gaba_b_receptor_antagonist float gastric_antisecretory float antifungal float angiotensin_at2_receptor_antagonist float interleukin_8_antagonist float adenosine_a2_receptor_antagonist float miotic float cholecystokinin_antagonist float antibiotic float antibiotic_aminoglycoside-like float melatonin_antagonist float anesthetic_inhalation float phospholipase_inhibitor float antibiotic_macrolide-like float acetylcholine_agonist float gp_iib/iiia_receptor_antagonist float hcv_serine_protease_inhibitor float antiemetic float potassium_channel_activator float estrogen_agonist float respiratory_analeptic float sodium_channel_blocker_class_ib float erythropoietin float leukotriene_b4_antagonist float hmg_coa_synthase_inhibitor float liver_fibrosis_treatment float benzodiazepine_inverse_agonist float anticonvulsant float benzodiazepine_agonist_partial float 5_hydroxytryptamine_3_agonist float antispirochetal float dopamine_d2_antagonist float phosphodiesterase_i_inhibitor float antioxidant float hypolipemic float mao-b_inhibitor float tnf-alpha_release_inhibitor float vitamin_d-like float angiotensin_converting_enzyme_inhibitor float lipid_peroxidase_inhibitor float purine_nucleoside_phosphorylase_inhibitor float mineralocorticoid float neurokinin_antagonist float alpha_2_adrenoreceptor_agonist float camp_phosphodiesterase_inhibitor float keratolytic float spasmolytic_papaverin-like float androgen_antagonist float multiple_sclerosis_treatment float estrogen_antagonist float dopamine_d2_agonist float anesthetic float chymotrypsin_inhibitor float alpha_1_adrenoreceptor_agonist float antipsychotic float mannosidase_inhibitor float antidyskinetic float ampa_receptor_antagonist float antidiabetic_symptomatic float septic_shock_treatment float neuropeptide_antagonist float pancreatic_disorders_treatment float carcinogenic float alzheimer's_disease_treatment float motilin-like float adenosine_a3_receptor_antagonist float cardiotonic float leukotriene_a4_hydrolase_inhibitor float parathyroid_hormone_antagonist float 5_hydroxytryptamine_1_antagonist float antibiotic_carbacephem-like float platelet_activating_factor_antagonist float dopamine_d3_antagonist float antitrichomonal float dihydrofolate_reductase_inhibitor float purinergic_p2t_antagonist float mediator_release_inhibitor float h+/k+-transporting_atpase_inhibitor float s-adenosyl-l-homocysteine_hydrolase_inhibitor float dopamine_uptake_inhibitor float opioid_delta_receptor_agonist float interleukin_agonist float gastrin_inhibitor float camp_modulator float neurotrophic_factor float anorexic float dopamine_agonist float farnesyltransferase_inhibitor float glutamate_(mglur6)_antagonist float antiasthmatic float antimitotic_podophyllotoxin-like float glutamate_(mglur1a)_agonist float maillard_reaction_inhibitor float melatonin_agonist float antineoplastic_antibiotic float saluretic float anticholelithogenic float gaba_a_receptor_agonist float hypnotic float coagulant float opioid_partial_agonist float beta_lactamase_inhibitor float treponemicidal float ribonucleotide_reductase_inhibitor float uricosuric float hcv_ns3-4a_protease_inhibitor float dna_intercalator float squalene_synthetase_inhibitor float endothelin_receptor_antagonist float beta_adrenoreceptor_agonist float thromboxane_synthase_inhibitor float antibiotic_tribactam-like float analgesic float calpain_inhibitor float cns_active_muscle_relaxant float hcv_ns3_protease_inhibitor float 5_hydroxytryptamine_2_antagonist float protease_inhibitor float narcotic_antagonist float ophthalmic_drug float acetyl_coa_transferase_inhibitor float hypotermic float antihistaminic float dopamine_d4_antagonist float irritable_bowel_syndrome_therapy float platelet_adhesion_inhibitor float spasmolytic_urinary float atherosclerosis_treatment float nucleotide_metabolism_regulator float prolyl_endopeptidase_inhibitor float hair_growth_promoter float calcium_channel_antagonist float histamine_h1_receptor_antagonist float |
never | ||||||
| E_PATENT_LINK_PAGE | blob (switchable between blob diskfile url) |
A page with US patent links generated from E_PATENT_SET into the Google patent database. | imgproperty: { value: E_SVG_IMAGE description: Property to use to generate the structure header image datatype: string constraints: property} imgparameters: { value: {} description: Override attributes for the image computation datatype: dictionary} filename: { value: {} datatype: string constraints: writeable} ncols: { value: 4 minvalue: 1 maxvalue: 12 datatype: int} |
Tcl script | E_PATENT_SET | atomchange bondchange atom bond | e_patent_link_page.xpd | |||
| E_PATENT_SET | compoundvector | Patent countries and IDs associated with compound, plus s link into Google patents | country string id string date date url url |
filterduplicates: { value: 1 description: If set, make patent numbers unique (can be duplicates with SS/SIM queries in E_SCRIPDB_URL) datatype: boolean}
|
Tcl script | E_SCRIPDB_URL | atomchange bondchange atom bond | e_patent_set.xpd | ||
| E_PATHCODE | shortvector | Path length similiarity code | maxlen: { value: 8 description: Maximum path length to consider datatype: int} coreligands: { value: 0 description: If set, hetero atom embedded in core (for example, heteroaromats) are counted as substituents datatype: boolean} xarocore: { value: 0 description: If set, the core includes heteroaromatic rings, not just the carbon skeleton datatype: boolean} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange | mod_e_pathcode.so | |||
| E_PATH_FINGERPRINT | bitvector | Hashed fingerprint of paths between subset of structure atoms | size: { value: 256 datatype: int} minpathlen: { value: 2 datatype: int} maxpathlen: { value: 5 datatype: int} pathproperties: { value: A_SYMBOL datatype: string constraints: propertylist} nbitsperpath: { value: 5 datatype: int} atomfilter: { value: anormal !hydrogen datatype: string constraints: filterlist} usebondtype: { value: 0 datatype: boolean} maxcount: { value: 1 datatype: int} power: { value: 2 datatype: int} usesymmetry: { value: 1 datatype: boolean} useringclosures: { value: 1 datatype: boolean} maxpathsperatom: { value: -1 datatype: int} ignorechainch2: { value: 0 datatype: boolean} pathflags: { value: {} enumeration: none:noringchaincrossing,norccrossing datatype: string} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER A_RING_COUNT | atomchange bondchange ring | mod_e_path_fingerprint.so | |||
| E_PATRAN_STRING | string | Query encoded (as far as possible) as a LHASA Patran string | Compiled C module | A_QUERY B_QUERY A_ELEMENT B_ORDER | atomchange bondchange atom bond | mod_e_patran_string.so | ||||
| E_PDB_LIGAND_EXPO_URL | url | URL for data in the PDB ligand repository | Tcl script | E_PDB_LIGAND_ID | atomchange bondchange stereochange atom bond | e_pdb_ligand_expo_url.xpd | ||||
| E_PDB_LIGAND_ID | string | ID of ligand in PDB database | Tcl script | atomchange bondchange stereochange atom bond | e_pdb_ligand_id.xpd | |||||
| E_PDB_LIGAND_URL | url | URL for data in the PDB ligand repository | Tcl script | E_PDB_LIGAND_ID | atomchange bondchange stereochange atom bond | e_pdb_ligand_url.xpd | ||||
| E_PDB_STRING | string | PDB record as a string | Tcl script | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond | e_pdb_string.xpd | |||||
| E_PDF3D_IMAGE | diskfile (switchable between blob diskfile) |
3D PDF interactive PDF image | height: { value: 250 datatype: int} width: { value: 250 datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 datatype: int} frame: { value: 1 datatype: boolean} title: { value: {} datatype: string} keywords: { value: {} datatype: string constraints: list} compression: { value: 0 datatype: boolean} showtree: { value: 0 datatype: boolean} showtoolbar: { value: 0 datatype: boolean} javascriptfile_3d: { value: {} datatype: diskfile constraints: readable} javascriptfile_doc: { value: {} datatype: diskfile constraints: readable} previewpngfile: { value: {} datatype: diskfile constraints: readable} bgcolor: { value: grey20 datatype: color} message: { value: {} datatype: string} messagecolor: { value: red datatype: color} framecolor: { value: black datatype: color} measure: { value: 0 datatype: boolean} disclose: { value: 1 datatype: boolean} ownerpassword: { value: {} datatype: string} userpassword: { value: {} datatype: string} downloadfilename: { value: {} datatype: string} header: { value: {} datatype: string} headeralignment: { value: center enumeration: left,w:center,c:right,e:topcenter,n:bottomcenter,s:bottomleft,sw:bottomright,se:topright,ne:topleft,nw datatype: string} footer: { value: {} datatype: string} footeralignment: { value: center enumeration: left,w:center,c:right,e:topcenter,n:bottomcenter,s:bottomleft,sw:bottomright,se:topright,ne:topleft,nw datatype: string} footerproperty: { value: {} datatype: string constraints: property} footercolor: { value: red datatype: color} headerproperty: { value: {} datatype: string constraints: property} headercolor: { value: red datatype: color} font: { value: Helvetica datatype: string} headerfontsize: { value: 12 datatype: double} footerfontsize: { value: 12 datatype: double} fullscreen: { value: 0 datatype: boolean} |
Compiled C module | E_U3D_MODEL | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd | mod_e_pdf3d_image.so | |||
| E_PDF_IMAGE | diskfile (switchable between string blob diskfile) |
A 2D-plot of the structure as PDF image file | filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} width: { value: 180 minvalue: 10 maxvalue: 1000 datatype: string} height: { value: 180 minvalue: 10 maxvalue: 1000 datatype: string} keywords: { value: {} datatype: string} frame: { value: 0 datatype: boolean} framecolor: { value: black datatype: color} bgcolor: { value: transparent datatype: color} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1.0 datatype: double} linewidth: { value: 1.3 datatype: double} linespacing: { value: 2.5 datatype: double} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} colormode: { value: gray enumeration: mono,bw,b/w,black,monochrome:gray,grey,grayscale,greyscale:color,colour datatype: int} wedges: { value: 1 datatype: boolean} dashes: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} checkintersection: { value: 0 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} showcharge: { value: 1 datatype: boolean} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} showstereogroups: { value: 0 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: int} wigglecount: { value: 10 datatype: int} wiggleamplitude: { value: 3.0 datatype: double} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} border: { value: 12 minvalue: 0 maxvalue: 25 datatype: int} bonds: { value: 8 minvalue: 3 maxvalue: 25 datatype: int} symbolfontsize: { value: -1 datatype: int} annotationfontsize: { value: -1 datatype: double} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} markcolor: { value: blue datatype: color} highlightcolor: { value: red datatype: color} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} contractgroups: { value: 0 datatype: boolean} isotopemapping: { value: none datatype: string} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} highlightbonds: { value: {} datatype: intvector} highlightgroups: { value: {} datatype: intvector} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} font: { value: Helvecica datatype: string} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filtername} annotationcolor: { value: {} datatype: color} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} usesubscripts: { value: 1 datatype: boolean} downloadfilename: { value: {} datatype: string} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} uselinecaps: { value: 1 datatype: boolean} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION | atomchange bondchange stereochange merge hadd | mod_e_pdf_image.so | |||
| E_PESTICIDE_COMPENDIUM_URL | url | Data display link into the Compendium of Pesticide Common Names (http://www.alanwood.net/pesticides) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_pesticide_compendium_url.xpd | ||||
| E_PHARAO_PHARMACOPHORES | compoundvector | Pharamcophores as detected by Silicos' pharao program. This is used in the PHAR format I/O module. | AROM:HDON:HACC:LIPO:POSC:NEGC:HYBH:HYBL:EXCL |
code int coords floatvector spread double norm boolean normal floatvector |
atomchange bondchange stereochange 3drelative | |||||
| E_PHASE | byte | Phase of ensemble | unknown:solid:liquid:gas,gaseous |
atomchange bondchange merge | ||||||
| E_PHEROBASE_URL | string | Data display URL in PheroBase (pherobase.com) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_pherobase_url.xpd | ||||
| E_PICT_IMAGE | diskfile (switchable between blob diskfile) |
PICT format structure drawing, for Apple platforms | width: { value: 180 datatype: int} height: { value: 180 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 0 datatype: boolean constraints: property} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.4 datatype: double} colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: string} groupcolor: { value: purple datatype: color} annotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} usehatch: { value: 0 datatype: boolean} frame: { value: 1 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: int} linespacing: { value: 2.0 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 6 datatype: int} wiggleamplitude: { value: 1.5 datatype: double} checkintersection: { value: 0 datatype: boolean} showstereogroups: { value: 0 datatype: boolean} usesubscript: { value: 1 datatype: boolean} font: { value: Arial datatype: string} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR A_ANNOTATION B_FLAGS A_FLAGS | atomchange bondchange stereochange merge hadd | mod_e_pict_image.so | |||
| E_PLANTCYC_ID | string | PlantCyc structure ID (http://pmn.plantcyc.org) | Tcl script | E_STDINCHI | atomchange bondchange stereochange atom bond | e_plantcyc_id.xpd | ||||
| E_PLANTCYC_URL | url | PlantCyc structure display URL (http://pmn.plantcyc.org) | Tcl script | E_PLANTCYC_ID | atomchange bondchange stereochange atom bond | e_plantcyc_url.xpd | ||||
| E_PMI | floatmatrix | Principial moments of inertia, computed on A_XYZ or a custom coordinate property | useh: { value: 1 datatype: boolean} coordinateproperty: { value: A_XYZ datatype: string constraints: property} |
Compiled C module | A_XYZ A_TYPE A_WEIGHT E_CENTER A_ELEMENT | atomchange bondchange 3drelative hadd atom | mod_e_pmi.so | |||
| E_POGO_CIDS | compoundvector | cid int score double obj1 int obj2 int |
maxcids: { value: 50 datatype: int} mode: { value: none enumeration: none:bond:ringsystemsubsitution:ringsystemresize datatype: string} label: { value: 0 description: The bond or ringsystem label to operate on datatype: string} minordirection: { value: 0 description: If set, use the minor (reverse) direction for bond operations datatype: boolean} database: { value: pogochem datatype: string} dbtype: { value: mysql datatype: string} dbuser: { value: {} datatype: string} dbpassword: { value: {} datatype: string} dbhost: { value: localhost datatype: string} dbsocket: { value: /var/run/mysql/mysql.sock datatype: string} bondscoring: { value: hc enumeration: hc:cc:cl:xc:cx datatype: string} |
Tcl script | atomchange bondchange atom bond | e_pogo_cids.xpd | ||||
| E_POGO_DISPLAY | diskfile (switchable between blob diskfile xmlstring) |
SVG combim image of structures for the Pogochem service | width: { value: 1024 minvalue: 640 maxvalue: 4096 datatype: int} height: { value: 800 minvalue: 640 maxvalue: 4096 datatype: int} satelliteclick: { value: {} datatype: url} bondclick: { value: {} datatype: url} showaidstats: { value: 0 datatype: boolean} frame: { value: 0 datatype: boolean} framecolor: { value: black datatype: color} usescoredistance: { value: 1 datatype: boolean} ringsystemclick: { value: {} datatype: url} filename: { value: {} datatype: diskfile constraints: writeable} maxitems: { value: 12 minvalue: 4 maxvalue: 24 datatype: int} satellitewidth: { value: 150 minvalue: 50 maxvalue: 500 datatype: int} satelliteheight: { value: 150 minvalue: 50 maxvalue: 500 datatype: int} centerwidth: { value: 300 minvalue: 50 maxvalue: 500 datatype: int} centerheight: { value: 300 minvalue: 50 maxvalue: 500 datatype: int} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} |
Tcl script | E_POGO_CIDS | atomchange bondchange atom bond | e_pogo_display.xpd | |||
| E_POLARIZABILITY | float | Mean Polarizability. Computed indirectly via property E_HEAT_OF_FORMATION | A_XYZ | atomchange bondchange | ||||||
| E_POLYLINE_ANNOTATION | compound | Polyline as structure drawing annotation. This is one of the choice variants of property E_ANNOTATON. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float style bitset headskip double tailskip double headwidth double tailwidth double headlength double taillength double headflags bitset tailflags bitset arcangle double curved boolean |
A_XY | never | ||||
| E_POLYMERSET | dataset | Expanded polymer structures generated from SGroups | maxexpansion: { value: 35 minvalue: 1 maxvalue: 999 datatype: int} minexpansion: { value: 0 minvalue: 0 maxvalue: 999 datatype: int} maxmw: { value: 500 minvalue: 1 maxvalue: 999999 datatype: double} |
Tcl script | G_SGROUP | atomchange bondchange groupchange | e_polymerset.xpd | |||
| E_POLYMER_HASH | uint64 | Tcl script | E_POLYMERSET | never | e_polymer_hash.xpd | |||||
| E_PPI_LIKENESS_VIOLATIONS | byte | Hamon, Bourgeas, Ducrot, Theret, Xuereb, Basse, Brunel, Combes, Morelli, Roche, J. R. Soc. Interface 2013, 11, 20130860 | Tcl script | E_WEIGHT E_NRINGS E_NHACCEPTORS | atomchange bondchange atom bond | e_ppi_likeness_violations.xpd | ||||
| E_PRICE | compound | Price per mol for various package sizes | screening currency lab currency bulk currency |
Tcl script | atomchange bondchange stereochange atom bond | e_price.xpd | ||||
| E_PROTECTED_SET | dataset | Input structure modified by attaching alternate protecting groups to acids, amines, ketones, aldehydes and alcohols. No support yet for other groups with standard protection methodologies (1,2-diols, terminal acetylenes, indoles, sulfonamides, phosphates). These modified structures are intended to be used as alternative query input to find pre-protected starting materials. | testaflags: { value: 0 description: If set, use only groups flagged in A_FLAGS as protected datatype: boolean} maxtransformproducts: { value: -1 description: Maximum number of transform results to allow for each application of a FG protection transform, -1 for unlimited datatype: int} includeinputstructure: { value: 1 description: If set, a duplicate of the original input structure is part of the result set datatype: boolean} maxlevel: { value: 1 description: Maximum obscurity level to apply - more obscure PGs have higher level datatype: int} groups: { value: acid|amine|carbonyl|hydroxyl description: Types of groups to protect enumeration: none:acid,acids:amine,amines:carbonyl,carbonyls:hydroxyl,hydroxyls,alcohol,alcohols datatype: bitset} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange hadd atom bond | e_protected_set.xpd | |||
| E_PROTONATIONSET | dataset | Set of likely protomers, collected in dataset object | maxtotalcharge: { value: 3 datatype: int} mintotalcharge: { value: -3 datatype: int} |
Tcl script | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange merge | e_protonationset.xpd | |||
| E_PUBCHEMQC_URL | string | Data URL for the PubchemQC database (http://pubchemqc.riken.jp) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_pubchemqc_url.xpd | ||||
| E_PUBCHEM_3D_IMAGE | diskfile | 3D structure rendering | never | |||||||
| E_PUBCHEM_3D_THUMBNAIL | diskfile | 3D structure rendering preview | never | |||||||
| E_PUBCHEM_AID_COUNT | intvector | PubChem assay screening results. The result is a vector of 4 elements indicating the number of assays where the compound tested, in this order, active, inactive or inconclusive plus the total number of assays the compound was tested in. | active int inactive int inconclusive int total int |
Tcl script | E_CID | atomchange bondchange stereochange merge | e_pubchem_aid_count.xpd | |||
| E_PUBCHEM_COMPOUND | structure | Processed PubChem database structure | opseq: { value: hydrogens-made-explicit superatoms-expanded groupV-tetravalent-charged charge-neutralized atoms-verified bonds-verified atomstereo-3d-perceived bondstereo-3d-perceived stereochemistry-verified valence-bond-standardized plot-coordinates-beautified datatype: string} maxtautomers: { value: 200 datatype: string} |
Tcl script | never | e_pubchem_compound.xpd | ||||
| E_PUBCHEM_COMPOUND_CANONICALIZED | boolean | Flag indicating whether compound is canonicalized | atom bond | |||||||
| E_PUBCHEM_COMPOUND_ID | compound | PUBCHEM compound identifier | deposited:standardized:component:neutralized:mixture:tautomer:pka-state:unset=254:unknown=255 cid=0:sid=1:xid=2:unset=254:unknown=255 |
type int idtype int id int |
never | |||||
| E_PUBCHEM_CONFORMER | compoundvector | NCBI conformer data, filled by reading PubChem 3D SD files | id uint64 energy double volume double selfoverlap double rmsd double multipoles doublevector diverseorder shortvector shapefingerprint compoundvector |
atomchange bondchange stereochange merge 3drelative 3dabsolute mol atom bond | ||||||
| E_PUBCHEM_DEPOSITOR_RECORD_DATE | datetime | Depositor's record date of a submission | never | |||||||
| E_PUBCHEM_DIFFERENCE_FLAGS | uint64 | Flags for differences found in structure standardization processing | never | |||||||
| E_PUBCHEM_DIFFERENCE_TIMESTAMP | datetime | Timestamp for a structure standardization processing difference check | never | |||||||
| E_PUBCHEM_EXT_DATASOURCE_CID | int | CID from depositor representing the data item | never | |||||||
| E_PUBCHEM_EXT_DATASOURCE_INCHI | string | InChI string from depositor representing the data item | never | |||||||
| E_PUBCHEM_EXT_DATASOURCE_NAME | string | Depositor's datasource name | never | |||||||
| E_PUBCHEM_EXT_DATASOURCE_REGID | string | Depositor's unique external registry ID | never | |||||||
| E_PUBCHEM_EXT_DATASOURCE_SMILES | string | Kekulized SMILES string from depositor representing the data item | never | |||||||
| E_PUBCHEM_EXT_DATASOURCE_URL | url | Depositor's external source/database URL | never | |||||||
| E_PUBCHEM_EXT_SUBSTANCE_URL | url | Depositor's external individual substance URL | never | |||||||
| E_PUBCHEM_GENBANK_GENERIC_ID | stringvector | NCBI/NLM/NIH GenBank general ID(s) | never | |||||||
| E_PUBCHEM_GENERIC_REGISTRY_NAME | stringvector | Generic registry name(s) | never | |||||||
| E_PUBCHEM_NCBI_BIOSYSTEM_ID | intvector | NCBI/NLM/NIH BIOSYSTEM ID(s) | never | |||||||
| E_PUBCHEM_NCBI_MMDB_ID | stringvector | NCBI/NLM/NIH MMDB ID(s) | never | |||||||
| E_PUBCHEM_NCBI_PROBE_ID | intvector | NCBI/NLM/NIH PROBE ID(s) | never | |||||||
| E_PUBCHEM_NCBI_TAXONOMY_ID | stringvector | NLM/NIH Taxonomy ID reference(s) | never | |||||||
| E_PUBCHEM_PATENT_REFERENCES | compoundvector | User-supplied patent references of compounds registered in PubChem (i.e. with a CID) | patentdate date patentid string patenttitle string patentsubmissiondate date patentgrantdate date patenturl url |
Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_pubchem_patent_references.xpd | |||
| E_PUBCHEM_PATENT_URL | url | PubChem patent display via CID | Tcl script | atomchange bondchange atom bond | e_pubchem_patent_url.xpd | |||||
| E_PUBCHEM_PUBLICATION_DATE | datetime | Depositor's publication date of journal article associated with compound | never | |||||||
| E_PUBCHEM_PUBMED_ID | stringvector | NLM/NIH PubMed ID for an article or abstract | never | |||||||
| E_PUBCHEM_PUBMED_REFERENCES | compoundvector | User-supplied PubMed references of compounds registered in PubChem (i.e. with a CID) | date date pmid int title string journal string |
Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_pubchem_pubmed_references.xpd | |||
| E_PUBCHEM_REVOKE_SUBSTANCE | stringvector | Substance revocation comments | never | |||||||
| E_PUBCHEM_SHAPE_FINGERPRINT | compoundvector | Property holding PubChem 3D fingerprint data | shapecid int lid int packedmatrix uint64 |
atomchange bondchange stereochange merge 3drelative 3dabsolute atom bond | ||||||
| E_PUBCHEM_SID_DATA | compoundvector | Data on PubChem depositor records | sid int source string sourceid string sourcecategory stringvector sourcereleasedate date depositdate date modifydate date registrynumber string dburl url sburl url |
Tcl script | E_SIDSET | atomchange bondchange stereochange merge | e_pubchem_sid_data.xpd | |||
| E_PUBCHEM_STANDARDIZED_STRUCTURE | structure | Structure standardized by the PubChem structure standardization service | transferformat: { value: serialized datatype: string}
|
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT | atomchange bondchange stereochange merge | mod_e_pubchem_standardized_structure.so | |||
| E_PUBCHEM_SUBSTANCE_COMMENT | stringvector | Substance comments | never | |||||||
| E_PUBCHEM_URL | url | PubChem compound database URL | Tcl script | E_CID | atomchange bondchange stereochange merge | e_pubchem_url.xpd | ||||
| E_PUBCHEM_XLOGP3 | double | Processed PubChem database structure | atom bond | |||||||
| E_PUBCHEM_XREF_EXT_ID | stringvector | Depositor's external source/database crossreference ID | never | |||||||
| E_PUBMED_IDS | intvector | PubMed reference IDs for structures found in PubChem | Tcl script | E_CID | atomchange bondchange atom bond | e_pubmed_ids.xpd | ||||
| E_PUBMED_LINK_PAGE | blob (switchable between blob diskfile url) |
A page with links generated from E_PUBCHEM_PUBMED_REFERENCES into the PubMed literature database. | imgproperty: { value: E_SVG_IMAGE description: Property to use to generate the structure header image datatype: string constraints: property} imgparameters: { value: {} description: Override attributes for the image computation datatype: dictionary} filename: { value: {} datatype: string constraints: writeable} ncols: { value: 2 minvalue: 1 maxvalue: 12 datatype: int} |
Tcl script | E_PUBCHEM_PUBMED_REFERENCES | atomchange bondchange atom bond | e_pubmed_link_page.xpd | |||
| E_PUBMED_URLS | urlvector | Display links for the PubMed entries identified via E_PUBMED_IDS | Tcl script | E_PUBMED_IDS | atomchange bondchange atom bond | e_pubmed_urls.xpd | ||||
| E_PYTHON_TEST | string | Python test function | param1: { value: one datatype: string} param2: { value: 2 datatype: int} param3: { value: 3.3 datatype: double} |
Python script | atomchange bondchange atom bond | e_python_test.xpd | ||||
| E_QUERY | compound | Ensemble-level search options | none:unwrapped_recursive_smarts undefined:lt:le:eq:ge:gt:ne:in:notin:range:bitset_and {} none:and:or:xor,eor |
flags bitset prefixoperator int prefixvalue int chainoperator int chainsubstructure substructure |
never | |||||
| E_QUERY_SCREEN | bitvector | Bitvector optimized for standard substructure queries, with focus on ring systems and ring substitutions as well as the capability to generalized heteroatoms and standard element classes (halogens, N/O/S, etc.). | size: { value: 1952 description: Vector size minvalue: 256 maxvalue: 4096 datatype: int} version: { value: 3 description: Versioning switch to compare evolution of algorithm datatype: int} power: { value: 2 description: Count step escalation minvalue: 1 maxvalue: 3 datatype: int} nbitsperpath: { value: 4 description: Bit positions to ser per unique path minvalue: 1 maxvalue: 16 datatype: int} maxcount: { value: 3 description: Maximum path count to use minvalue: 1 maxvalue: 16 datatype: int} minpathlen: { value: 2 description: Minimum length of paths fo hash minvalue: 2 maxvalue: 5 datatype: int} maxpathlen: { value: 5 description: Maximum length of pathes to hash minvalue: 2 maxvalue: 10 datatype: int} maxpathsperatom: { value: -1 description: Maximum nmber of paths to find per atom, -1 is unlimited minvalue: -1 maxvalue: 9999 datatype: int} isquery: { value: 0 description: Whether structure is a query sub/superstructure, or a complete structure datatype: boolean} ignoreh: { value: 0 description: If set, do not create any codes involving hydrogen datatype: boolean} tauto: { value: 0 description: If set, do not set any bits with H, or involving bond orders in tauo systems datatype: boolean} debug: { value: 0 description: If set, print found paths datatype: boolean} useringcombos: { value: 1 description: If set, add ring combo screen bits datatype: boolean} tracebit: { value: -1 description: Trace which pattern sets this bit position minvalue: -1 maxvalue: 4096 datatype: int} cmpflags: { value: bondorder|useatomtree|usebondtree description: Comparison flags which will be used in subsequent atom-by-atom matching. Some flags can be used for increasing the filter efficiency enumeration: one:wedge,wedges:charge:stereo:bondorder,bo:terminal:nozwitterioncollapse:nosinglaonaro:nodoubleonaro:isotope:tautomer:arotautomer:matchbondringcount:lazymatchbondringcount:kekule,kekuleodd:strictnomatch:nochainonaro:lazymatchatomringcount:matchatomringcount:bondreaction:pionaro:noaliphaticonaro:relativestereo:fixedframework,fixedframe:nomultibondfg:noarobondfg:noheterofg:useatomtree,atomtree:usebondtree,bondtree:excludesmartsenvironment:openhcount:varbondglobal:varbondindividual:kekuleeven:unsetaromaticisaliphatic:implicitonsingleoraro:nullsubstructureismismatch:nochainonring:atomlistidentity:splitfragments:generalizeheteroatoms:nosuperatomonh:singleattachmentsuperatomsonly:remembercomplexmatches:matchallheavyatoms:fullringsystem:noatomstereook:nobondstereook:multibondorder,singleonany,singleisany:matchfullmolecule,matchfullmol:matchfullensemble,matchfullens:nosmallerrings:noalkyllinks:containedatomlists:chained:no3dcoordinatecomputation,no3dcoordinatescomputation datatype: bitset} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER B_ISAROMATIC A_ISAROMATIC E_ELEMENT_COUNT R_TYPE R_AROMATIC A_HASH A_RING_COUNT B_RING_COUNT | atomchange bondchange hadd atom bond ring | mod_e_query_screen.so | |||
| E_RACEMIC_STEREO_HASH | uint64 | Ensemble hashcodes for racemic mixtures. These are identical to the minimum molecule stereo hashcod es of the present structure, or its enantiomer. For example, the racemic stereo hashcode for both L-alanine and D-alanine input structures (with known stereochemistry) is, by chance, that of L-alanine, and not that of DL-alanine (with unknown stereochemistry) | Compiled C module | M_RACEMIC_STEREO_HASH M_RACEMIC_STEREO_HASH_GROUP | atomchange bondchange stereochange merge | mod_e_racemic_stereo_hash.so | ||||
| E_RADIOACTIVE | boolean | Indicator whether ensemble is radioactive as per atom isotope labelling | Tcl script | A_RADIOACTIVE | atomchange bondchange atom bond | e_radioactive.xpd | ||||
| E_RAMANIRGIF | diskfile | IR/RAMAN spectrum as GIF file | width: { value: 660 datatype: int} height: { value: 300 datatype: int} filename: { value: {} datatype: string} type: { value: ir enumeration: ir:raman datatype: string} multigif: { value: 0 datatype: boolean} backgrcolor: { value: transparent datatype: color} axiscolor: { value: black datatype: color} ircolor: { value: blue datatype: color} ramancolor: { value: red datatype: color} legend: { value: 0 datatype: boolean} interlace: { value: 1 datatype: boolean} yscalemax: { value: auto datatype: string} changeyunit: { value: 0 datatype: boolean} |
Tcl script | E_RAMANSPECTRUM E_IRSPECTRUM | atomchange bondchange | e_ramanirgif.xpd | |||
| E_RAMANSPECTRUM | compound | Measured or computed Raman spectrum. This is a spectrum type which can be read and written in JCAMP and Galactic SPC format. | experimental boolean origin string author string date date spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum xyvector peaks floatvector peakshape stringvector peakintensity floatvector peakname stringvector |
A_XYZ A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange 3drelative | |||||
| E_RAMANSPECTRUM_IMAGE | diskfile (switchable between string blob diskfile url) |
Raman spectrum rendering | height: { value: 250 datatype: int} width: { value: 500 datatype: int} bgcolor: { value: white datatype: color} title: { value: {} datatype: string} filename: { value: {} datatype: string constraints: writeable} format: { value: gif enumeration: png,png24:gif:png8 datatype: string} titlecolor: { value: black datatype: color} framecolor: { value: black datatype: color} signalcolor: { value: #DD0000 datatype: color} ystyle: { value: transmittance enumeration: transmittance:absorbance datatype: int} xdirection: { value: reverse enumeration: normal:reverse datatype: int} xstyle: { value: 1/cm enumeration: 1/cm:um datatype: int} |
Tcl script | E_RAMANSPECTRUM | atomchange bondchange merge mol | e_ramanspectrum_image.xpd | |||
| E_RAYTRACE_IMAGE | diskfile | Raytraced image of 3D structure, using the povray raytracer as external application | background: { value: black datatype: color} height: { value: 250 datatype: int} width: { value: 250 datatype: int} quality: { value: 8 datatype: int} lightx: { value: 60 datatype: int} lighty: { value: 66 datatype: int} antialias: { value: 1 datatype: bitset} preview: { value: 0 datatype: double} fog: { value: 0 datatype: boolean} includepath: { value: /usr/local/lib/pov/include datatype: string} style: { value: ballstick enumeration: wireframe:capped:ball&stick:spacefill datatype: string} vdwscaling: { value: 25 datatype: double} bcolor: { value: white datatype: color} bondradius: { value: 15 datatype: string} uselabel: { value: 0 datatype: boolean} usebo: { value: 0 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} atomhighlightcolor: { value: red datatype: color} bondhighlightcolor: { value: red datatype: color} transparency: { value: 0 datatype: double} highlightatoms: { value: {} datatype: intvector} highlightbonds: { value: {} datatype: intvector} format: { value: png enumeration: gif:png,png24:ppm:tga datatype: string} zoom: { value: 100 datatype: double} ignoreh: { value: 0 datatype: boolean} |
Tcl script | A_XYZ A_TYPE B_TYPE | atomchange bondchange stereochange merge 3drelative 3dabsolute | e_raytrace_image.xpd | |||
| E_REACTION_ROLE | byte | Role of ensemble in reaction. | undef,undefined:reagent,educt,reactant,reagents,educts,reactants:product,products:solvent,solvents:catalyst,catalysts:intermediate,intermediates:impurity,impurities:byproduct,byproducts:agent,agents:waste:precursor,precursors:altreagent,altreagents |
Compiled C module | never | mod_e_reaction_role.so | ||||
| E_RECAP_FRAGMENTS | structure | Structure fragmented according to the RECAP rules | J. Chem. Inf. Comput. Sci. 38, 1998, 511-522 | useextratransforms: { value: 0 description: Whether to use extra transforms not in original paper, but in transform library (e.g. aronitrogen-arocarbon cut) datatype: boolean} useisotopelabels: { value: 0 description: If set, set isotope labels as described in original publication in additon to A_REACP_LINKER_TYPE property datatype: boolean} patternfile: { value: recap.smirks datatype: diskfile constraints: readable} |
Tcl script | A_ELEMENT A_TYPE B_TYPE B_ORDER B_FRAGMENT_CARBON_COUNT | atomchange bondchange atom bond ring | e_recap_fragments.xpd | ||
| E_RECONNECTED_STRUCTURE | structure | Reconnect structure components by identifying potential complex-bond (carbon monoxide, etc.) and ionic (ion and metal counterion) in metal-centric complex and salt compounds. This is primarily intended to facilitate substructure seach on such compounds. | Tcl script | atomchange bondchange stereochange atom bond | e_reconnected_structure.xpd | |||||
| E_RECTANGLE_ANNOTATION | compound | Rectangle as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float bgcolor color style bitset |
A_XY | never | ||||
| E_REGISTRATION_ID | string | Registration ID | never | |||||||
| E_REOS_FILTER | boolean | An implementation template for the Vertex REOS drug-likeness filter | Adv. Drug Delivery Reviews 54, 2002, 255-271 | minweight: { value: 200 datatype: double} maxweight: { value: 500 datatype: double} minlogp: { value: -5 datatype: double} maxlogp: { value: 5 datatype: double} minhdonors: { value: 0 datatype: int} maxhdonors: { value: 5 datatype: int} minhacceptors: { value: 0 datatype: int} maxhacceptors: { value: 10 datatype: int} mincharge: { value: -2 datatype: int} maxcharge: { value: 2 datatype: int} minrotbonds: { value: 0 datatype: int} maxrotbonds: { value: 8 datatype: int} minheavyatoms: { value: 20 datatype: int} maxheavyatoms: { value: 50 datatype: int} patternfile: { value: reos.sma datatype: diskfile constraints: readable} |
Tcl script | atomchange bondchange atom bond | e_reos_filter.xpd | |||
| E_REPULSION_ENERGY | float | Measured or computed Core-Core Repulsion Energy. Computed indirectly via E_HEAT_OF_FORMATION. | A_XYZ A_ELEMENT A_TYPE B_ORDER | atomchange bondchange hadd | ||||||
| E_RESONANCE_SET | dataset | Create a resonance set. Adapted from test suite by Bruno Bienfait of Molecular Networks GmbH | maxens: { value: 1000 datatype: int} timeout: { value: 0 datatype: int} |
Tcl script | atomchange bondchange atom bond | e_resonance_set.xpd | ||||
| E_RHEA_IDS | stringvector | IDs of reactions involving the structure in the RHEA reaction database (www.rhea-db.org) | Tcl script | E_CHEBI_ID | atomchange bondchange atom bond | e_rhea_ids.xpd | ||||
| E_RHEA_LINK_PAGE | blob (switchable between blob diskfile url) |
Page with links to RHEA (www.ebi.ac.uk/rhea) reactions | imgproperty: { value: E_SVG_IMAGE description: Property to use to generate the structure header image datatype: string constraints: property} imgparameters: { value: {} description: Override attributes for the image computation datatype: dictionary} filename: { value: {} datatype: string constraints: writeable} ncols: { value: 5 minvalue: 1 maxvalue: 12 datatype: int} |
Tcl script | E_RHEA_IDS | atomchange bondchange atom bond | e_rhea_link_page.xpd | |||
| E_RIGID_BOND_COUNT | int | Number of bonds which are not rotatable because they are in a ring, or have multiple bond order. | Compiled C module | B_ROTATABILITY | atomchange bondchange hadd | mod_e_rigid_bond_count.so | ||||
| E_RINGSYSTEM_COUNT | short | Ringsystem count | Compiled C module | atomchange bondchange atom bond | mod_e_ringsystem_count.so | |||||
| E_RINGSYSTEM_FRAGMENTS | dataset | Generate a complete set of fragments, or a set only containing fragments from a single ringsystem, by removing all combinations of ring systems and chain atoms. | singleonly: { value: 0 description: If set, only isolate single ring systems, not combination connected by brdige atoms datatype: boolean}
|
Tcl script | atomchange bondchange atom bond | e_ringsystem_fragments.xpd | ||||
| E_RING_SIZE_COUNT | intvector | Counts of ring sizes in structure (array element index is size. array size is maximum ring size plus one) | Compiled C module | R_SIZE | atomchange bondchange | mod_e_ring_size_count.so | ||||
| E_ROSDAL_STRING | string | Rosdal Line Notation structure representation | atomchange bondchange stereochange merge atom bond | |||||||
| E_ROUNDED_RECTANGLE_ANNOTATION | compound | Rounded ectangle as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float bgcolor color style bitset arcwidth float archeight float |
A_XY | never | ||||
| E_RTECS_NUMBER | string | CDC RTECS number of structure | Tcl script | E_CAS | atomchange bondchange atom bond | e_rtecs_number.xpd | ||||
| E_RULE_OF_3_VIOLATIONS | byte | Carr Rule of 3 violation count (hydrogen donor count, hydrogen acceptor count, logp, weight/100, polar surface area, number of rotatable bonds over 3) | Congreve, M., Carr, R., Murray, C. and Jhoti, H. A 'Rule of Three' for fragment-based lead discovery, Drug Discov. Today 2003, 8, 876-877 | Tcl script | E_NHDONORS E_NHACCEPTORS E_XLOGP E_WEIGHT E_TPSA E_NROTBONDS | atomchange bondchange merge atom bond | e_rule_of_3_violations.xpd | |||
| E_RULE_OF_5_VIOLATIONS | byte | Count of violated Lipinski Rule of 5 conditions in structure | Lipinski CA, Lombardo F, Dominy BW, Feeney PJ, Adv. Drug Deliv. Rev. 46 (1-3): 3–26 | uselowermwbound: { value: 0 description: If set, also test for a minimum weight of 150 Dalton datatype: boolean}
|
Tcl script | E_NHDONORS E_NHACCEPTORS E_WEIGHT E_XLOGP2 | atomchange bondchange merge atom bond | e_rule_of_5_violations.xpd | ||
| E_SCAFFOLD_KEYS | shortvector | Keys for natural scaffold ordering | J. Chem. Inf. Model. 2014, 54, 1617-1622 | Tcl script | A_FRAMEWORK A_TYPE A_ELEMENT A_RING_COUNT R_CONJUGATED | atomchange bondchange atom bond ring | e_scaffold_keys.xpd | |||
| E_SCAFFOLD_TREE_SEQUENCE | dataset | The order set of subsequent simplifications of the Ertl/Schuffenhauer scaffold tree. | J. Chem. Inf. Model. 2007, 47, 47-58 | includeoriginal: { value: 0 datatype: boolean}
|
Tcl script | atomchange bondchange mol ring | e_scaffold_tree_sequence.xpd | |||
| E_SCAFFOLD_TREE_STRUCTURE | structure | Simplified scaffold structure, as per the Schuffenhauer/Ertl paper. This returns the next step in simplification, or an error if no more simplification is possible. | Schuffenhauer et al., J. Chem. Inf. Model. 2007, 47, 47-58 | Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER Y_AROMATIC R_AROMATIC R_SIZE R_HETEROATOM_COUNT E_NMOLECULES E_RINGSYSTEM_COUNT E_HASHY | atomchange bondchange merge atom bond ring | e_scaffold_tree_structure.xpd | |||
| E_SCALED_SCAFFOLD_KEYS | floatvector | Keys for natural scaffold ordering, scaled for equal weights (recomputed from 10000 mosty comst commen scaffolds in ChEMBL19 (via F_SCAFFOLD_TABLE) from Cactvs property E_SCAFFOLD_KEYS | J. Chem. Inf. Model. 2014, 54, 1617-1622 | Tcl script | E_SCAFFOLD_KEYS | atomchange bondchange atom bond ring | e_scaled_scaffold_keys.xpd | |||
| E_SCRAMBLED_STRUCTURE | structure | Ensemble with randomized atom and bond sequence | seed: { value: {} description: A numerical random seed value. If empty, use clock clicks. datatype: string} scrambleatoms: { value: 1 datatype: boolean} scramblebonds: { value: 1 datatype: boolean} scramblewedges: { value: 0 datatype: boolean} |
Tcl script | A_TYPE B_TYPE B_ORDER A_ELEMENT | atomchange bondchange stereochange merge | e_scrambled_structure.xpd | |||
| E_SCREEN | bitvector | Screening bits for substructure search | usevariants: { value: 0 datatype: string} maxvariants: { value: 10 datatype: string} extended: { value: 2 datatype: string} tauto: { value: none datatype: string} ignoreh: { value: 0 datatype: string} usebo: { value: 1 datatype: string} |
(builtin) | A_ELEMENT A_TYPE B_TYPE B_ORDER R_TYPE B_ISTAUTOMERIC R_SIZE B_ISAROMATIC | atomchange bondchange hadd mol | ||||
| E_SCRIPDB_URL | url | Query URL for University of Toronto SCRIBDP IBM patent database interface | startyear: { value: 2001 description: First patent year to query minvalue: 2001 maxvalue: 2099 datatype: int} endyear: { value: 2020 description: Last patent year to query minvalue: 2001 maxvalue: 2099 datatype: int} verify: { value: 1 description: If set, check whether there are matches datatype: boolean} reactionsonly: { value: 0 description: If set, look only for patents containing synthetic procedures datatype: boolean} threshold: { value: 0.8 description: The threshold for similarity queries minvalue: 0.1 maxvalue: 1.0 datatype: double} querytype: { value: 0 description: The query type (fullstructure, substructure, similarity) enumeration: fs,fullstructure:ss,substructure:sim,similarity datatype: int} |
Tcl script | atomchange bondchange atom bond | e_scripdb_url.xpd | ||||
| E_SDBS_ID | int | Database ID of structure on AIST SDBS (RioDB) spectral database (http://riodb01.ibase.aist.go.jp) | Tcl script | E_CAS | atomchange bondchange atom bond | e_sdbs_id.xpd | ||||
| E_SDBS_URL | url | Database URL for display of structure in AIST SDBS (RioDB) spectral database (http://riodb01.ibase.aist.go.jp) | Tcl script | E_SDBS_ID | atomchange bondchange atom bond | e_sdbs_url.xpd | ||||
| E_SDF_STRING | string | SDF structure encoding | writelist: { value: {} datatype: string constraints: propertylist} subformat: { value: 2d enumeration: mol2d,2d,mol,std,standard:mol3d,3d:reaction,rxn,rdf:spectrum:volume:mol0d,0d datatype: int} eolchars: { value: default enumeration: default:win,windows,crlf:mac,cr:linux,unix,nl datatype: int} hydrogens: { value: asis enumeration: add:asis:strip:stripall datatype: int} nitrostyle: { value: asis enumeration: ionic:asis:penta,pentavalent datatype: int} usev3000: { value: 1 enumeration: ionic:asis:penta,pentavalent datatype: boolean} writeend: { value: blockend enumeration: blockend:none datatype: int} |
Tcl script | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond | e_sdf_string.xpd | ||||
| E_SERIALIZED_JAVA_OBJECT | blob | Transport container for Java objects. This is used for example in the KNIME native table I/O module for CDKCells. | never | |||||||
| E_SHARC_ACCESS | byte | Access mode for a record in the SHARC archive | private:groupheader::group,groupfull::header::gradient::::::::everybody,open,full |
never | ||||||
| E_SHARC_GROUP | string | Group of owner or contributor of a data record in the SHARC archive | never | |||||||
| E_SID | int | PubChem SID structure identifier | Tcl script | atomchange bondchange stereochange merge atom bond ring | e_sid.xpd | |||||
| E_SIDSET | intvector | PubChem SIDs associated with structure identified by its CID | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_sidset.xpd | ||||
| E_SIDSET_URL | url | PubChem substance database URL which displays the collection of SIDs associated with a structure | Tcl script | E_SIDSET | atomchange bondchange stereochange merge | e_sidset_url.xpd | ||||
| E_SIGMAALDRICH_IDS | compoundvector | SigmaAldrich catcalog name and catalog ID | catalog string id string mfcd string |
Tcl script | E_SDF_STRING E_SMILES | atomchange bondchange stereochange atom bond | e_sigmaaldrich_ids.xpd | |||
| E_SIGMAALDRICH_URLS | urlvector | Catalog data display URL for SigmaAldrich | Tcl script | E_SIGMAALDRICH_IDS | atomchange bondchange stereochange atom bond | e_sigmaaldrich_urls.xpd | ||||
| E_SIMULATION_BOX | xyzvector | Box for MM simulations (used for example in Gromacs file format). The values are three xyz vectors, defining the box coordinates. Modulo arithmetic is used to map points outside the box back into it. | v1 floatvector v2 floatvector v3 floatvector |
A_XYZ | atomchange bondchange stereochange merge hadd | |||||
| E_SKETCHER_URL | url | URL suitable for loading the structure into the Xemistry Web Sketcher (www.xemistry.com/edit) | baseurl: { value: http://www.xemistry.com/edit description: The base URL of the sketcher installation to use datatype: url} transferformat: { value: blob description: The transfer format to use datatype: string} |
Tcl script | atomchange bondchange atom bond | e_sketcher_url.xpd | ||||
| E_SLN_STRING | string | SLN structure encoding | minimal: { value: 0 description: If set, omit compound level property section (>name=xxx<) etc. datatype: boolean} fold: { value: 0 description: Whether to use multiline format with continuation characters datatype: boolean} extended: { value: 0 description: Whether to encode extended attributes, such as 2D and 3D coordinates datatype: boolean} propertylist: { value: {} description: List of ensemble properties to include datatype: string constraints: propertylist} droplist: { value: {} description: List of ensemble properties to exclude. Overrides inclusion list. datatype: string constraints: propertylist} computeprops: { value: 0 description: Whether to attempt to compute properties in the inclusion list datatype: boolean} dimension: { value: -1 description: Coordinate handling. -1: automatic, 0: no coordinates, 2:force 2D, 3: force 3D (both with computation if necessary) minvalue: -1 maxvalue: 3 datatype: int} usesuperatom: { value: 0 description: Whether to use A_SUPERATOMSTRING for superatoms (default: use unspecified R group symbol) datatype: boolean} |
Compiled C module | atomchange bondchange stereochange merge hadd atom bond | mod_e_sln_string.so | ||||
| E_SMALLMOLECULES_URL | url | Structure lookup URL for smallmolecules.com | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_smallmolecules_url.xpd | ||||
| E_SMALLWORLD_NETWORK | network | Sample implementation of R. Sayles SmallWorld network for accelerated MCSS searching | useelements: { value: 1 datatype: boolean} usebondorders: { value: 1 datatype: boolean} addsingleatomfragments: { value: 0 datatype: boolean} |
Compiled C module | E_HASHY B_HASHGROUP A_ELEMENT A_LABEL B_LABEL A_TYPE B_TYPE B_ISAROMATIC B_RING_COUNT A_SUBSTITUENT_COUNT E_NMOLECULES E_HEAVY_ATOM_COUNT | atomchange bondchange atom bond | mod_e_smallworld_network.so | |||
| E_SMARTS | string | Encoded structure in SMARTS format | J. Chem. Inf. Comput. Sci. 1988, 28, 31-36 | usearo: { value: 1 datatype: boolean} unique: { value: 0 datatype: boolean} usestereo: { value: 1 datatype: boolean} usesuperatom: { value: 0 datatype: boolean} useisotope: { value: 1 datatype: boolean} usemapping: { value: 1 datatype: boolean} usestereogroup: { value: 0 datatype: boolean} smarts: { value: 1 datatype: boolean} usehcount: { value: 1 datatype: boolean} useexplicithcount: { value: 0 datatype: boolean} singleringupdownbond: { value: 1 datatype: boolean} useexplicith: { value: 1 datatype: boolean} queryhatoms: { value: {} datatype: intvector} checkstereo: { value: 1 datatype: boolean} hideautoh: { value: 1 datatype: boolean} atomaroproperty: { value: A_ARORING_COUNT datatype: string constraints: property} |
Compiled C module | A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL | atomchange bondchange stereochange merge hadd | mod_e_smarts.so | ||
| E_SMARTSVIEWER_IMAGE | diskfile (switchable between string blob diskfile mapfile url) |
SMARTS query visualization | http://smartsview.zbh.uni-hamburg.de/home/auto_retrieving | format: { value: png enumeration: png:pdf:svg label: Image Format: datatype: int} visualization: { value: complete enumeration: complete:symbols label: Visualization Mode: datatype: int} legend: { value: both enumeration: none:static:dynamic:both label: Legend: datatype: int} |
Tcl script | E_SMARTS | atomchange bondchange stereochange merge mol | e_smartsviewer_image.xpd | ||
| E_SMCM | float | Synthetic and molecular complexity | T. K. Allu, T. Oprea, J. Chem. Inf. Model. 2005, 45, 1237-1243 | Tcl script | A_TYPE B_TYPE B_ORDER A_SYMBOL A_STEREOGENIC B_STEREOGENIC E_ELEMENT_COUNT B_ISAROMATIC E_RING_SIZE_COUNT E_RINGSYSTEM_COUNT | atomchange bondchange stereochange | e_smcm.xpd | |||
| E_SMILES | string | Encoded structure in SMILES format | J. Chem. Inf. Comput. Sci. 1988, 28, 31-36 | usearo: { value: 0 datatype: string} unique: { value: 0 datatype: string} usestereo: { value: 1 datatype: string} usesuperatom: { value: 0 datatype: string} useisotope: { value: 1 datatype: string} usemapping: { value: 1 datatype: string} usestereogroup: { value: 0 datatype: string} smarts: { value: 0 datatype: string} usehcount: { value: 1 datatype: string} singleringupdownbond: { value: 1 datatype: string} useexplicith: { value: 0 datatype: string} queryhatoms: { value: {} datatype: string} checkstereo: { value: 1 datatype: string} hideautoh: { value: 0 datatype: string} firstatom: { value: -1 datatype: string} lastatom: { value: -1 datatype: string} useextrabondtypes: { value: 1 datatype: string} generalization: { value: none datatype: string} reuseringlinks: { value: 0 datatype: string} useexplicithcount: { value: 0 datatype: string} atomaroproperty: { value: A_ARORING_COUNT datatype: string} atommapproperty: { value: A_MAPPING datatype: string} usename: { value: 0 datatype: string} canonicalizationmethod: { value: cactvs datatype: string} |
(builtin) | A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL_STEREO B_LABEL_STEREO A_ISOTOPE A_MAPPING A_QUERY B_QUERY | atomchange bondchange stereochange merge hadd | |||
| E_SMOOTHED_PATHCODE | floatvector | Smoothed path length similiarity code | Tcl script | E_PATHCODE | atomchange bondchange | e_smoothed_pathcode.xpd | ||||
| E_SOLUBILITY_URL | url | Link to predict solubility (showme.physics.drexel.edu/onsc/models/multisolvent.php) | Tcl script | atomchange bondchange atom bond | e_solubility_url.xpd | |||||
| E_SORT_FORMULA | string | Sortable string for sorting E_FORMULA according to C, H, X element rank | useimplicith: { value: 1 description: If set, add implicit Hs to formula datatype: boolean}
|
Tcl script | E_ELEMENT_COUNT | atomchange hadd | e_sort_formula.xpd | |||
| E_SORT_NAME | string | Sortable string for sorting E_NAME | Tcl script | E_NAME | never | e_sort_name.xpd | ||||
| E_SOURCE | stringvector | Source of structure data, in free-form string array format | never | |||||||
| E_SPAN | int | The maximum of all M_SPAN property values of the ensemble. | Compiled C module | M_SPAN | atomchange bondchange merge mol atom bond | mod_e_span.so | ||||
| E_SPECIFIC_ROTATION | float | Specific rotation [alpha] | atomchange bondchange atom bond | |||||||
| E_SPECTRABASE_ID | string | Record ID in the Spectrabase database (spectrabase.com) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_spectrabase_id.xpd | ||||
| E_SPECTRABASE_URL | url | Display URL in the Spectrabase database (spectrabase.com) | Tcl script | E_SPECTRABASE_ID | atomchange bondchange stereochange atom bond | e_spectrabase_url.xpd | ||||
| E_SPHINX_SCIENTIFIC_ID | string | ID in Sphinx Scientific catalogue (www.sphinxscientificlab.com) | Tcl script | atomchange bondchange atom bond | e_sphinx_scientific_id.xpd | |||||
| E_SPHINX_SCIENTIFIC_URL | url | Display URL for Sphinx Scientific catalog (www.sphinxscientificlab.com) | Tcl script | E_SPHINX_SCIENTIFIC_ID | atomchange bondchange atom bond | e_sphinx_scientific_url.xpd | ||||
| E_SRS_ID | int | Substance ID in the EPA/FDA Substance Registry Services (SRS) | Tcl script | E_CAS | atomchange bondchange atom bond | e_srs_id.xpd | ||||
| E_SRS_URL | url | Structure data display page in the EPA/FDA Substance Registry Services (SRS) | Tcl script | E_SRS_ID | atomchange bondchange atom bond | e_srs_url.xpd | ||||
| E_STANDARDIZED_STRUCTURE | structure | A collection of structure standardization steps. | nitrostyle: { value: penta enumeration: ignore,asis,default:ionic,charged:pentavalent,penta,uncharged,neutral:xionic,extendedionic,extendedcharged,xcharged:xpentavalent,extendedpentavalent,xpenta,extendedpenty,xneutral,extendedneutral,xuncharged,extendeduncharged datatype: int} sulfoxidestyle: { value: asis enumeration: ignore,asis,default:ionic,charged:neutral,tetravalent datatype: string} desalt: { value: 1 datatype: boolean} clearinorganic: { value: 1 datatype: boolean} uncharge: { value: 1 datatype: boolean} chargebalance: { value: 0 datatype: boolean} saltfile: { value: ions.smi description: Standard counterions datatype: diskfile constraints: readable} cutmetalsalts: { value: 1 datatype: boolean} singlefragment: { value: 1 datatype: boolean} |
Tcl script | A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange stereochange mol atom bond ring | e_standardized_structure.xpd | |||
| E_STANDARD_ATOM_COUNT | int | Number of normal (non-query, non-superatom, etc.) atoms in ensemble | Compiled C module | A_TYPE | atomchange merge hadd | mod_e_standard_atom_count.so | ||||
| E_STDBLE | float | Standard bond length for plot | (builtin) | A_XY | never | |||||
| E_STDINCHI | string | Standard InChI identifier | options: { value: DONOTADDH description: Set of default option words as defined to standard comment: Many of the option words listed for E_INCHI implicitly switch off standard mode. See INChI lib docs. datatype: string constraints: list} fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean} autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean} stereoperception: { value: 1 datatype: boolean} stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int} prefix: { value: 1 datatype: boolean} stripstereolayer: { value: 0 datatype: boolean} stripisotopelayer: { value: 0 datatype: boolean} stripfixedhlayer: { value: 0 datatype: boolean} stripreconnectlayer: { value: 0 datatype: boolean} stripchargelayer: { value: 0 datatype: boolean} |
Compiled C module | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange merge atom bond | mod_e_stdinchi.so | |||
| E_STDINCHIKEY | string | Hash of InChI string | prefix: { value: 1 datatype: boolean}
|
Compiled C module | E_STDINCHI | atomchange bondchange stereochange atom bond | mod_e_stdinchikey.so | |||
| E_STDINCHI_AUXINFO | string | Standard InChI auxiliary information | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange hadd atom bond | ||||||
| E_STEREOGENIC | intpair | Sum of M_STEREOGENIC stereogenic atoms and bond counts | Compiled C module | M_STEREOGENIC | atomchange bondchange stereochange atom bond | mod_e_stereogenic.so | ||||
| E_STEREOISOMERS | dataset | Set of stereoisomers from input structure | flipatoms: { value: all description: Select atoms where stereochemistry should be flipped enumeration: undefined:defined:all:none datatype: int} flipbonds: { value: all description: Select bonds where stereochemistry should be flipped enumeration: undefined:defined:all:none datatype: int} allowundefinedatoms: { value: 1 description: If not set, result ensembles with undefined atom stereochemistry are deleted datatype: boolean} allowundefinedbonds: { value: 1 description: If not set, result ensembles with undefined bond stereochemistry are deleted datatype: boolean} maxisomers: { value: -1 datatype: int} |
Tcl script | A_LABEL_STEREO B_LABEL_STEREO A_TYPE A_ELEMENT A_STEREOGENIC B_STEREOGENIC | atomchange bondchange stereochange 3drelative atom bond | e_stereoisomers.xpd | |||
| E_STEREOSET | dataset (switchable between diskfile dataset) |
Set of stereoisomers and diastereomers (atom and/or bonds) of base compound | coupledbridgeheads: { value: 1 description: iif set, bridgehead atoms are coupled, only synchronous stereo flips allowed datatype: boolean} filename: { value: {} description: Output file name (only used if datatype is set to diskfile) datatype: string constraints: writeable} atomsubset: { value: {} description: if set to non-empty set, perform stereo flips only on listed atoms datatype: intvector} bondsubset: { value: {} description: if set to non-empty set, perform stereo flips only on listed bonds datatype: intvector} processatoms: { value: 1 description: if set, perform atom inversions datatype: boolean} processbonds: { value: 0 description: if set, perform double bond flips datatype: boolean} synthesizeatomstereo: { value: 0 description: if set, assign initial arbitary stereochemistry to stereogenic atoms if no descriptor set datatype: boolean} synthesizebondstereo: { value: 0 description: if set, assign initial arbitary stereochemistry to stereogenic bonds if no descriptor set datatype: boolean} nmax: { value: -1 description: maximum number of result structures datatype: int} feedback: { value: 0 description: if set, print progress info datatype: boolean} mincouplingringsize: { value: 9 description: minimum size of rings considered coupled via trhe bridgehead criterion datatype: int} expectduplicates: { value: 1 description: if not set, any stereo duplicate generated is reported datatype: boolean} |
Tcl script | A_ELEMENT B_TYPE A_TYPE B_ORDER A_LABEL_STEREO B_FLAGS B_LABEL_STEREO | atomchange bondchange stereochange merge hadd ring | e_stereoset.xpd | |||
| E_STEREO_ATOMHASH_COUNT | int | Number of different stereospecific basic atom hash codes | (builtin) | E_HASHGROUP_COUNT_AS | atomchange bondchange merge | |||||
| E_STEREO_COUNT | intvector | Stereo descriptor counts for atom and bond stereochemistry (potential/set/unset counts for both, as a vector with six elements) | apossible int adefined int aundefined int bpossible int bdefined int bundefined int |
Compiled C module | M_STEREO_COUNT | atomchange bondchange stereochange | mod_e_stereo_count.so | |||
| E_STEREO_DEFINITION | intpair | Count separately number of set atom and bond stereo descriptors on stereogenic atoms and bonds, stored as an integer pair | (builtin) | A_STEREOGENIC B_STEREOGENIC A_DL_STEREO A_CIP_STEREO A_LABEL_STEREO A_HASH_STEREO B_CIP_STEREO B_LABEL_STEREO B_CISTRANS_STEREO B_HASH_STEREO | atomchange bondchange stereochange | |||||
| E_STEREO_HASH128 | uint128 | Perturbed stereo-sensitive ensemble hashcode, extended to 128 bits | Compiled C module | M_STEREO_HASHGROUP128 M_STEREO_HASH128 | atomchange bondchange merge hadd | mod_e_stereo_hash128.so | ||||
| E_STEREO_MOLHASH_COUNT | int | Number of different stereospecific perturbed molecule hash codes | (builtin) | E_HASHGROUP_COUNT_MS | atomchange bondchange merge hadd | |||||
| E_STEREO_STATUS | byte | n,nostereo:u,undefined:p,partial:d,defined |
Compiled C module | M_STEREO_STATUS | atomchange bondchange stereochange merge mol atom bond | mod_e_stereo_status.so | ||||
| E_STEREO_TAUTO_HASH | uint64 | Perturbed tautomer-agnostic ensemble stereo hashcode. Only stero infomation outside tautomer systems is used - bond and atom stereochemistry inside tauto systems is assumed to be lost in tautomerization. | maxtautomers: { value: 250 minvalue: 1 maxvalue: 9999 datatype: int} loghandle: { value: {} description: Tcl molfile handle for writing a log generated structures datatype: string} scramble: { value: 0 description: If set, scramble hashcodes to move them into new hashcode namespace datatype: int} setcanonictautomer: { value: 0 description: If set, also set E_CANONIC_TAUTOMER property datatype: boolean} usekekuleset: { value: 1 description: If set, start from Kekule set of initial structure datatype: boolean} stereobondmalus: { value: 1 description: If set, downgrade tautomers with bond stereochemistry potential in tauto system datatype: boolean} restrictedtransforms: { value: 0 description: If set, use smaller transform set datatype: boolean} setcount: { value: 1 description: If set, also set E_TAUTOMER_COUNT datatype: boolean} lockringpielectroncount: { value: 0 description: If set, allow only transform results where the pi electroin count of the rings is constant datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_HASHSY | atomchange bondchange stereochange merge | mod_e_stereo_tauto_hash.so | |||
| E_STEREO_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant ensemble stereo hashcode, 128 bit version | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_STEREO_HASH128 | atomchange bondchange stereochange merge | mod_e_stereo_tauto_hash128.so | |||
| E_STRUCTURE_VARIANTS | dataset | Generate variants of a structure by inserting or deleting CH2 groups, by substituting them with hetero atoms, or by moving functional groups. | addch2: { value: 1 description: If >0, add CH2 groups in weighted propotion datatype: int} delch2: { value: 1 description: If >0, remove CH2 groups in weighted proportion datatype: int} subch2: { value: 1 description: If >0, replace unsubstituted C by hetero atoms in weighted proportion datatype: int} movegroups: { value: 2 description: If >0, move functional groups in weighted proportion datatype: int} maxdistance: { value: 2 description: Maximum distance for moved functional groups datatype: int} minringsize: { value: 4 description: No ring contraction below this size datatype: int} maxringsize: { value: 8 description: No ring expansion beyond this size datatype: int} alisubelements: { value: N O S datatype: string constraints: list} arosubelements: { value: N datatype: string constraints: list} seed: { value: 0 description: Pseudo-random generator seed datatype: int} maxvariants: { value: 10 description: Maximum number of variants to generate datatype: int} maxfailures: { value: 350 description: Maximum allowed number of serially failed attempts to generate new structure datatype: int} chainmods: { value: 1 description: If set, allow chain modifications datatype: boolean} ringmods: { value: 1 description: If set, allow ring modifications datatype: boolean} addoriginal: { value: 0 description: If set, add original structure to set datatype: boolean} |
Tcl script | B_ISAROMATIC B_ORDER A_FG_SUBSTITUENTS A_FG_PARTICIPATION A_ARORING_COUNT B_RING_SIZE_BITS A_RING_SIZE_BITS | atomchange bondchange 3dabsolute atom bond | e_structure_variants.xpd | |||
| E_SUPRABANK_ID | int | Structure ID in Suprabank (suprabank.org) | Tcl script | atomchange bondchange stereochange atom bond | e_suprabank_id.xpd | |||||
| E_SUPRABANK_URL | url | Display URL in Suprabank (suprabank.org) | Tcl script | atomchange bondchange stereochange atom bond | e_suprabank_url.xpd | |||||
| E_SURECHEMBL_ID | string | Database ID of structure in the SureChEMBL database (www.surechembl.org) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_surechembl_id.xpd | ||||
| E_SURECHEMBL_URL | url | Data display URL for structure in SureChEMBL database (www.surechembl.org) | Tcl script | E_SURECHEMBL_ID | atomchange bondchange stereochange atom bond | e_surechembl_url.xpd | ||||
| E_SVG_IMAGE | diskfile (switchable between string blob diskfile url xmlstring) |
Ensemble image in SVG vector format | width: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int} height: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 minvalue: 3 maxvalue: 25 datatype: double} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 minvalue: 0 maxvalue: 25 datatype: string} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: string} header: { value: {} datatype: string} footer: { value: {} datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} secondarycolor: { value: #00D000 datatype: color} highlightbonds: { value: {} datatype: intvector} secondxarybonds: { value: {} datatype: intvector} highlightatoms: { value: {} datatype: intvector} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.2 datatype: double} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} symbolfontsize: { value: -1 datatype: double} annotationfontsize: { value: -1 datatype: double} bondannotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showlabel: { value: 0 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} frame: { value: 1 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: int} linespacing: { value: 1.8 datatype: double} unit: { value: {} datatype: string} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} circleatoms: { value: {} datatype: intvector} atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 10 datatype: int} wiggleamplitude: { value: 3.0 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} showstereogroups: { value: 0 datatype: boolean} font: { value: Helvetica datatype: string} usewebfont: { value: 0 datatype: boolean} usesubscripts: { value: 1 datatype: boolean} uselinecaps: { value: 1 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} standalone: { value: 1 datatype: boolean} xmlheader: { value: 1 datatype: boolean} id: { value: {} datatype: string} title: { value: {} datatype: string} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} showempty: { value: 0 datatype: boolean} saverendercoordinates: { value: 0 datatype: boolean} suppressedmols: { value: {} datatype: intvector} framecolor: { value: black datatype: color} rawcoordinates: { value: 0 datatype: boolean} atomclick: { value: {} description: Javascript function to call, substitute %i id, %a atom label, %b bond label, %r ring label, %y ringsystem label datatype: string} bondclick: { value: {} datatype: string} ringclick: { value: {} datatype: string} ringsystemclick: { value: {} datatype: string} headerclick: { value: {} datatype: string} footerclick: { value: {} datatype: string} bgclick: { value: {} datatype: string} ringclickcolor: { value: {} datatype: color constraints: emptycolor} ringsystemclickcolor: { value: {} datatype: color constraints: emptycolor} bondclickcolor: { value: {} datatype: color constraints: emptycolor} ringhovercolor: { value: {} datatype: color constraints: emptycolor} ringsystemhovercolor: { value: {} datatype: color constraints: emptycolor} atomhovercolor: { value: {} datatype: color constraints: emptycolor} bondhovercolor: { value: {} datatype: color constraints: emptycolor} activehbonds: { value: 0 description: If set, undrawn bonds to H become active on hovering and are clickable if a bond click action has been set datatype: boolean} style: { value: default description: General plot style. Can either be default, or patran for Patran-style atom and bond annotations enumeration: default:patran datatype: int} maxannotationlength: { value: -1 description: Maximum character length of atom and bond annotations. If an annotation is longer, the plotted value is abbreviated, and a SVG title attribute with the full string added datatype: int} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} extrabondannotationproperty: { value: {} datatype: string constraints: property} |
Compiled C module | A_TYPE A_ELEMENT A_XY A_HSPECIAL A_CSPECIAL B_TYPE B_ORDER A_ANNOTATION B_ANNOTATION B_FLAGS A_FLAGS A_QUERY B_QUERY | atomchange bondchange stereochange merge atom bond | mod_e_svg_image.so | |||
| E_SYMMETRY | string | Molecular Point Group | A_XYZ | atomchange bondchange stereochange hadd | ||||||
| E_SYNTHETIC_ACCESSIBILITY | double | Estimation of synthetic acessibility by the Ertl/Schuffenhauer algorithm | Ertl, Schuffenhauer, J. Cheminf. 2009, 1:8 | fragfile: { value: echash_toheavy_usebo.db datatype: diskfile constraints: readable} defaultscore: { value: -6.047372 description: value to use if encountering an unknown sphere hash, corresponds to score of singleton in hash db datatype: double} scale: { value: -0.801403346304195 description: experimental parameter to scale result between range 1(simplest) to 10(most complex) datatype: double} offset: { value: 6.1171206468215455 description: experimental parameter to scale result between range 1(simplest) to 10(most complex) datatype: double} |
Tcl script | A_ELEMENT A_TYPE B_TYPE B_ORDER A_EC_HASH | atomchange bondchange atom bond | e_synthetic_accessibility.xpd | ||
| E_SYNTHONIX_ID | string | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_synthonix_id.xpd | |||||
| E_SYNTHONIX_URL | url | Tcl script | E_SYNTHONIX_ID | atomchange bondchange stereochange atom bond | e_synthonix_url.xpd | |||||
| E_T3DB_ID | string | Toxin and Toxin Target Database (T3DB) structure ID (http://www.t3db.ca) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_t3db_id.xpd | ||||
| E_T3DB_URL | url | Toxin and Toxin Target Database (T3DB) structure display URL (http://www.t3db.ca) | Tcl script | E_T3DB_ID | atomchange bondchange stereochange atom bond | e_t3db_url.xpd | ||||
| E_TAUTOMER_COUNT | int | Number of tautomers found for compound | A_TYPE B_TYPE B_ORDER A_ELEMENT | atomchange merge atom bond | ||||||
| E_TAUTOMER_NETWORK | network | The network of tautomers, with V_STRUCTURE nodes containing the structures and C_NAME indicating the transform which generated it | storeimages: { value: 0 description: If set, store an image of the structures in the nodes in property V_GRAPHICS datatype: boolean} maxtautomers: { value: 1000 description: The maximum number of unique tautmer structures generated minvalue: 0 datatype: int} usekekuleset: { value: 1 description: Whether to start with a Kekule form set (recommended) datatype: boolean} restricted: { value: 0 description: Whether to use a restricted transform set datatype: boolean} maxtransforms: { value: -1 description: If not negative, the maximum number of transforms to apply minvalue: -1 datatype: int} preservegroups: { value: 0 description: Whether to preserve group information on the tautomers datatype: boolean} imgparameters: { value: width 100 height 100 bgcolor grey80 atomcolor black bondcolor black format png frame 0 bonds 6 description: Image parameters datatype: dictionary} transformfile: { value: {} description: If set, read transform set from specified file datatype: diskfile constraints: readable autodatapath} |
Compiled C module | atomchange bondchange atom bond | mod_e_tautomer_network.so | ||||
| E_TAUTOMER_SCORE | int | Scoring function for tautomers | stereobondmalus: { value: 1 description: If set, give malus to stereogenic bonds (which may appear stereochemically defined, but are not really) datatype: boolean} explain: { value: 0 description: If set, print the score components datatype: boolean} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT B_ISAROMATIC R_TYPE R_AROMATIC A_FORMAL_CHARGE | atomchange bondchange atom bond ring | mod_e_tautomer_score.so | |||
| E_TAUTOSET | dataset | Set of structure tautomers generated by application of a standard set of tautomer SMIRKS transforms | maxtautomers: { value: 1000 description: Maximum number of tautomers to create datatype: int} usekekuleset: { value: 1 description: Generate a Kekule set as first step, and then apply tuatomer transforms on this set datatype: boolean} restricted: { value: 0 description: If set, use smaller set of transforms datatype: boolean} nametransforms: { value: 0 description: If set, set E_NAME of result molecules to transform sequence datatype: boolean} maxtransforms: { value: -1 description: Maximum number of transform applications datatype: int} preservegroups: { value: 0 description: If set, lock ensemble group subobjects datatype: boolean} sorted: { value: 0 description: If set, sort entries according to sortproperty parameter, using the hash code for tie breaking, with the top-rated structure first in the dataset datatype: boolean} hashcode: { value: E_HASHY description: The hashcode to use for duplicate checks datatype: string constraints: property} sortproperty: { value: E_TAUTOMER_SCORE description: The property to use for dataset element comparisons if the sort flag is set datatype: string constraints: property} transformfile: { value: {} description: If set, read transform set from specified file datatype: diskfile constraints: readable autodatapath} |
Compiled C module | A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange merge atom bond | mod_e_tautoset.so | |||
| E_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant ensemble hashcode, independent of isotope labelling and stereochemistry | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} stereobondmalus: { value: 0 datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_HASHY | atomchange bondchange merge | mod_e_tauto_hash.so | |||
| E_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant ensemble hashcode, 128 bit version | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_HASH128 | atomchange bondchange stereochange merge | mod_e_tauto_hash128.so | |||
| E_TCM_TAIWAN_ID | int | Compound ID for TCL@Taiwan Traditional Chinese Medicine database (tcm.cmu.edu.tw) | Tcl script | atomchange bondchange atom bond | e_tcm_taiwan_id.xpd | |||||
| E_TCM_TAIWAN_URL | url | URL for display of compound in TCL@Taiwan Traditional Chinese Medicine database (tcm.cmu.edu.tw) | Tcl script | E_TCM_TAIWAN_ID | atomchange bondchange atom bond | e_tcm_taiwan_url.xpd | ||||
| E_TEXT_ANNOTATION | compound | Annotation string for a structure drawing. It is one possiblöe type of the property-class data values of choice vector property E_ANNOTATION. This data is for example read from and written to CDX/CDXML files. | {} {} {} center:left:right center:top:bottom {} {} ^none:bold:italic:underline:outline:shadow:subscript:superscript:formula |
coords floatpair text stringvector color color align int valign int font string fontsize float style bitset charset string width double height double autosize boolean autoresize boolean autoalign boolean preferredwidth double |
A_XY | never | ||||
| E_TEX_IMAGE | diskfile (switchable between blob diskfile) |
Structure drawing representation for the chemfig Tex macro packge (http://www.ctan.org/pkg/chemfig/) by Christian Tellechea | filename: { value: {} datatype: string constraints: writeable} downloadfilename: { value: {} datatype: string} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} showstereo: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showcharge: { value: 1 datatype: boolean} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} showstereogroups: { value: 0 datatype: boolean} footer: { value: {} datatype: string} footerproperty: { value: {} datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} usesubscripts: { value: 1 datatype: boolean} contractgroups: { value: 0 datatype: boolean} wedges: { value: 1 datatype: boolean} dashes: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} highlightgroups: { value: {} datatype: intvector} eolchars: { value: {} description: Empty string is platform default datatype: string} fulldocument: { value: 0 description: If set, create a complete minimal text document. By default. only include file is created datatype: boolean} |
Compiled C module | atomchange bondchange stereochange merge mol atom bond | mod_e_tex_image.so | ||||
| E_TGI | compound | TGI tumor screen data in the NCI cancer screening database | concunit shortstring lcconc float panel shortstring cell string panelnumber short cellnumber short nlog_tgi float ntest_this short ntest_max short |
atomchange bondchange merge | ||||||
| E_TIMESTAMP | datetime | Timestamp | Tcl script | atomchange bondchange stereochange merge | e_timestamp.xpd | |||||
| E_TITLE | string | Title string in free format | never | |||||||
| E_TOTAL_ENERGY | float | Measured or computed singlepoint energies | Tcl script | E_ELECTRONIC_ENERGY E_REPULSION_ENERGY | atomchange bondchange 3drelative 3dabsolute | e_total_energy.xpd | ||||
| E_TOTAL_SUBSTRUCTURE_COUNT | int | Total number of connected substructures in the molecule. This includes topological duplicates. By default, the snip path count from E_SMALLWORLD_NETWORK is used, not the real substructure count, which is usually not exactly the same. | usessmatch: { value: 0 description: If set, do explicit counted substructure matching instead of snap path counts datatype: boolean}
|
Compiled C module | E_SMALLWORLD_NETWORK | atomchange bondchange atom bond | mod_e_total_substructure_count.so | |||
| E_TOTAL_WALK_COUNT | double | Sum of M_TOTAL_WALK_COUNT values | J. Chem. Inf. Comput. Sci. 2000, 40, 99-106 | Compiled C module | M_TOTAL_WALK_COUNT | atomchange bondchange mol atom bond | mod_e_total_walk_count.so | |||
| E_TOXICOPHORE_COUNT | intpair | Count of toxicophores | Kazius, McGuire, Bursi, J. Med. Chem. 2005, 48, 321-320 | Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange merge ring | e_toxicophore_count.xpd | |||
| E_TPSA | float | Computed topological polar surface area | P. Ertl, B. Rohde, P. Selzer, J. Med. Chem. 43, 3714-3717, 2000 | usechemaxonextensions: { value: 1 datatype: boolean} trace: { value: 0 datatype: boolean} pentavalentnitrogroups: { value: 1 datatype: boolean} |
Tcl script | A_ELEMENT A_VB_NEIGHBOR_COUNT A_HCOUNT R_SIZE B_ISAROMATIC B_ORDER A_FORMAL_CHARGE B_ORDER B_ORDER | atomchange bondchange hadd | e_tpsa.xpd | ||
| E_TRAFO_ARO | uint64 | Hash code transformation (isolated aromatic core) | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_aro.xpd | |||
| E_TRAFO_AROCSKEL | uint64 | Hash code transformation - aromatic systems and carbon skeleton | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_arocskel.xpd | |||
| E_TRAFO_AROCSKEL_ALPHA | uint64 | Hash code transformation - aromatic systems plus carbon skeleton plus alpha atoms | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_arocskel_alpha.xpd | |||
| E_TRAFO_AROCSKEL_ALPHA_OXO | uint64 | Hash code transformation (C skeleton plus aromatic ring plus alpha atoms, then oxidation) | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE A_IUPAC_GROUP A_FREE_ELECTRONS | atomchange bondchange merge atom bond | e_trafo_arocskel_alpha_oxo.xpd | |||
| E_TRAFO_AROCSKEL_SUB | uint64 | Hash code transformation (aromatic and carbon skeleton, followed by generalization of substituents) | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_arocskel_sub.xpd | |||
| E_TRAFO_ARO_ALPHA | uint64 | Hash code transformation (aromatic system plus alpha atom, then h-addition) | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE E_CANONIC_TAUTOMER | atomchange bondchange merge atom bond | e_trafo_aro_alpha.xpd | |||
| E_TRAFO_ARO_ALPHA_OXO | uint64 | Hash code transformation - aromatic system and alpha atoms, followed by oxidation | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE A_IUPAC_GROUP E_CANONIC_TAUTOMER A_FREE_ELECTRONS | atomchange bondchange merge atom bond | e_trafo_aro_alpha_oxo.xpd | |||
| E_TRAFO_ARO_SUB | uint64 | Hash code transformation - aromatic system and generalized substituents | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_aro_sub.xpd | |||
| E_TRAFO_CSKEL | uint64 | Hash code transformation - isolate carbon skeleton | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_cskel.xpd | |||
| E_TRAFO_CSKEL_ALPHA | uint64 | Hash code transformation - carbon skeleton plus alpha atoms | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: string constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_cskel_alpha.xpd | |||
| E_TRAFO_CSKEL_ALPHA_OXO | uint64 | Hash code transformation - isolate carbon skeleton and alpha atoms, followed by oxidation | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_cskel_alpha_oxo.xpd | |||
| E_TRAFO_CSKEL_SUB | uint64 | Hash code transformation - isolate carbon skeleton and mark substitution points | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_cskel_sub.xpd | |||
| E_TRAFO_FRAME | uint64 | Hash code transformation: Isolate the framework, i.e. replace all non-H non-carbon atoms with carbon. | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_frame.xpd | |||
| E_TRAFO_OXIDATION | uint64 | Hash code transformation - standard oxidation | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_oxidation.xpd | |||
| E_TRAFO_REDUCTION | uint64 | Hash code transformation - standard reduction | log: { value: 0 datatype: string} logfile: { value: trafolog.cbin datatype: string} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_reduction.xpd | |||
| E_TRAFO_RING | uint64 | Hash code transformation - isolate ring system | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ring.xpd | |||
| E_TRAFO_RINGCSKEL | uint64 | Hash code transformation - isolate rings and carbon skeleton | log: { value: 0 datatype: int} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ringcskel.xpd | |||
| E_TRAFO_RINGCSKEL_ALPHA | uint64 | Hash code transformation - rings and carbon skeleton and alpha atom | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ringcskel_alpha.xpd | |||
| E_TRAFO_RINGCSKEL_ALPHA_OXO | uint64 | Hash code transformation - isolate rings and carbon skeleton plus alpha atoms, then oxidize | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ringcskel_alpha_oxo.xpd | |||
| E_TRAFO_RINGCSKEL_SUB | uint64 | Hash code transformation- isolate ring and carbon skeleton, then mark substition points | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ringcskel_sub.xpd | |||
| E_TRAFO_RING_ALPHA | uint64 | Hash code transformation - isolate ring system and alpha atoms | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ring_alpha.xpd | |||
| E_TRAFO_RING_ALPHA_OXO | uint64 | Hash code transformation - isolate ring syetem and alpha atoms, then oxidation | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ring_alpha_oxo.xpd | |||
| E_TRAFO_RING_SUB | uint64 | Hash code transformation - isolate ring system with generalized substituent site markers | log: { value: 0 datatype: boolean} logfile: { value: trafolog.cbin datatype: diskfile constraints: writeable} |
Tcl script | A_ELEMENT B_TYPE B_ORDER A_TYPE | atomchange bondchange merge atom bond | e_trafo_ring_sub.xpd | |||
| E_U3D_MODEL | diskfile | 3D structure model in Intel U3D format, converted from the IDTF representation (E_IDTF_MODEL). This is used for inclusion of interactive 3D PDF file (property E_PDF3D_IMAGE) | filename: { value: {} datatype: diskfile constraints: writeable} debug: { value: 0 datatype: boolean} excludenormals: { value: 0 datatype: boolean} removezerofaces: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: diskfile} checklibs: { value: 0 datatype: boolean} |
Compiled C module | E_IDTF_MODEL | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd | mod_e_u3d_model.so | |||
| E_UNICHEM_URL | url | EBI Unichem link page for the structure (www.ebi.ac.uk) | Tcl script | E_STDINCHIKEY | atomchange bondchange atom bond | e_unichem_url.xpd | ||||
| E_UNII | stringvector | FDA Unique Ingredient Identifier (UNII) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_unii.xpd | ||||
| E_UNIPROT_URL | url | Data display URL in Uniprot database (www.uniprot.org) | Tcl script | E_CHEBI_ID | atomchange bondchange stereochange atom bond | e_uniprot_url.xpd | ||||
| E_UNIQUE_SUBSTRUCTURE_COUNT | int | Unqiue number of connected substructures in the molecule. This includes duplicates - e.g. butane has one butane, one propane, one ethane and one methane substructures. | Compiled C module | E_SMALLWORLD_NETWORK | atomchange bondchange atom bond | mod_e_unique_substructure_count.so | ||||
| E_UNIT_CELL | floatvector | Crystallographic unit cell., in a/b/c/alpha/beta/gamma sequence. Used in the CIF file format I/O module. | a float b float c float alpha float beta float gamma float |
atomchange bondchange stereochange merge 3drelative 3dabsolute | ||||||
| E_UNSPECIFIED_AIDSET | intvector | Set of PubChem assay IDs testing this compound as unspecified | Tcl script | E_CID | atomchange bondchange stereochange | e_unspecified_aidset.xpd | ||||
| E_URL | url | URL of molecular data file | never | |||||||
| E_UUUTS_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: uuuTS datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} forcemagic: { value: 0 datatype: string} useisotope: { value: 0 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_UUUTS_STRUCTURE datatype: string} secondarytag: { value: 01-xx datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 0 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} csbasehash: { value: E_HASHSY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_uuuts_id.xpd | |||
| E_UUUTS_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_UUUTU_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: uuuTu datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} forcemagic: { value: 0 datatype: string} useisotope: { value: 0 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_UUUTU_STRUCTURE datatype: string} secondarytag: { value: 01-xx datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 0 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} csbasehash: { value: E_HASHY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_uuutu_id.xpd | |||
| E_UUUTU_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_UUUUS_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: uuuuS datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} forcemagic: { value: 0 datatype: string} useisotope: { value: 0 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_UUUUS_STRUCTURE datatype: string} secondarytag: { value: 01-xx datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 1 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} csbasehash: { value: E_HASHSY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_uuuus_id.xpd | |||
| E_UUUUS_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_UUUUU_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: uuuuu datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} forcemagic: { value: 0 datatype: string} useisotope: { value: 0 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_UUUUU_STRUCTURE datatype: string} secondarytag: { value: 01-xx datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 1 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} csbasehash: { value: E_HASHY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_uuuuu_id.xpd | |||
| E_UUUUU_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_UUUXX_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: uuuxx datatype: string} scope: { value: private datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} forcemagic: { value: 0 datatype: string} useisotope: { value: 0 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_UUUXX_STRUCTURE datatype: string} secondarytag: { value: 01-xx datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 1 hsaturation 1 tautomer 0 singleHalogenAtoms 1 uncharge 1 deleteMetalComplexCenter 1 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 radical 1 stereo 1 singleHydrogenAtoms 1 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 1 grabLargestFragment 1} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 1 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 1 {} !normal {nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} csbasehash: { value: E_HASHY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 1 singleHalogenAtoms 1 radical 1 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 1 deleteMetalComplexCenter 1 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 1 desalt 1 resonance 1 deleteIsotopeLabels 1 grabLargestFragment 1} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_uuuxx_id.xpd | |||
| E_UUUXX_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_UVSPECTRUM | compound | UV/Vis spectrum, usually read from JCAMP files. This property is also computable via a look-up in the NIST WebBook. | experimental boolean origin string author string date int spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum floatvector |
Tcl script | atomchange bondchange | e_uvspectrum.xpd | ||||
| E_UVSPECTRUM_IMAGE | diskfile (switchable between string blob diskfile url) |
UV/Vis spectrum rendering | height: { value: 250 datatype: int} width: { value: 500 datatype: int} bgcolor: { value: white datatype: color} title: { value: {} datatype: string} filename: { value: {} datatype: string constraints: writeable} format: { value: gif enumeration: gif:png,png24:png8 datatype: string} titlecolor: { value: black datatype: color} framecolor: { value: black datatype: color} signalcolor: { value: #DD0000 datatype: color} |
Tcl script | E_UVSPECTRUM | atomchange bondchange merge mol | e_uvspectrum_image.xpd | |||
| E_VEBER_BIOAVAILABILITY_FLAG | boolean | Veber bioavailability flag (E_TPSA<=140 && E_NROTBONDS<=10) | Journal of Medicinal Chemistry, Vol. 45, pp. 2615-2623, 2002 | Compiled C module | E_NROTBONDS E_TPSA | atomchange bondchange atom bond | mod_e_veber_bioavailability_flag.so | |||
| E_VIBRATION_VRML | diskfile | VRML scene of the normal vibrations of the molecule(s) | vibscale: { value: 0.5 datatype: string} index: { value: 0 datatype: string} filename: { value: {} datatype: string} nframes: { value: 10 datatype: string} stdinterval: { value: 1.0 datatype: string} bcolor: { value: white datatype: string} usebo: { value: 1 datatype: string} step: { value: 0 datatype: string} usefreq: { value: 0 datatype: string} |
Tcl script | A_XYZ A_ELEMENT A_TYPE B_TYPE B_ORDER A_NORMAL_VIBRATIONS | atomchange bondchange stereochange merge 3dabsolute | e_vibration_vrml.xpd | |||
| E_VRML | diskfile (switchable between blob diskfile url) |
VRML scene of molecular ensemble | style: { value: ballstick enumeration: ballstick:capped:wireframe:spacefill:all datatype: string} vdwscaling: { value: 25 datatype: double} bondcolor: { value: atomsplit datatype: string} bondradius: { value: 15 datatype: double} annotationsize: { value: 15 datatype: double} labelsize: { value: 15 datatype: double} showlabel: { value: 0 datatype: boolean} labelcolor: { value: purple datatype: color} annotationcolor: { value: cyan datatype: color} annotationproperty: { value: A_SHIELDING datatype: string constraints: property} showbondorder: { value: 0 datatype: boolean} showproperty: { value: 0 datatype: boolean} useabsolute: { value: 0 datatype: boolean} suppress: { value: none enumeration: none:neg:neg0:pos:pos0:zero:nonzero:all datatype: string} nicsgrid: { value: 0 datatype: boolean} colorcode: { value: 0 datatype: boolean} positivecolor: { value: red datatype: color} neutralcolor: { value: white datatype: color} negativecolor: { value: green datatype: color} transform: { value: none enumeration: none:log:loglog:root2:root3:pow2:pow3 datatype: string} mincubesize: { value: 4 datatype: double} maxcubesize: { value: 40 datatype: double} glossfactor: { value: 75 datatype: double} scaling: { value: auto datatype: string} transparency: { value: 0 datatype: double} structure: { value: 0 datatype: boolean} filename: { value: {} datatype: string constraints: writeable} geometry: { value: 0 datatype: boolean} atomhighlightcolor: { value: red datatype: color} highlightatoms: { value: {} datatype: intvector} bondhighlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} animation: { value: 0 datatype: boolean} cycletime: { value: 1 datatype: double} playoption: { value: 0 datatype: boolean} httpheader: { value: 0 datatype: int} ignoreh: { value: 0 datatype: boolean} setviewpoint: { value: 1 datatype: boolean} downloadfilename: { value: {} datatype: string} |
Compiled C module | A_XYZ A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange merge | mod_e_vrml.so | |||
| E_WEB_STRUCTURE_QUERY_URL | url | Perform various structure queries on Internet databases and return a URL which can be used to display the results. Depending on the database contacted, this URL may either just display results, with the query already having been executed, or perform the actual query without prior job submission. | database: { value: pcstructure enumeration: pcstructure:pcsubstance:chebi:hmdb:chembl:chemspider datatype: string} querytype: { value: fullstructure enumeration: fullstructure,fs:identity,id:substructure,ss,sub:superstructure,su,super:similarity,sim:formula,form,frm datatype: int} trace: { value: 0 datatype: boolean} threshold: { value: 95 description: Minimum required similarity value in percent datatype: int} stereomode: { value: absolute enumeration: ignore:absolute:relative:nonconflicting datatype: int} isotopemode: { value: ignore enumeration: ignore:isotope datatype: int} tautomode: { value: ignore enumeration: ignore:tautomer datatype: int} maxhits: { value: 500 minvalue: -1 maxvalue: 999999 datatype: int} maxurllength: { value: 2048 minvalue: -1 maxvalue: 999999 datatype: int} |
Tcl script | atomchange bondchange atom bond | e_web_structure_query_url.xpd | ||||
| E_WEIGHT | float | Molecular weight of ensemble | allisotopes: { value: 0 datatype: string} useimplicith: { value: 1 datatype: string} |
(builtin) | A_WEIGHT | atomchange merge | ||||
| E_WIKIPEDIA_CHEMBOX | diskfile (switchable between string blob diskfile) |
Text to use by editors in Wikipedia chembox, as defined in http://en.wikipedia.org/wiki/Template:Chembox | trycas: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} verifycas: { value: 1 datatype: boolean} threaded: { value: 0 description: If set, computed with multiple threads datatype: boolean} |
Tcl script | E_CID E_CHEMSPIDER_ID E_DRUGBANK_ID E_CHEBI_ID E_EINECS_ID E_UNII E_EC_NUMBER E_RTECS_NUMBER E_IUPHAR_ID E_CHEMBL_ID | atomchange bondchange stereochange merge hadd | e_wikipedia_chembox.xpd | |||
| E_WIKIPEDIA_DRUGBOX | diskfile (switchable between string blob diskfile) |
Text suitable for use by editors in Wikipedia drugbox template, pre-filled with standard attributes computed by Internet lookup | filename: { value: {} datatype: diskfile constraints: writeable} threaded: { value: 0 datatype: boolean} trycas: { value: 1 datatype: boolean} verifycas: { value: 1 datatype: boolean} |
Tcl script | E_IUPAC_PREFERRED_NAME E_CID E_CHEMSPIDER_ID E_DRUGBANK_ID E_CHEBI_ID E_CAS E_CHEMBL_ID E_IUPHAR_ID E_UNII | atomchange bondchange stereochange merge hadd | e_wikipedia_drugbox.xpd | |||
| E_WIKIPEDIA_URL | url | Wikipedia compound id URL. Lookup is performed by CAS number, PubChem CID, InChI, StdInChI in that order | language: { value: en enumeration: en:de:es:fr:ru:ja comment: language set selected to contain reasonable chemistry content, e.g. a pyrdine entry datatype: string} trycas: { value: 1 datatype: string} trycid: { value: 1 datatype: string} tryinchi: { value: 1 datatype: string} trystdinchi: { value: 1 datatype: string} trycomputedcas: { value: 0 datatype: string} |
Tcl script | E_CID E_CAS E_INCHI E_STDINCHI | atomchange bondchange stereochange merge | e_wikipedia_url.xpd | |||
| E_WILEY_URL | url | URL to display references in Wiley/VCH literature (www.compoundsearch.com) | Tcl script | E_STDINCHIKEY | atomchange bondchange atom bond | e_wiley_url.xpd | ||||
| E_WLN_STRING | string | Wisswesser Line Notation structure representation. The computation function only identifies a WLN string in the names in E_NAMESET (which ususally comes from the NCI resolver). It.does not algorithmically compute the name. | Tcl script | E_NAMESET | atomchange bondchange stereochange merge atom bond | e_wln_string.xpd | ||||
| E_WOLFRAMALPHA_URL | url | Link into the WolframAlpha database (wolframalpha.com) | Tcl script | atomchange bondchange atom bond | e_wolframalpha_url.xpd | |||||
| E_WOODHEAD_FRAGMENTLIKENESS_VIOLATIONS | byte | This is a stricter verion of E_JHOTI_FRAGMENTLIKENESS_VIOLATIONS | Congreve, Chessari, Tisi, Woodhead, J. Med. Chem. 2008, 51, 3661 | Tcl script | E_WEIGHT E_NHDONORS E_NHACCEPTORS E_XLOGP2 E_NROTBONDS E_TPSA | atomchange bondchange atom bond | e_woodhead_fragmentlikeness_violations.xpd | |||
| E_XLOGP | float | Calculating the XLOGP value according to the algorithm published in R. Wang, Y. Fu, L.Lai J. Chem. Inf. Comput. Sci. 37, 1997, 615-621 | R. Wang, Y. Fu, L.Lai J. Chem. Inf. Comput. Sci. 37, 1997, 615-621 | Tcl script | A_ELEMENT A_TYPE | atomchange bondchange | e_xlogp.xpd | |||
| E_XLOGP2 | float | Calculating the XLOGP value (version 2) | R. Wang, Y. Gao, L. Lai, Persp. Drug Disc. Design 19, 2000, 47-66 | logcomputation: { value: 0 datatype: boolean}
|
Tcl script | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange | e_xlogp2.xpd | ||
| E_XSCREEN | bitvector | Extended path-based screening bit set. Superceded by E_QUERY_SCREEN. | length: { value: 1024 datatype: int} space: { value: 4096 datatype: int} depth: { value: 3 datatype: int} nohdepth: { value: 1 datatype: int} tauto: { value: 0 datatype: boolean} usech: { value: 1 datatype: boolean} nobranchdepth: { value: 3 datatype: int} traceatom: { value: -1 datatype: int} tracebit: { value: -1 datatype: int} maxatoms: { value: 8 datatype: int} tracefile: { value: {} datatype: diskfile constraints: writeable} maxfork: { value: 3 datatype: int} maxnfork: { value: 2 datatype: int} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange atom bond | mod_e_xscreen.so | |||
| E_XYEXTENT | floatvector | 2D display coordinate bounding box | xmin double xmax double ymin double ymax double |
(builtin) | A_XY A_FLAGS | atomchange merge hadd | ||||
| E_XYZEXTENT | floatvector | 3D coordinate bounding box | xmin double xmax double ymin double ymax double zmin double zmax double |
coordinateproperty: { value: A_XYZ datatype: string}
|
(builtin) | A_XYZ | atomchange merge 3drelative 3dabsolute hadd | |||
| E_YEAST_SCREEN | compound | NCI yeast screen data (used as a field in the NCI database browser) | concentration float strain string diff_inhibit float avg_inhibit float |
atomchange bondchange merge | ||||||
| E_YMDB_ID | string | Yeast metabolome structure ID (http://www.ymdb.ca) | Tcl script | atomchange bondchange stereochange atom bond | e_ymdb_id.xpd | |||||
| E_YMDB_URL | url | Yeast metabolome structure display URL (http://www.ymdb.ca) | Tcl script | E_YMDB_ID | atomchange bondchange stereochange atom bond | e_ymdb_url.xpd | ||||
| E_ZEROPOINT_ENERGY | float | Computed zeropoint energy. This can be indireclty obtained via E_HEAT_OF_FORMATION with a VAMP computation in the standard set-up. | A_XYZ | atomchange bondchange 3dabsolute | ||||||
| E_ZINC_ID | string | zinc.docking.org ID | Tcl script | E_STDINCHI | atomchange bondchange stereochange merge | e_zinc_id.xpd | ||||
| E_ZINC_URL | url | zinc.docking.org URL | Tcl script | E_ZINC_ID | atomchange bondchange stereochange merge | e_zinc_url.xpd | ||||
| E_ZMATRIX | compoundvector | Z matrix of structure. This is for example used in the I/O modules for Gaussian Archive, Mopac Input and Ouptut. and Gaussian Input. | distance double angle double torsion double atom1 int atom2 int atom3 int |
atomchange bondchange stereochange merge 3drelative 3dabsolute shuffle hadd | ||||||
| F_AUTHOR | compound | Structure or reaction file author data, computation copies these from the internal object author fields | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
Tcl script | never | f_author.xpd | ||||
| F_AVERAGE_ATOM_COUNT | double | Average atom count of compounds in file | Tcl script | never | f_average_atom_count.xpd | |||||
| F_AVERAGE_RING_COUNT | double | Average ESSSR ring count of compounds in file | Tcl script | never | f_average_ring_count.xpd | |||||
| F_AVERAGE_WEIGHT | double | Average molecular weight of compounds in file | Tcl script | never | f_average_weight.xpd | |||||
| F_COMMENT | string | Free comment attached to file | never | |||||||
| F_DATE | date | File creation date | atomchange bondchange atom bond | |||||||
| F_DIVERSITY_SET | dataset | Select a diverse subset from the source dataset. | property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property} query: { value: all description: Structure filter query expression datatype: string} feedback: { value: 0 description: Output a dot to stderr for every n structures added to the set - 0 for no feedback datatype: int} size: { value: 50 description: Target size minvalue: 1 datatype: int} startindex: { value: -1 description: First structure source index, -1 is random. This is an index into the eligible records, not directly a file record number. datatype: int} minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int} |
Tcl script | atomchange bondchange atom bond | f_diversity_set.xpd | ||||
| F_GAUSSIAN_JOB_PARAMS | compound | Parameters for a Gaussian job. These are intergrated into the output of structure files in Gaussian Input file format, and filled when reading Gaussian input structure files. | link0 stringvector route stringvector title stringvector charge_spin intpair redundant stringvector |
never | ||||||
| F_IDENT | string | Ident string of structure file | Tcl script | atomchange bondchange atom bond | f_ident.xpd | |||||
| F_MARVIN | typeddictionary | Marvin GUI Props | never | |||||||
| F_QUERY | compound | Statistics on last query executed on the file. Set by "molfile scan" command. | ens,structure:enslist,elist,structures:record,rec:recordlist,reclist:bitvector,bit:count,cnt:delete,del:property,prop:propertylist,proplist:file,molfile:filelist:table,qtable,hitlist:reaction:reactionlist,xlist,reactions:array,tclarray,pythonarray:vrecord,vrec:vrecordlist,vreclist:custom:customlist:ensblob:reactionblob:exists:tablecollection:vertex:vertexlist:row,index:rowlist,indexlist |
mode int query string retrieve string timeout int maxhits int date datetime startpos int endpos int nhits int nexamined int querytime int eof boolean comment string displayquery string |
never | |||||
| F_QUERY_GIF | diskfile (switchable between string blob diskfile url) |
Depiction of last query executed on file | width: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int} height: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int} bgcolor: { value: transparent datatype: color} suppressnodes: { value: E_LIVE_IN_ENTREZ datatype: string} frame: { value: 0 datatype: int} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int} crop: { value: 2 minvalue: -1 datatype: int} format: { value: gif datatype: string} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} fixiepngsize: { value: 1 datatype: boolean} molimgwidth: { value: 75 minvalue: 25 maxvalue: 500 datatype: int} molimgheight: { value: 75 minvalue: 25 maxvalue: 500 datatype: int} font: { value: arialn datatype: string} fontsize: { value: 8 datatype: string} interlace: { value: 1 datatype: string} suppressedproperties: { value: {} datatype: string constraints: propertylist} downloadfilename: { value: {} datatype: string} |
Compiled C module | F_QUERY | never | mod_f_query_gif.so | |||
| F_SCAFFOLD_TABLE | table | A list of Ertl-type scaffolds extracted from a file. The table contains the counts and SMILES strings as columns, plus row-attached structures. | maxrecs: { value: -1 description: The maximum number of records to process, -1 is infinite datatype: int} maxscaffolds: { value: -1 description: The maximum number of scaffolds to record, -1 is infinite datatype: int} maxsimplification: { value: 1 description: The maximum number of scaffolds simplification steps to perform, -1 is infinite datatype: int} compoundfilter: { value: all description: A compound filter expression (see 'ens scan' command) scaffolds must match datatype: string} |
Tcl script | E_SMILES E_SCAFFOLD_TREE_STRUCTURE | atomchange bondchange stereochange atom bond | f_scaffold_table.xpd | |||
| F_SCAFFOLD_TREE | datatree | The scaffolds of the structures in the dataset in sorted, hierarchical order. The first node a an empty root node, and its children are the irreducible scaffolds. The individual scaffold nodes of the tree contain SMILES strings as value and the (non-stereo/non-isotope) ensemble hashcode as name, followed by all more complex scaffolds which are reduced to the current scaffold by one simplification step. | maxlevel: { value: -1 description: Maximum tree depth to generate, -1 for unlimited datatype: int} includeoriginals: { value: 0 description: If set, include the base structures. By default, only the scaffolds are included datatype: boolean} hashcode: { value: E_HASHY description: The hashcode property to be used to check structure identity datatype: string constraints: property} nodenameproperty: { value: E_HASHY description: Instance values of this property are stored as node names. datatype: string constraints: property} auxproperties: { value: {} description: Instance data of these properties is appended to the right of the SMILES data in the nodes datatype: string constraints: propertylist} |
Tcl script | atomchange bondchange atom bond | f_scaffold_tree.xpd | ||||
| F_TREE_DATA_GIF | diskfile (switchable between string blob diskfile url) |
Rendering of tree-style property data (must be of property datatype "datatree") as a GIF/PNG image using a modified Reingold-Tilford tree layout algorithm. | property: { value: F_SCAFFOLD_TREE description: Property to read rendered data from datatype: string constraints: property} treeindex: { value: 0 datatype: string} maxlevel: { value: -1 datatype: int} boxwidth: { value: 100 datatype: int} boxheight: { value: 100 datatype: int} treedistance: { value: 10 description: Minimum horizontal distance between boxes on a level which do not have the same parent datatype: int} siblingdistance: { value: 5 description: Minimum horizontal distance between boxes on a level which do have the same parent datatype: int} leveldistance: { value: 25 description: Distance between lower box Y of parent level and upper box Y of child level datatype: int} border: { value: 5 description: Unused pixels around tree datatype: int} decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean} showname: { value: 0 description: If set, include the node name in rendering datatype: boolean} showcount: { value: 0 description: If set, include non-negative count node fields in rendering datatype: boolean} interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean} alignstructures: { value: 1 description: If structures are rendered, align them hierarchically datatype: boolean} excluderoot: { value: 0 description: If set, do not render root node datatype: boolean} framewidth: { value: 0 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} linecolor: { value: red datatype: color} boxframecolor: { value: blue datatype: color} boxbgcolor: { value: grey90 datatype: color} format: { value: png enumeration: gif:png,png24:png8 datatype: string} font: { value: arialn datatype: string} fontsize: { value: 8.0 datatype: double} filename: { value: {} description: Output file name, if data type is diskfile. If empty, generate /tmp file datatype: diskfile constraints: writeable} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} |
Compiled C module | atomchange bondchange atom bond | mod_f_tree_data_gif.so | ||||
| F_VECTOR_SUM | intvector | property: { value: E_SCREEN datatype: string constraints: property} filter: { value: all datatype: string} |
Compiled C module | atomchange bondchange atom bond | mod_f_vector_sum.so | |||||
| G_AROMATIC | short | Group aromaticity status, indicating whether none, some or all atoms in the group are aromatic. | no,none:some,partially:full,all |
Compiled C module | B_ISAROMATIC B_TYPE | atomchange bondchange groupchange atom bond ring group | mod_g_aromatic.so | |||
| G_ATOMS | intvector | Atoms in each group, extracted as labels from the internal group object. Group objects which are not atoms are skipped. | Compiled C module | G_TYPE A_LABEL | atomchange bondchange groupchange atom bond group | mod_g_atoms.so | ||||
| G_AUTODOCK4_BRANCH | compound | Autodock 4 torsion branch data. Used by the Autodock PDBQT file I/O module. This property is also computable from general geometric principles. | level int linkatom1 int linkatom2 int |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT B_ROTATABILITY A_AUTODOCK4_TYPE | atomchange bondchange groupchange merge atom bond ring group | mod_g_autodock4_branch.so | |||
| G_BGCOLOR | color | If set to a real color, use it is as background rendered square behind the group atoms | never | |||||||
| G_BONDS | intvector | Labels of bonds linking atoms within the group, or explicit group bond set, if the group has bond elements. Impplicit bonds are the same as containment bonds in MDL nomenclature | filters: { value: {} description: Set of filters the returned bonds need to pass datatype: string constraints: filterlist}
|
Tcl script | B_LABEL | atomchange bondchange atom bond group | ||||
| G_CONSTRAINT | compound | Constraints for 3D searching, mirroring the MDL 3D query standards | none:point_distance,distance:point_angle,angle:point_torsion,torsion:centroid:sphere:linepoint_abs,linepoint_absolute:linepoint_rel,linepoint_relative:plane:line:point_line_distance:point_plane_distance:line_line_angle:plane_plane_angle:linepoint_vector:line_from_plane:plane_from_line |
type int range floatpair name string color string comment string flag boolean alist intvector |
never | |||||
| G_ELEMENT_COUNT | shortvector | Count of element types of atoms of group | ? short h short he short li short be short b short c short n short o short f short ne short na short mg short al short si short p short s short cl short ar short k short ca short sc short ti short v short cr short mn short fe short co short ni short cu short zn short ga short ge short as short se short br short kr short rb short sr short y short zr short nb short mo short tc short ru short rh short pd short ag short cd short in short sn short sb short te short i short xe short cs short ba short la short ce short pr short nd short pm short sm short eu short gd short tb short dy short ho short er short tm short yb short lu short hf short ta short w short re short os short ir short pt short au short hg short tl short pb short bi short po short at short rn short fr short ra short ac short th short pa short u short np short pu short am short cm short bk short cf short es short fm short md short no short lr short rf short db short sg short bh short hs short mt short ds short |
Compiled C module | A_ELEMENT A_TYPE | atomchange groupchange merge hadd group | mod_g_element_count.so | |||
| G_FG_COUNT | shortvector | Count of functional groups in group | ^cf:cx:ccdb:cctb |
groupindex: { value: -1 datatype: int} add_h_on_c: { value: 0 datatype: boolean} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange groupchange group | mod_g_fg_count.so | ||
| G_FORMAL_CHARGE | short | Sum of the formal atom charges in the group | Compiled C module | A_TYPE A_FORMAL_CHARGE | atomchange groupchange atom group | mod_g_formal_charge.so | ||||
| G_FORMULA | string | Elemental formula of the group | usecharges: { value: 0 datatype: boolean} format: { value: ascii enumeration: ascii:html datatype: int} useimplicith: { value: 0 datatype: boolean} usequeryatoms: { value: 0 datatype: boolean} |
Compiled C module | G_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_QUERY A_ISOTOPE A_FORMAL_CHARGE | atomchange groupchange atom group | mod_g_formula.so | |||
| G_HACCEPTOR_COUNT | int | Number hydrogen acceptors in group | Tcl script | A_HYDROGEN_BONDING | atomchange bondchange groupchange group | g_hacceptor_count.xpd | ||||
| G_HASHGROUP_COUNT | intvector | Group-oriented population of basic atom hash groups | Compiled C module | A_EXTENDED_GROUPHASH A_GROUP_NUMBER | atomchange bondchange groupchange merge hadd group | mod_g_hashgroup_count.so | ||||
| G_HASHY | uint64 | Perturbed group hashcode | usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string}
|
Compiled C module | atomchange bondchange groupchange hadd group | mod_g_hashy.so | ||||
| G_HDONORS_COUNT | int | Number of hydrogen donors in group | Tcl script | A_HYDROGEN_BONDING | atomchange bondchange groupchange group | g_hdonor_count.xpd | ||||
| G_LABEL | int | Arbitrary group label | (builtin) | never | ||||||
| G_MOL_NUMBER | short | Number of molecule (A_MOL_NUMBER) group belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge group | |||||
| G_NAME | string | Name of a group | never | |||||||
| G_PI_ELECTRON_COUNT | short | Number of pi electrons in group | Compiled C module | A_FREE_ELECTRONS A_TYPE B_TYPE B_ORDER B_ISAROMATIC | ring | mod_g_pi_electron_count.so | ||||
| G_QUERY | compound | Query attributes for matched substructure groups | ^none:aromatic,fullyaromatic:aliphatic,fullyaromatic:saturated:unsaturated,insaturated:carbocyclic:heterocyclic:monocyclic:polycyclic:mixed,mixedaromaticaliphatic:partiallyaromatic:partiallyaliphatic:topoequivalent,fullytopoequivalent:topodistinct,fullytopodistinct:mixedtopoequivalent:partiallytopoequivalent:partiallytopodistinct |
flags bitset formula formulamatch substituentcount bitset valencecount bitset neighborcount bitset hydrogencount bitset heterosubstituentcount bitset ringbondcount bitset pielectroncount bitset query querytree alphaformula formulamatch topodistance bitset |
atomchange bondchange atom bond | |||||
| G_RING_COUNT | int | Number of ESSR rings intersecting with group atoms | Tcl script | R_TYPE | bondchange groupchange ring group | g_ring_count.xpd | ||||
| G_SGROUP | compound | MDL SGroup Data | none,non:superatom,sup:multigroup,mul:sru:monomer,mon:mer:copolymer,cop:crosslink,cro:modification,mod:graft,gra:component,com:mixture,mix:formulation,for:datagroup,dat:anypolymer,any:generic,gen:stereo,ste:query,que:match,mat:fgroup,fg none:alt:ran:blo none:hh:ht:eu {} {} {} {} {} F:N:T |
type int subtype int connectivity int label int text string bracket1 xyvector bracket2 xyvector name string fieldtype int units string data stringvector coords floatpair class string minmultiplier int maxmultiplier int |
Compiled C module | never | mod_g_sgroup.so | |||
| G_SIZE | int | Size of groups, measured in number of objects in each group. There is no discrimination between atoms, bonds or groups as objects in the count. | Compiled C module | groupchange group | mod_g_size.so | |||||
| G_STANDARD_GROUP_NAME | string | Detection of functional groups and abbreviated strings | groupsubstructures: { value: {C(=O)[OH] COOH} {[NH2] NH2} {N([CH3])[CH3] NMe2} {N([CH2][CH3])[CH2][CH3] NEt2} {C(=O)O[CH2][CH3] COOEt} {C(=O)O[CH3] COOMe} {N(=O)O NO2} {S(=O)(=O)[OH] SO3H} {S(=O)(=O)O[Na] SO3Na} {O[CH2][CH3] OEt} {[CH]=O CHO} {O[CH2][CH2][CH3] OPr} {O[CH]([CH3])[CH3] OiPr} {[OH] OH} {C#N CN} {[Si]([CH3])([CH3])[CH3] TMS} datatype: string}
|
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange groupchange hadd ring group | g_standard_group_name.xpd | |||
| G_SURFACEINFO | compound | Data on surface sections, as read from files in the the IFF/RIFF/VEGA file formats | {} {} dotted:mesh:solid {} {} ^visible:alpha |
id int name string type int alpha int dotsize int flags bitset |
never | |||||
| G_TITRATION | byte | Create an atom group set which describes standard functional groups as protonable or deprotonable. | deprotonation=-1:neutral=0:protonation=1 |
deprotfgs: { value: [H]O[S,P,Se,Te,As,Sb,Cl,Br,I](=O) [H]OC=O [H]O[C;a] [H]C(C=O)C=O [H]OC=CC=O description: Standard SMARTS substructures of groups which can be deprotonated datatype: string} protfgs: { value: [N;A;+0;!$(N-C=O);!$(N=O)] description: Standard SMARTS substructures of groups which can be protonated datatype: string} |
Tcl script | atomchange bondchange groupchange merge hadd atom bond group | g_titration.xpd | |||
| G_TOPO_EQUIVALENCE | short | Group topological equivalence status, indicating whether none, some or all atoms in the group are in the same topological class, as defined by an atom hashcode | no,none:some,partially:full,all |
topoproperty: { value: A_ISOTOPE_STEREO_HASH description: Atom property used to determined topological atom class datatype: string constraints: property}
|
Compiled C module | A_ISOTOPE_STEREO_HASH | atomchange bondchange stereochange groupchange atom bond ring group | mod_g_topo_equivalence.so | ||
| G_TYPE | int | Group classifiction, following the MDL Molfile convention. Computation is performed indirectly via G_SGROUP, which contains the same information has first element in compound datastructure. |
none,non:superatom,sup:multigroup,mul:sru:monomer,mon:mer:copolymer,cop:crosslink,cro:modification,mod:graft,gra:component,com:mixture,mix:formulation,for:datagroup,dat:anypolymer,any:generic,gen:stereo,ste:query,que:match,mat:fgroup,fg |
never | ||||||
| G_XBONDS | intvector | Labels of bonds linking group atoms to non-group atoms (crossing bonds in MDL nomenclature) | filters: { value: {} description: Filter set the returned bonds must pass datatype: string constraints: filterlist}
|
Tcl script | B_LABEL | atomchange bondchange groupchange group | ||||
| G_XYEXTENT | floatvector | Bounding box of group elements, computed from A_XY | Compiled C module | A_XY A_FLAGS | groupchange merge group | mod_g_xyextent.so | ||||
| G_XYZ | floatvector | Group 3D coordinates (may be planes, vectors) | (builtin) | A_XYZ | atomchange bondchange merge 3drelative 3dabsolute group | |||||
| H_IDENT | string | Free-form ID of the hierarchy | Tcl script | never | h_ident.xpd | |||||
| H_LEVEL | short | Level of the hierarchy object within a hierarchy. The hierarchy root is level 0. | Compiled C module | never | mod_h_level.so | |||||
| H_NAME | string | Free-form name of the hierarchy | never | |||||||
| I_ID | compound | Bioitem (biologics component) item class (class identifier and element number or index into superatom or fragment table) | undefined=-1:none:element,atom:fragment,biofragment:superatom |
class int fragmentid int |
never | |||||
| I_LABEL | int | Bioitem (biologics component) label | Compiled C module | never | mod_i_label.so | |||||
| I_SYMBOL | shortstring | Bioitem (biologics component) item symbol (i.e. amino acid abbreviation, superatom symbol, element symbol, etc.) | Compiled C module | never | mod_i_symbol.so | |||||
| J_LABEL | int | Biolink (biologics component join) label | Compiled C module | never | mod_j_label.so | |||||
| J_LINK | compound | Biolink (biologics component join) item link data | undefined=-1:none:simple:amide:disulfide:ester:ether |
bondclass int label1 int label2 int bondtype int order short |
never | |||||
| K_LABEL | int | Arbitrary label for bond angle objects | (builtin) | never | ||||||
| K_MOL_NUMBER | short | Number of molecule (A_MOL_NUMBER) bondangle object belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge bondangle | |||||
| L_1DPATTERN_SVG_IMAGE | diskfile (switchable between string blob diskfile url xmlstring) |
SVG depiction of the 1D patterns applicable to the currently loaded transform | boxwidth: { value: 250 datatype: int} boxheight: { value: 250 datatype: int} |
Tcl script | E_SVG_IMAGE | never | l_1dpattern_svg_image.xpd | |||
| L_2DPATTERN_SVG_IMAGE | diskfile (switchable between string blob diskfile url xmlstring) |
SVG depiction of the 2D patterns applicable to the currently loaded transform | boxwidth: { value: 250 datatype: int} boxheight: { value: 250 datatype: int} |
Tcl script | E_SVG_IMAGE | never | l_2dpattern_svg_image.xpd | |||
| L_CODE_COVERAGE | intpairvector | Accumulated bytecode execution coverage, as a per-line (accumulated across libraries) integer pair vector. First element value 0: Not executed, 2: executed, 1: partially executed, i.e. there are multiple bytecodes generated from a single source line and some, but not all of them were executed. The second element holds the source file index. | Compiled C module | never | mod_l_code_coverage.so | |||||
| L_NEW1DPATTERN_SVG_IMAGE | diskfile (switchable between string blob diskfile url xmlstring) |
SVG depiction of the NEW1D patterns applicable to the currently loaded transform | boxwidth: { value: 250 datatype: int} boxheight: { value: 250 datatype: int} |
Tcl script | E_SVG_IMAGE | never | l_new1dpattern_svg_image.xpd | |||
| M_3DSIZE | floatvector | Various 3D size measures for molecules, computed from property A_XYZ and the geometrical molecule center in M_CENTER. The property is a float vector, fields: index 0: diameter (maximum 3D atom distance in molecule) index 1: radius (maximum atom distance from molecule center in smae molecule) index 2: radius of gyration (squared atom distances from center divided by number of atoms in molecule) index 3: separation (sum of intramolecular atom distances divided by number of atoms in molecule) |
diameter float radius float radiusofgyration float separation float |
Compiled C module | A_XYZ M_CENTER A_MOL_LABEL | atomchange bondchange stereochange 3drelative mol atom bond | mod_m_3dsize.so | |||
| M_AMINO_ACID_SEQUENCE | string | Amino acid sequence in 1- or 3-letter letter code. Can be computed from molecular structure with standard amino acid set. | nomenclature: { value: a description: Whether to use single-letter amino acid codes (a) or 3-letter codes (aaa) enumeration: a,letter1=1:aaa,letter3=3 datatype: int} encodeterminals: { value: 0 description: If set, include H- and -OH terminal encodings datatype: boolean} encodebridges: { value: 0 description: If set, encode SS disulfide bridges in (x) format datatype: boolean} separator: { value: {} description: Separator character between AA encodings (can be empty) datatype: string} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange mol atom bond | mod_m_amino_acid_sequence.so | |||
| M_AMOUNT | double | atomchange bondchange mol atom bond | ||||||||
| M_ASCII_IMAGE | string (switchable between string unicode) |
ASCII (or Unicode) rendering of a chemical structure. Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the alst line. |
width: { value: 40 minvalue: 25 maxvalue: 256 datatype: int} height: { value: 30 minvalue: 25 maxvalue: 256 datatype: int} showcharge: { value: 0 datatype: boolean} useunicode: { value: 1 datatype: boolean} bonds: { value: 10 minvalue: 3 maxvalue: 25 datatype: double} usecolor: { value: 0 datatype: boolean} usefontstyle: { value: 0 datatype: boolean} showradical: { value: 0 datatype: boolean} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,exten ded,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,y es datatype: int} csymbol: { value: all enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: white datatype: color} highlightcolor: { value: red datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} frame: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} crop: { value: left|right|top|bottom enumeration: ^none:left:right:top:bottom datatype: bitset} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} usealtcharset: { value: 0 datatype: boolean} leadnewline: { value: 0 datatype: boolean} tailnewline: { value: 0 datatype: boolean} framecolor: { value: black datatype: color} hcolor: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} unicodeforringbonds: { value: macrocycles enumeration: no,never:macrocycles,largerings:yes,always datatype: int} badunicodechars: { value: 0x2571 0x2572 0x2573 0x2afd description: Codes of Unicode chars which should not be used, for example because they are missing in the terminal font comment: 0x2afd: double slash, 0x244a: double backslash, 0x2500: horizontal single line, 0x2501: horizontal bold single line, 0x2502: vertical single line, 0x2504: vertical bold single line, 0x2504: horizontal dotted line, 0x2506: vertical dotted line, 0x250c: corner lower right, 0x2510: corner lower left, 0x2514: corner upper right, 0x2518: corner upper left, 0x2550: horizontal double line, 0x2551: vertical double line, 0x2554: double corner lower right, 0x2557: double corner lower left, 0x255A: double corner upper right, 0x255D: double corner upper left, 0x2571: diagonal lower left to upper right, 0x2572: diagonal upper left to lower right, 0x2573: cross, 0x2630: horizontal triple line datatype: string constraints: list} lineprefix: { value: {} description: Characters to add to the 2nd and later lines, for example to compensate for database table formatting datatype: string} |
Compiled C module | A_TYPE A_ELEMENT A_FLAGS B_FLAGS A_QUERY B_QUERY A_FORMAL_CHARGE A_RESIDUE A_SYMBOL A_XSYMBOL A_XY A_HSPECIAL A_CSPECIAL A_COLOR A_ANNOTATION B_TYPE B_LABEL B_ORDER B_COLOR R_TYPE | atomchange bondchange stereochange merge mol atom bond | mod_m_ascii_image.so | |||
| M_ATOM_RANGE | intpair | Ids of first and last atom of molecule | (builtin) | M_STANDARD_ATOM_COUNT | atomchange bondchange merge shuffle hadd | |||||
| M_BENZENOID_INDEX | double | The count of benzene ESSSR rings divided by the total number of aromatic ESSSR rings. Zero in case there are no aromatic rings. | Roughley and Jordan, J. Med. Chem. 2011, 54, 3451-3479 | Compiled C module | R_TYPE R_AROMATIC R_HETEROATOM_COUNT R_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_benzenoid_index.so | |||
| M_BP | floatpair | Boiling point in Kelvin, with optional temperature range | value float range float |
pressure: { value: 760 datatype: double} pressureunit: { value: Torr datatype: string} |
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE | atomchange bondchange mol | ||||
| M_CARBON_COUNT | int | Number of carbon atoms in fragment - the same as M_ELEMENT_COUNT(6) | Compiled C module | A_TYPE A_ELEMENT A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_carbon_count.so | ||||
| M_CAS | string | Chemical Abstracts registry number for ensemble | useresolver: { value: 1 datatype: boolean} usepubchem: { value: 1 datatype: boolean} uselookchem: { value: 0 datatype: boolean} |
Tcl script | M_HASHISY M_CID | atomchange bondchange stereochange groupchange merge 3drelative 3dabsolute shuffle hadd dup mol atom bond ring sigma pi group reaction dataset file table network vertex edge surface ringsystem bondangle torsion hierarchy biological bioitem biolink 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | m_cas.xpd | |||
| M_CENTER | compound | Box, geometric and mass-weighted molecule centers | box floatvector geo floatvector mass floatvector |
coordinateproperty: { value: A_XYZ datatype: string} useh: { value: 1 datatype: string} |
(builtin) | E_XYZEXTENT A_WEIGHT A_XYZ A_MOL_NUMBER | atomchange bondchange 3drelative 3dabsolute mol | |||
| M_CHARACTER | byte | Classification of 3D molecular structure (minimum,transition,etc) | unknown,u,?:minimum,n,m,nu,mu:transition,t:fixed,f,x |
A_XYZ | atomchange bondchange stereochange 3drelative hadd mol | |||||
| M_CHARGE | short | Sum of charges in the molecules | (builtin) | A_FORMAL_CHARGE A_MOL_NUMBER | atomchange mol | |||||
| M_CHARGED_ATOM_COUNT | int | Number of atoms in the molecule which are formally charged and not direclty adjacent to an atom of opposite formal charge (such as in ionic nitro groups). | Compiled C module | A_TYPE A_FORMAL_CHARGE B_TYPE A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_charged_atom_count.so | ||||
| M_CHARGED_GROUP_COUNTS | intpair | Counts of groups charged positively or negatively under neutral conditions in protic solvents. This is a simple guestimate from A_HYDROGEN_BONDING, using acidic and basic groups as starting points and combining close centers (i.e. a P(=O)(OH)2 group with 2 acidic protons only gets a single positive charge count). | positive int negative int |
Compiled C module | A_TYPE A_ELEMENT A_HYDROGEN_BONDING B_TYPE A_ARORING_COUNT A_UNSATURATION A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_charged_group_counts.so | |||
| M_CHIRALITY | byte | Stereo status or potential of molecule | none:meso:unspecified:chiral:contradictory |
Compiled C module | A_LABEL A_STEREOGENIC A_MOL_NUMBER E_NMOLECULES A_HASH A_ALLENE A_HASH_STEREO B_HASH_STEREO A_LABEL_STEREO | atomchange bondchange stereochange 3drelative mol atom bond | mod_m_chirality.so | |||
| M_CID | int | PubChem CID structure identifier | Tcl script | E_SMILES E_STDINCHIKEY | atomchange bondchange stereochange merge hadd | m_cid.xpd | ||||
| M_COLOR | color | Background color to use in plots | never | |||||||
| M_COMPLEXITY | float | Molecular complexity according to modified Bertz/Hendrickson algorithm | W. D. Ihlenfeldt, Ph.D. Thesis, TU Munich 1991 | Compiled C module | A_ELEMENT B_TYPE B_ORDER B_HASH | atomchange bondchange merge mol | mod_m_complexity.so | |||
| M_CONVENTION | string | Description of structure encoding convention. This is for example used in CML files, where you can legally encode your data in any way you please, without regard to capabilities of software inputting that data again. | never | |||||||
| M_DENSITY | float | Density of molecule at room temperature in kg/L | Tcl script | A_ELEMENT A_ISOTOPE | atomchange bondchange mol | m_density.xpd | ||||
| M_ELEMENT_COUNT | shortvector | Count of element types of atoms of molecules | ? short h short he short li short be short b short c short n short o short f short ne short na short mg short al short si short p short s short cl short ar short k short ca short sc short ti short v short cr short mn short fe short co short ni short cu short zn short ga short ge short as short se short br short kr short rb short sr short y short zr short nb short mo short tc short ru short rh short pd short ag short cd short in short sn short sb short te short i short xe short cs short ba short la short ce short pr short nd short pm short sm short eu short gd short tb short dy short ho short er short tm short yb short lu short hf short ta short w short re short os short ir short pt short au short hg short tl short pb short bi short po short at short rn short fr short ra short ac short th short pa short u short np short pu short am short cm short bk short cf short es short fm short md short no short lr short rf short db short sg short bh short hs short mt short ds short |
(builtin) | A_MOL_NUMBER A_ELEMENT A_TYPE | atomchange bondchange merge shuffle hadd mol | ||||
| M_EMF_IMAGE | diskfile (switchable between blob diskfile url) |
A 2D-plot of the structure as a WMF or EMF file | width: { value: 180 datatype: int} height: { value: 180 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: smiles datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.4 datatype: double} colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} symbolfontsize: { value: -1 datatype: double} annotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} usehatch: { value: 0 datatype: boolean} format: { value: wmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int} frame: { value: 1 datatype: int} showchirality: { value: none enumeration: none:simple:extended datatype: int} linespacing: { value: 2.0 datatype: double} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 6 datatype: int} wiggleamplitude: { value: 1.5 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} crop: { value: -1 datatype: int} showstereogroups: { value: 0 datatype: int} font: { value: Arial datatype: string} usesubscripts: { value: 1 datatype: boolean} usereactionscaling: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION | atomchange bondchange stereochange merge hadd mol | mod_m_emf_image.so | |||
| M_EXACT_MASS | floatpair | Exact mass of most abundant compound isotope combination, assuming natural abundance | weight double abundance double |
useimplicith: { value: 1 description: Whether to include implicit hydrogens datatype: boolean}
|
Compiled C module | A_TYPE A_ELEMENT A_ISOTOPE | atomchange merge mol atom | mod_m_exact_mass.so | ||
| M_FG_COUNT | shortvector | Count of functional groups in molecule | ^cf:cx:ccdb:cctb |
groupindex: { value: -1 datatype: int} add_h_on_c: { value: 0 datatype: boolean} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange mol | mod_m_fg_count.so | ||
| M_FORMULA | string | Molecular formula of molecules | usecharges: { value: 0 datatype: string} format: { value: ascii datatype: string} useimplicith: { value: 1 datatype: string} usequeryatoms: { value: 0 datatype: string} |
(builtin) | A_ISOTOPE A_MOL_NUMBER | atomchange merge mol | ||||
| M_FSP3 | double | Carbon flatness score - the ratio of SP3 hybridized carbon atoms to total carbon atom count | Lovering, F. et al., J.Med.Chem. 2009, 52, 6752-6756 | Compiled C module | A_TYPE A_ELEMENT A_HYBRIDIZATION A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_fsp3.so | |||
| M_GIF | diskfile (switchable between string blob diskfile url) |
A 2D-plot of the structure as a GIF or PNG file | width: { value: 180 datatype: int} height: { value: 180 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black description: A color name, the magic value "atomsplit", or a bond color property. In case of an empty string, use B_COLOR comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} footer: { value: {} datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: string} interlace: { value: 1 datatype: boolean} commenttype: { value: property enumeration: none:text:property,prop datatype: string} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} highlightbonds2: { value: {} datatype: intvector} highlightatoms: { value: {} datatype: intvector} explicithydrogens: { value: {} datatype: intvector} linkatoms: { value: {} description: Atom pairs between which a dotted line should be drawn datatype: intpairvector} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} crop: { value: -1 datatype: int} wedges: { value: 1 datatype: boolean} saverendercoordinates: { value: 0 description: If set, try to set A_RENDER_XY to indicate the atom image coordinates datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} format: { value: gif datatype: string} markcolor: { value: blue datatype: diskfile} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} font: { value: arialn datatype: string} symbolfontsize: { value: -1 datatype: int} annotationfontsize: { value: -1 datatype: double} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} showisotope: { value: 1 datatype: boolean} isotopemapping: { value: none datatype: string} showstereoh: { value: 1 datatype: boolean} suppressedmols: { value: {} datatype: intvector} linewidth: { value: 1.4 datatype: double} showempty: { value: 0 datatype: boolean} voronoicolorproperty: { value: {} datatype: color constraints: emptycolor} voronoifilter: { value: {} datatype: string constraints: filtername} showmapping: { value: 0 datatype: boolean} showstereogroups: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} showchirality: { value: none enumeration: none:simple:extended datatype: int} frame: { value: 0 datatype: int} linespacing: { value: 2.0 datatype: double} headerfontsize: { value: -1 datatype: int} footerfontsize: { value: -1 datatype: int} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 6 datatype: int} wiggleamplitude: { value: 2.0 datatype: double} fixiepngsize: { value: 1 datatype: boolean} rawcoordinates: { value: 0 datatype: boolean} checkintersection: { value: 0 datatype: boolean} usesubscripts: { value: 1 datatype: boolean} usereactionscaling: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} usegrouplabels: { value: 0 datatype: boolean} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION | atomchange bondchange stereochange merge hadd mol | mod_m_gif.so | |||
| M_HALIDE_FRACTION | double | Fraction of molecular weight of the fragment contributed by halogen atoms | Compiled C module | A_TYPE A_ELEMENT A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_halide_fraction.so | ||||
| M_HASH | uint64 | Basic molecule hashcode | (builtin) | A_HASHGROUP A_MOL_NUMBER A_HASH | atomchange bondchange | |||||
| M_HASH128 | uint128 | Perturbed molecule hashcode, extended to 128 bits | Compiled C module | A_HASH A_HASHGROUP M_HASHGROUP_COUNT | atomchange bondchange hadd mol | mod_m_hash128.so | ||||
| M_HASHGROUP | index | Hash group id index for basic molecule hash code | (builtin) | M_HASH | atomchange bondchange merge | |||||
| M_HASHGROUP128 | index | Hash group id index for perturbated molecule hash code, based on M_HASH128 | Compiled C module | M_HASH128 | atomchange bondchange merge mol | mod_m_hashgroup128.so | ||||
| M_HASHGROUP_COUNT | intvector | Molecule-oriented population of basic atom hash groups | (builtin) | A_HASH | atomchange bondchange merge hadd mol | |||||
| M_HASHGROUP_Y | index | Hash group id index for perturbated molecule hash code | (builtin) | M_HASHY | atomchange bondchange merge | |||||
| M_HASHISY | uint64 | Isotopic stereospecific perturbed molecule hashcode | (builtin) | A_ISOTOPE_STEREO_HASHGROUP A_ISOTOPE_STEREO_HASH A_MOL_NUMBER | atomchange bondchange stereochange merge hadd | |||||
| M_HASHIY | uint64 | Perturbed molecule hashcode with isotopes | (builtin) | A_ISOTOPE_HASHGROUP A_ISOTOPE_HASH M_ISOTOPE_HASHGROUP_COUNT | atomchange bondchange merge hadd | |||||
| M_HASHS | uint64 | Stereospecific basic molecule hashcode | (builtin) | A_STEREO_HASHGROUP A_STEREO_HASH A_MOL_NUMBER | atomchange bondchange stereochange merge hadd | |||||
| M_HASHSY | uint64 | Perturbed stereospecific molecule hashcode | useisotope: { value: 0 datatype: string}
|
(builtin) | A_STEREO_HASH A_STEREO_HASHGROUP M_STEREO_HASHGROUP_COUNT | atomchange bondchange hadd | ||||
| M_HASHY | uint64 | Perturbed molecule hashcode | useisotope: { value: 0 datatype: string}
|
(builtin) | A_HASH A_HASHGROUP M_HASHGROUP_COUNT | atomchange bondchange hadd | ||||
| M_HEAVY_ATOM_COUNT | int | Number of non-hydrogen atoms in the molecule | Compiled C module | A_MOL_NUMBER A_ELEMENT A_TYPE | atomchange bondchange mol atom bond | mod_m_heavy_atom_count.so | ||||
| M_HETEROATOM_CARBON_RATIO | double | Number of hetero atoms devided by number of carbon atoms | Compiled C module | A_TYPE A_ELEMENT A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_heteroatom_carbon_ratio.so | ||||
| M_HETEROATOM_COUNT | int | Number of hetero (not C or H) atoms in the molecules/fragments | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange mol atom bond | mod_m_heteroatom_count.so | ||||
| M_HYDROGEN_COMPLETE | boolean | Boolean flag indicating whether there are no open hydrogen sites | Compiled C module | A_HYDROGENS_NEEDED A_MOL_NUMBER | atomchange bondchange hadd mol atom bond | mod_m_hydrogen_complete.so | ||||
| M_IDENT | string | Freeform molecule ID | Tcl script | never | m_ident.xpd | |||||
| M_INCHI | string | Fragment-level InChI string | options: { value: DONOTADDH FIXEDH RECMET NOWARNINGS description: Set of option words as used in the original NIST software comment: Supported option words: NOLABELS SAVEOPT AUXNONE MISMATCHISERROR OUTERRINCHI Key XHash1 XHash2 SNON NEWPSOFF DONOTADDH LooseTSACheck SREL ChiralFlagOFF SUU SLUUD FIXEDH RECMET KET 15T PT_22_00 PT_16_00 PT_06_00 PT_39_00 LargeMolecules Polymers Polymers105 NPZz NoWarnings MergeHash NoInChI FoldCRU FoldSRU FrameShift: NoFrameShift NoEdits SATZZ FNUDOFF FixSp3bugOFF FBOFF FB2OFF SPXYZOFF SASXYZOFF Polymers105+. Record processing options INPAUX START: END: RECORD: have no effect. datatype: string constraints: list} fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean} stereoperception: { value: 1 description: If set, perceive stereochemistry, if no, use what is presently set on the structure datatype: boolean} stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int} autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean} prefix: { value: 1 description: If set, include InChI= prefix in output datatype: boolean} stripstereolayer: { value: 0 datatype: boolean} stripisotopelayer: { value: 0 datatype: boolean} stripfixedhlayer: { value: 0 datatype: boolean} stripreconnectlayer: { value: 0 datatype: boolean} stripchargelayer: { value: 0 datatype: boolean} |
Compiled C module | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange hadd mol atom bond | mod_m_inchi.so | |||
| M_INCHI_AUXINFO | string | InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting M_INCHI | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange hadd mol atom bond | ||||||
| M_ISOTOPE_COUNT | int | Number of isotopically labelled atoms in molecule | Compiled C module | A_TYPE A_ISOTOPE A_MOL_NUMBER | atomchange merge mol atom bond | mod_m_isotope_count.so | ||||
| M_ISOTOPE_HASH128 | uint128 | Perturbed molecule hashcode, extended to 128 bits, with isotopes | Compiled C module | A_ISOTOPE_HASH A_ISOTOPE_HASHGROUP M_ISOTOPE_HASHGROUP_COUNT | atomchange bondchange hadd mol | mod_m_isotope_hash128.so | ||||
| M_ISOTOPE_HASHGROUP128 | index | Hash group id index for perturbated molecule hash code, based on M_ISOTOPE_HASH128 | Compiled C module | M_ISOTOPE_HASH128 | atomchange bondchange merge mol | mod_m_isotope_hashgroup128.so | ||||
| M_ISOTOPE_HASHGROUP_COUNT | intvector | Molecule-oriented population of isotope atom hash groups | (builtin) | A_ISOTOPE_HASH | atomchange bondchange merge hadd mol | |||||
| M_ISOTOPE_HASHGROUP_Y | index | Hash group id index for perturbed isotopic molecule hash code | (builtin) | M_HASHIY | atomchange bondchange merge hadd | |||||
| M_ISOTOPE_STEREO_HASH128 | uint128 | Perturbed molecule hashcode, extended to 128 bits, with stereochemistry and isotopes | Compiled C module | A_STEREO_HASH A_STEREO_HASHGROUP M_STEREO_HASHGROUP_COUNT | atomchange bondchange hadd mol | mod_m_isotope_stereo_hash128.so | ||||
| M_ISOTOPE_STEREO_HASHGROUP128 | index | Hash group id index for perturbated molecule hash code, based on M_ISOTOPE_STEREO_HASH128 | Compiled C module | M_ISOTOPE_STEREO_HASH128 | atomchange bondchange merge mol | mod_m_isotope_stereo_hashgroup128.so | ||||
| M_ISOTOPE_STEREO_HASHGROUP_COUNT | intvector | Molecule-oriented population of isotope stereo atom hash groups | (builtin) | A_ISOTOPE_STEREO_HASH | atomchange bondchange merge hadd mol | |||||
| M_ISOTOPE_STEREO_HASHGROUP_Y | index | Hash group id index for isotopic stereospecific perturbed molecule hash code | (builtin) | M_HASHISY | atomchange bondchange merge hadd | |||||
| M_ISOTOPE_STEREO_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant molecule isotope stereo hashcode | M_HASHISY E_HASHISY E_ISOTOPE_STEREO_TAUTO_HASH | atomchange bondchange mol | ||||||
| M_ISOTOPE_STEREO_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant molecule isotope stereo hashcode, 128 bit version | M_ISOTOPE_STEREO_HASH128 E_ISOTOPE_STEREO_HASH128 E_ISOTOPE_STEREO_TAUTO_HASH128 | atomchange bondchange mol | ||||||
| M_ISOTOPE_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant molecule hashcode, without stereochemistry but with isotope labelling | M_HASHIY E_HASHIY E_ISOTOPE_TAUTO_HASH | atomchange bondchange mol | ||||||
| M_ISOTOPE_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant molecule isotope hashcode, 128 bit version | M_ISOTOPE_HASH128 E_ISOTOPE_HASH128 E_ISOTOPE_TAUTO_HASH128 | atomchange bondchange mol | ||||||
| M_LABEL | int | Arbitrary molecule label | (builtin) | never | ||||||
| M_LIPINSKI_ACCEPTOR_COUNT | int | Number of hydrogens on N and O atoms - H-bond acceptors according to simple Lipinski definition. For a more refined definition, use property E_NHACCEPTORS. |
Compiled C module | A_TYPE A_ELEMENT A_MOL_NUMBER A_FREE_ELECTRONS | atomchange bondchange mol atom bond | mod_m_lipinski_acceptor_count.so | ||||
| M_LIPINSKI_DONOR_COUNT | int | Number of oxygen and nitrogen atoms according to really simple Lipinski definition. For a more refined definition, use E_NHDONORS. | Compiled C module | A_TYPE A_ELEMENT A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_lipinski_donor_count.so | ||||
| M_MAX_CHAIN_FRAGMENT_SIZE | int | The maximum value of A_CHAIN_LENGTH in the molecule, i.e. the size of the largest fragment of connected non-ring non-hydrogen atoms. | Compiled C module | A_CHAIN_LENGTH A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_max_chain_fragment_size.so | ||||
| M_MAX_CONJUGATED_SYSTEM_SIZE | int | The maximum size of a conjugated system in the fragment according to the Shoichet definition (see literature reference). | J. Med. Chem. 2003, 46, 4477-4486 | Compiled C module | A_CONJUGATED_SYSTEM_SIZE | atomchange bondchange mol atom bond | mod_m_max_conjugated_system_size.so | |||
| M_MAX_LINEAR_CHAIN_FRAGMENT_SIZE | int | The maximum value of A_LINEAR_CHAIN_LENGTH in the molecule, i.e. the size of the largest fragment of connected non-ring non-branching non-hydrogen atoms. | Compiled C module | A_LINEAR_CHAIN_LENGTH A_MOL_NUMBER | atomchange bondchange mol atom bond | mod_m_max_linear_chain_fragment_size.so | ||||
| M_MESO | boolean | Flag indicating that the molecule is mesomeric (i.e. all stereogenic sites are defined, and the enantiomer of the molecule is the same compound (example: R.S. and S.R tartric acid, but not the R.R. or S.S. variants. | Tcl script | A_STEREOGENIC A_HASH_STEREO E_ENANTIOMER | atomchange bondchange stereochange atom bond | m_meso.xpd | ||||
| M_METADATA | dictionary | Dublin Core metadata for structure fragment | never | |||||||
| M_MOLNAME | string | Molecule name(s) | atomchange bondchange | |||||||
| M_MOL_NUMBER | short | Number of molecule | (builtin) | atomchange bondchange merge shuffle mol | ||||||
| M_MONOISOTOPIC_MASS | float | Mass computed with most abundant isotope only, not natural abundance | useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean}
|
Compiled C module | A_ELEMENT A_TYPE A_ISOTOPE | atomchange mol | mod_m_monoisotopic_mass.so | |||
| M_MP | floatpair | Melting Point in Kelvin, with optional range | value float range float |
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE | atomchange bondchange mol | |||||
| M_NAME | string | Free-form molecule name | Tcl script | never | m_name.xpd | |||||
| M_NATOMS | int | Number of atoms in molecule | (builtin) | A_MOL_NUMBER A_TYPE | atomchange bondchange hadd mol | |||||
| M_NBONDS | int | Number of bonds in molecule | (builtin) | B_MOL_NUMBER | bondchange mol | |||||
| M_NCBI_STANDARDIZER_HASH | uint64 | NCBI standardization hashcode (no h, no charges, bond order) | A_ELEMENT B_ORDER B_TYPE A_TYPE | atomchange bondchange merge | ||||||
| M_NCOLLISIONS | int | Number of atomic close contacts | Compiled C module | A_XYZ A_ELEMENT A_TYPE | atomchange 3drelative mol | mod_m_ncollisions.so | ||||
| M_NRINGS | int | Number of rings in molecule | Compiled C module | A_MOL_NUMBER R_SIZE M_LABEL | bondchange mol bond ring | mod_m_nrings.so | ||||
| M_ORGANIC | byte | Flag indicating whether molecule is organic (i.e. contains carbon, and is not one of a small set of simple compounds like carbon monoxide, carbon dioxide, a cyanide, etc.). Value: 0: no, 1:yes, -1:undecidable | undefined=-1:inorganic=0:organic=1 |
Compiled C module | A_TYPE A_ELEMENT A_MOL_NUMBER B_TYPE | atomchange bondchange mol | mod_m_organic.so | |||
| M_PMI | floatmatrix | Principial moments of inertia, computed on A_XYZ or a custom coordinate property | useh: { value: 1 datatype: boolean} coordinateproperty: { value: A_XYZ datatype: string constraints: property} |
Compiled C module | A_XYZ A_TYPE A_WEIGHT A_MOL_NUMBER A_ELEMENT | atomchange 3drelative hadd mol atom | mod_m_pmi.so | |||
| M_POINTGROUP | shortstring | Point group of molecule. Read for example from SHARC files. | atomchange bondchange stereochange 3drelative hadd mol | |||||||
| M_RACEMIC_STEREO_HASH | uint64 | Molecule hashcodes for racemic mixtures. These are identical to the minimum molecule stereo hashcodes of the present structure, or its enantiomer. For example, the racemic stereo hashcode for both L-alanine and D-alanine input structures (with known stereochemistry) is, by chance, that of L-alanine, and not that of DL-alanine (with unknown stereochemistry) | Compiled C module | A_STEREO_HASH M_HASHSY | atomchange bondchange stereochange mol | mod_m_racemic_stereo_hash.so | ||||
| M_RACEMIC_STEREO_HASH_GROUP | index | Group memberships of the racemic molecule stereo hash codes | Compiled C module | M_RACEMIC_STEREO_HASH | atomchange bondchange stereochange mol | mod_m_racemic_stereo_hash_group.so | ||||
| M_RADIALCODE | floatvector | Gasteiger radial distribution function structure encoding | B: { value: 400 datatype: int} rmax: { value: 6.4 datatype: double} codelen: { value: 128 datatype: int} normalize: { value: 0 datatype: boolean} |
Compiled C module | A_TYPE A_ELEMENT A_XYZ | atomchange bondchange 3drelative mol | mod_m_radialcode.so | |||
| M_REACTION_LABEL | int | Section number of reaction component in MDL RXN/RDF files | Tcl script | atomchange bondchange atom bond | ||||||
| M_REACTION_ROLE | int | Role of molecule in reaction. More fine-grained than E_REACTION_ROLE | undef,undefined:reagent,educt,reactant:product:solvent:catalyst:intermediate:impurity:byproduct:agent:waste |
Tcl script | atomchange bondchange atom bond | |||||
| M_RIGID_BOND_COUNT | int | Number of bonds which are not rotatable because they are in a ring, or have multiple bond order. | Compiled C module | B_ROTATABILITY A_MOL_NUMBER | atomchange bondchange hadd mol | mod_m_rigid_bond_count.so | ||||
| M_RINGSYSTEM_COUNT | short | Ringsystem count | Compiled C module | atomchange bondchange mol atom bond | mod_m_ringsystem_count.so | |||||
| M_ROTATABLE_BOND_COUNT | int | Number of bonds which are rotatable and where the rotation has a steric effect | Compiled C module | B_ROTATABILITY | atomchange bondchange hadd mol | mod_m_rotatable_bond_count.so | ||||
| M_SMILES | string | SMILES strings of individual molecules/fragments in an ensemble. | useexplicithcount: { value: 0 datatype: string} generalization: { value: none datatype: string} usehcount: { value: 1 datatype: string} firstatom: { value: -1 datatype: string} lastatom: { value: -1 datatype: string} checkstereo: { value: 1 datatype: string} reuseringlinks: { value: 0 datatype: string} usestereogroup: { value: 0 datatype: string} hideautoh: { value: 0 datatype: string} usestereo: { value: 1 datatype: string} unique: { value: 0 datatype: string} singleringupdownbond: { value: 1 datatype: string} usesuperatom: { value: 0 datatype: string} atomaroproperty: { value: A_ARORING_COUNT datatype: string} useexplicith: { value: 0 datatype: string} queryhatoms: { value: {} datatype: string} usemapping: { value: 1 datatype: string} smarts: { value: 0 datatype: string} usearo: { value: 0 datatype: string} useisotope: { value: 1 datatype: string} useextrabondtypes: { value: 1 datatype: string} usename: { value: 0 description: If set, append M_NAME to the SMILES after a blank datatype: boolean} |
Tcl script | E_SMILES | atomchange bondchange stereochange hadd mol atom bond | m_smiles.xpd | |||
| M_SPAN | int | Largest distance in bonds between any two atoms in molecule | Compiled C module | B_TYPE A_TOPO_DISTANCE | atomchange bondchange hadd mol atom bond | mod_m_span.so | ||||
| M_STANDARD_ATOM_COUNT | int | Number of traditional atoms in molecule | (builtin) | A_MOL_NUMBER A_TYPE | atomchange bondchange hadd mol | |||||
| M_STATE | byte | Molecule state (as used for example in a reaction) | unknown:solid:liquid:gas,gaseous:plasma:oil |
temperature: { value: 298.15 minvalue: 0 datatype: double}
|
Tcl script | M_BP M_MP | atomchange bondchange mol atom bond | m_state.xpd | ||
| M_STDINCHI | string | Standard InChI identifier of molecular fragments in ensemble | options: { value: DONOTADDH description: Set of default option words as defined to standard comment: Many of the option words listed for E_INCHI implicitly switch off standard mode. See INChI lib docs. datatype: string constraints: list} fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean} autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean} stereoperception: { value: 1 datatype: boolean} stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int} prefix: { value: 1 datatype: boolean} stripstereolayer: { value: 0 datatype: boolean} stripisotopelayer: { value: 0 datatype: boolean} stripfixedhlayer: { value: 0 datatype: boolean} stripreconnectlayer: { value: 0 datatype: boolean} stripchargelayer: { value: 0 datatype: boolean} |
Compiled C module | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange hadd atom bond | mod_m_stdinchi.so | |||
| M_STDINCHIKEY | string | Hash of InChI string | prefix: { value: 1 datatype: boolean}
|
Compiled C module | E_STDINCHI | atomchange bondchange stereochange mol atom bond | mod_m_stdinchikey.so | |||
| M_STDINCHI_AUXINFO | string | InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting M_STDINCHI | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange hadd mol atom bond | ||||||
| M_STEREOGENIC | intpair | Flags whether tthe molecule is stereogenic in the atom or bond set | Compiled C module | A_STEREOGENIC B_STEREOGENIC A_MOL_NUMBER | atomchange bondchange stereochange atom bond | mod_m_stereogenic.so | ||||
| M_STEREO_COUNT | intvector | Stereo counts | apossible int adefined int aundefined int bpossible int bdefined int bundefined int |
Compiled C module | A_LABEL_STEREO B_LABEL_STEREO A_STEREOGENIC B_STEREOGENIC A_MOL_LABEL B_MOL_LABEL | atomchange bondchange stereochange mol | mod_m_stereo_count.so | |||
| M_STEREO_HASH128 | uint128 | Perturbed molecule hashcode, extended to 128 bits, with stereochemistry | Compiled C module | A_STEREO_HASH A_STEREO_HASHGROUP M_STEREO_HASHGROUP_COUNT | atomchange bondchange hadd mol | mod_m_stereo_hash128.so | ||||
| M_STEREO_HASHGROUP | index | Hash group id index for stereospecific basic molecule hash code | (builtin) | M_HASHS | atomchange bondchange merge | |||||
| M_STEREO_HASHGROUP128 | index | Hash group id index for perturbated molecule hash code, based on M_STEREO_HASH128 | Compiled C module | M_STEREO_HASH128 | atomchange bondchange merge mol | mod_m_stereo_hashgroup128.so | ||||
| M_STEREO_HASHGROUP_COUNT | intvector | Molecule-oriented population of stereo atom hash groups | (builtin) | A_STEREO_HASH | atomchange bondchange merge hadd mol | |||||
| M_STEREO_HASHGROUP_Y | index | Hash group id index for stereospecific perturbated molecule hash code | (builtin) | M_HASHSY | atomchange bondchange stereochange merge | |||||
| M_STEREO_STATUS | byte | Check stereogenic atoms/bonds vs. stereo definition status, set overall status flag | n,nostereo:u,undefined:p,partial:d,defined |
Compiled C module | A_LABEL_STEREO B_LABEL_STEREO A_STEREOGENIC B_STEREOGENIC A_MOL_NUMBER A_STEREO_GROUP | atomchange bondchange stereochange atom bond | mod_m_stereo_status.so | |||
| M_STEREO_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant molecule stereo hashcode | M_HASHSY E_HASHSY E_STEREO_TAUTO_HASH | atomchange bondchange mol | ||||||
| M_STEREO_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant molecule stereo hashcode, 128 bit version | M_STEREO_HASH128 E_STEREO_HASH128 E_STEREO_TAUTO_HASH128 | atomchange bondchange mol | ||||||
| M_SVG_IMAGE | diskfile (switchable between string blob diskfile url xmlstring) |
Molecule images in SVG vector format | width: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int} height: { value: 180 minvalue: 10 maxvalue: 1000 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 minvalue: 3 maxvalue: 25 datatype: double} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 minvalue: 0 maxvalue: 25 datatype: string} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: string} header: { value: {} datatype: string} footer: { value: {} datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} secondarycolor: { value: #00D000 datatype: color} highlightbonds: { value: {} datatype: intvector} secondarybonds: { value: {} datatype: intvector} highlightatoms: { value: {} datatype: intvector} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.2 datatype: double} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} symbolfontsize: { value: -1 datatype: double} annotationfontsize: { value: -1 datatype: double} bondannotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showlabel: { value: 0 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} frame: { value: 1 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: int} linespacing: { value: 1.8 datatype: double} unit: { value: {} datatype: string} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} circleatoms: { value: {} datatype: intvector} atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 10 datatype: int} wiggleamplitude: { value: 3.0 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} showstereogroups: { value: 0 datatype: boolean} font: { value: Helvetica datatype: string} usewebfont: { value: 0 datatype: boolean} usesubscripts: { value: 1 datatype: boolean} usereactionscaling: { value: 0 datatype: boolean} uselinecaps: { value: 1 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} standalone: { value: 1 datatype: boolean} xmlheader: { value: 1 datatype: boolean} id: { value: {} datatype: string} title: { value: {} datatype: string} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} showempty: { value: 0 datatype: boolean} saverendercoordinates: { value: 0 description: If set, try to set A_RENDER_XY to indicate the atom image coordinates datatype: boolean} suppressedmols: { value: {} datatype: intvector} framecolor: { value: black datatype: color} rawcoordinates: { value: 0 datatype: boolean} atomclick: { value: {} description: Javascript function to call, substitute %i id, %a atom label, %b bond label, %r ring label, %y ringsystem label datatype: string} bondclick: { value: {} datatype: string} ringclick: { value: {} datatype: string} ringsystemclick: { value: {} datatype: string} headerclick: { value: {} datatype: string} footerclick: { value: {} datatype: string} bgclick: { value: {} datatype: string} ringclickcolor: { value: {} datatype: color} ringsystemclickcolor: { value: {} datatype: color} bondclickcolor: { value: {} datatype: color} ringhovercolor: { value: {} datatype: color} ringsystemhovercolor: { value: {} datatype: color} atomhovercolor: { value: {} datatype: color} bondhovercolor: { value: {} datatype: color} activehbonds: { value: 0 description: If set, undrawn bonds to H become active on hovering and are clickable if a bond click action has been set datatype: boolean} style: { value: default description: General plot style. Can either be default, or patran for Patran-style atom and bond annotations enumeration: default:patran datatype: int} maxannotationlength: { value: -1 description: Maximum character length of atom and bond annotations. If an annotation is longer, the plotted value is abbreviated, and a SVG title attribute with the full string added datatype: int} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} extrabondannotationproperty: { value: {} datatype: string constraints: property} |
Compiled C module | A_TYPE A_ELEMENT A_XY A_HSPECIAL A_CSPECIAL B_TYPE B_ORDER A_ANNOTATION B_ANNOTATION B_FLAGS A_FLAGS A_QUERY B_QUERY | atomchange bondchange stereochange merge mol atom bond | mod_m_svg_image.so | |||
| M_TAUTOMER_SCORE | int | Scoring function for tautomers | stereobondmalus: { value: 1 description: If set, give malus to stereogenic bonds (which may appear stereochemically defined, but are not really) datatype: boolean} explain: { value: 0 description: If set, print the score components datatype: boolean} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT B_ISAROMATIC R_TYPE R_AROMATIC A_FORMAL_CHARGE | atomchange bondchange atom bond ring | mod_m_tautomer_score.so | |||
| M_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant molecule hashcode, without stereochemistry and isotope labelling | M_HASHY E_HASHY E_TAUTO_HASH | atomchange bondchange mol atom bond | ||||||
| M_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant molecule hashcode, 128 bit version | M_HASH128 E_HASH128 E_TAUTO_HASH128 | atomchange bondchange mol | ||||||
| M_TITLE | string | Molecule title string | Tcl script | M_NAME | never | m_title.xpd | ||||
| M_TOTAL_WALK_COUNT | double | Total molecule walk count (as defined by Rücker and Rücker) | J. Chem. Inf. Comput. Sci. 2000, 40, 99-106 | excludebonds: { value: {} datatype: intvector} usexatoms: { value: 1 description: If set, use heteroatom vs. carbon for additional differentiation. By default, non-hydrogen atoms are anonymous datatype: boolean} usebo: { value: 1 description: If set, use bond order for additional walks datatype: boolean} |
Compiled C module | M_HEAVY_ATOM_COUNT B_TYPE B_ORDER B_ISAROMATIC A_TYPE A_ELEMENT | atomchange bondchange mol atom bond | mod_m_total_walk_count.so | ||
| M_VDW_VOLUME | double | Van der Waals molecular volume | Zhao, Abraham, Zissimos, J. Org. Chem. 2003, 68, 7368-7373 | Tcl script | A_TYPE A_ELEMENT | atomchange bondchange mol | m_vdw_volume.xpd | |||
| M_WEIGHT | float | Molecular weight of molecules | useimplicith: { value: 1 datatype: string}
|
(builtin) | A_MOL_NUMBER A_WEIGHT | atomchange merge mol | ||||
| M_XYEXTENT | floatvector | 2D display coordinate bounding box | (builtin) | A_XY A_MOL_NUMBER A_FLAGS | atomchange merge hadd | |||||
| M_XYZEXTENT | floatvector | 3D coordinate bounding box for molecules | (builtin) | A_XYZ | atomchange merge 3drelative 3dabsolute hadd | |||||
| N_AUTHOR | compound | Network author data, computation copies these from the internal object author fields | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
Tcl script | never | n_author.xpd | ||||
| N_COMMENT | string | Network object comment in free format | never | |||||||
| N_CONNECTION_COUNT | int | Connection count (number of connection objects in network) | Tcl script | never | n_connection_count.xpd | |||||
| N_CREATOR | string | Network creator information | never | |||||||
| N_DIRECTED | boolean | Flag indicating whether a network is directed | never | |||||||
| N_GIF | diskfile (switchable between string blob diskfile url) |
Network renderer | filename: { value: {} datatype: diskfile constraints: writeable} format: { value: png enumeration: png:png8:gif datatype: string} nodeproperty: { value: {} datatype: string constraints: property} boxwidth: { value: 100 datatype: int} boxheight: { value: 100 datatype: int} boxgap: { value: 50 datatype: int} interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean} framewidth: { value: 0 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} linecolor: { value: red datatype: color} boxframecolor: { value: blue datatype: color} boxbgcolor: { value: grey90 datatype: color} font: { value: arialn datatype: string} fontsize: { value: 8.0 datatype: double} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean} |
Compiled C module | V_XY V_GRAPHICS | atomchange bondchange atom bond vertex edge | mod_n_gif.so | |||
| N_GRAPHICS | compound | Global network graphics | none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon |
type int attributes dictionary |
never | |||||
| N_IDENT | string | Network identifier | Tcl script | never | n_ident.xpd | |||||
| N_IMAGE_URL | url | Network rendering reference URL | atomchange bondchange atom bond | |||||||
| N_LABEL_GRAPHICS | compound | Global network label graphics | none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon |
type int attributes dictionary |
never | |||||
| N_NAME | string | Network name string in free form | never | |||||||
| N_ONTOLOGY_HEADER | dictionary | ODO Ontology header data | never | |||||||
| N_ORGANISM | string | Organism identifier for the network | atomchange bondchange atom bond | |||||||
| N_SIZE | intpair | Counts of vertices(nodes) and connections(edges) | vertices int connections int |
Compiled C module | vertex edge | mod_n_size.so | ||||
| N_TEXT | string | Network text label | never | |||||||
| N_URL | url | Network reference URL | atomchange bondchange atom bond | |||||||
| N_VERTEX_COUNT | string | Vertex count of network | Tcl script | never | n_vertex_count.xpd | |||||
| N_XYEXTENT | floatvector | 2D display coordinate bounding box | xmin double xmax double ymin double ymax double |
Compiled C module | V_XY | atomchange merge hadd | mod_n_xyextent.so | |||
| O_AREA | double | Area of surface patch or other graphical object | O_XYZ | never | ||||||
| O_AREACHARGE | double | Partial charge associatd with a surface patch | O_XYZ O_CHARGE O_AREA | never | ||||||
| O_CHARGE | double | Surface patch partial charge. Read for example from COSMO output files (filex_cosmo). | O_XYZ | never | ||||||
| O_COLOR | colorvector | Color of surface area or point | atomchange bondchange 3drelative atom bond | |||||||
| O_DATA | double | Unclassified property data attached to surface elements | atomchange bondchange 3drelative atom bond | |||||||
| O_ID | int | Surface patch ID | atomchange bondchange 3drelative atom bond | |||||||
| O_IS_POINTVALUE | boolean | indicatesy whether O_DATA surface patch value belongs to O_POINTS (True) or to Triangles in O_TRIANGLE (False) | atomchange bondchange 3drelative atom bond | |||||||
| O_LABEL | int | Arbitrary label for surface elements and other graphics objects | (builtin) | never | ||||||
| O_MOL_NUMBER | int | Number of molecule (A_MOL_NUMBER) surface element belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange 3drelative 3dabsolute | |||||
| O_NORMALVECTOR | floatvector | Normal vectors for surface patches | O_XYZ | atomchange bondchange 3drelative atom bond | ||||||
| O_POINT | xyzvector | like O_XYZ but contains a list of coordinates (vertex points) for bigger surface patches. If required, a surface computation can be performed with the VAMP program. | filename: { value: {} datatype: string constraints: writeable} prgpath: { value: /usr/local/bin/vamp datatype: string} method: { value: AM1 datatype: string} |
Tcl script | A_XYZ | never | o_point.xpd | |||
| O_POINTINDEX | intvector | Indices of surface points (O_POINT) which make up a geometric shape (triangle or triangle patch) | O_XYZ O_TYPE | atomchange bondchange 3drelative atom bond | ||||||
| O_POTENTIAL | double | Surface patch potential potential (of undefined physical nature) | O_XYZ A_XYZ | never | ||||||
| O_TRIANGLE | xyzvector | Triangle point coordinates of surface element | O_XYZ | atomchange bondchange 3drelative atom bond | ||||||
| O_TYPE | byte | Type of surface patch | none:point:triangle:surface |
atomchange bondchange 3drelative atom bond | ||||||
| O_VALUE | doublevector | like O_DATA but contains a vector of values for bigger surface patches | O_POINT | atomchange bondchange 3drelative atom bond | ||||||
| O_XYZ | floatvector | Surface or other graphical object coordinates | A_XYZ | never | ||||||
| P_ATOMS | intvector | Labels of atoms in pi system | Tcl script | A_LABEL | atomchange bondchange stereochange groupchange merge 3drelative 3dabsolute shuffle hadd dup mol atom bond ring sigma pi group reaction dataset file table network vertex edge surface ringsystem bondangle torsion hierarchy biological bioitem biolink 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | p_atoms.xpd | ||||
| P_CLASS | short | Classification of pi systems | none:primary:orthogonal |
pi | ||||||
| P_ELECTRON_COUNT | int | Number of pi electrons in the pi system. | Compiled C module | A_FREE_ELECTRONS B_TYPE B_ORDER | atomchange bondchange atom bond pi | mod_p_electron_count.so | ||||
| P_ELEMENT_COUNT | shortvector | Count of element types of atoms of pi system | ? short h short he short li short be short b short c short n short o short f short ne short na short mg short al short si short p short s short cl short ar short k short ca short sc short ti short v short cr short mn short fe short co short ni short cu short zn short ga short ge short as short se short br short kr short rb short sr short y short zr short nb short mo short tc short ru short rh short pd short ag short cd short in short sn short sb short te short i short xe short cs short ba short la short ce short pr short nd short pm short sm short eu short gd short tb short dy short ho short er short tm short yb short lu short hf short ta short w short re short os short ir short pt short au short hg short tl short pb short bi short po short at short rn short fr short ra short ac short th short pa short u short np short pu short am short cm short bk short cf short es short fm short md short no short lr short rf short db short sg short bh short hs short mt short ds short |
Compiled C module | A_ELEMENT A_TYPE | atomchange merge hadd ring | mod_p_element_count.so | |||
| P_EXCESS_ELECTRONS | short | Electron count in excess to electron pair and bond electrons in set. Used in (now abandonded) Beilstein XML format (bxml) | A_FORMAL_CHARGE B_TYPE B_ORDER A_FREE_ELECTRONS | atomchange bondchange hadd atom bond | ||||||
| P_FORMULA | string | Elemental formula of the pi system | usecharges: { value: 0 datatype: boolean} format: { value: ascii enumeration: ascii:html datatype: int} useimplicith: { value: 0 datatype: boolean} usequeryatoms: { value: 0 datatype: boolean} |
Compiled C module | P_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_ISOTOPE A_FORMAL_CHARGE A_QUERY | atomchange atom pi | mod_p_formula.so | |||
| P_HUCKEL_ENERGIES | doublevector | Pi system energies computed with a plain connectivity-only (not extended) Huckel model. Energies are in arbitrary beta units, with higher values corresponding to lower MO energies. | trace: { value: 0 description: If set, print matrices datatype: boolean} hyperconjugation: { value: 1 description: If set, include alkyl substituents according to heteroatom hyperconjugation model datatype: boolean} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER P_ELECTRON_COUNT | atomchange bondchange atom bond pi | mod_p_huckel_energies.so | |||
| P_HUCKEL_HOMO_ENERGY | double | HOMO pi system energy, computed via plain Huckel approximation | atomchange bondchange atom bond pi | |||||||
| P_HUCKEL_LUMO_ENERGY | double | LUMO pi system energy, computed via plain Huckel approximation | atomchange bondchange atom bond pi | |||||||
| P_HUCKEL_MO_OCCUPANCY | bytevector | MO occupancy (electron count) according to plain Huckel model | P_HUCKEL_ENERGIES | atomchange bondchange atom bond pi | ||||||
| P_LABEL | int | Arbitrary pi system label | (builtin) | never | ||||||
| P_MOL_NUMBER | short | Number of molecule (A_MOL_NUMBER) pi system belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge pi | |||||
| P_NATOMS | int | Size of pi system | (builtin) | atomchange bondchange merge mol atom pi | ||||||
| Q_FILE | compound | Info about the file the biologics was read from | filename string startrecord int endrecord int line int format string offset int64 length int |
atomchange bondchange stereochange merge | ||||||
| Q_NAME | string | Free-text ID of biologics item | never | |||||||
| Q_URL | url | URL of molecular data file | never | |||||||
| R_AROMATIC | byte | Flags for aromatic (1) and antiaromatic (-1) rings | antiaromatic=-1:no=0:aromatic=1 |
strict: { value: 0 datatype: string} exodb1pe: { value: 0 datatype: string} |
(builtin) | A_PICENTER A_FREE_ELECTRONS A_FORMAL_CHARGE B_TYPE B_ORDER | atomchange bondchange ring | |||
| R_ATOMS | intvector | Labels of the atoms in the ring | (builtin) | A_LABEL | atomchange bondchange merge ring | |||||
| R_BONDS | intvector | Labels of the bonds in the ring | (builtin) | B_LABEL B_TYPE | atomchange bondchange ring | |||||
| R_CONJUGATED | boolean | Flag indicating a ring where all bonds are conjugated, as per the Ertl definition | J. Chem. Inf. Model. 2014, 54, 1617-1622 | Tcl script | atomchange bondchange atom bond | r_conjugated.xpd | ||||
| R_DAYLIGHT_AROMATIC | byte | Flags for aromatic (1) and anti-aromatic (-1) rings, according to the Daylight aromaticity definition. It is a companion to standard property R_AROMATIC, which uses the switchable global aromaticity model. This property is for example used for Daylight-style structure matching without altering the global aromaticity model. | @antiaromatic:no:aromatic |
strict: { value: 0 description: If set, always refuse aromaticity for rings where an atom partipicates in multiple multi-binds datatype: boolean} exodb1pe: { value: 0 description: If set, an exo DB is assumed to contribute one pi electron, not zero. This interpretation matches some Daylight tools. datatype: boolean} |
Compiled C module | A_PICENTER A_FREE_ELECTRONS A_FORMAL_CHARGE B_TYPE B_ORDER | atomchange bondchange ring | mod_r_daylight_aromatic.so | ||
| R_ELEMENT_COUNT | shortvector | Count of element types of atoms of ring | ? short h short he short li short be short b short c short n short o short f short ne short na short mg short al short si short p short s short cl short ar short k short ca short sc short ti short v short cr short mn short fe short co short ni short cu short zn short ga short ge short as short se short br short kr short rb short sr short y short zr short nb short mo short tc short ru short rh short pd short ag short cd short in short sn short sb short te short i short xe short cs short ba short la short ce short pr short nd short pm short sm short eu short gd short tb short dy short ho short er short tm short yb short lu short hf short ta short w short re short os short ir short pt short au short hg short tl short pb short bi short po short at short rn short fr short ra short ac short th short pa short u short np short pu short am short cm short bk short cf short es short fm short md short no short lr short rf short db short sg short bh short hs short mt short ds short |
Compiled C module | A_ELEMENT A_TYPE | atomchange merge hadd ring | mod_r_element_count.so | |||
| R_FORMULA | string | Elemental formula of the ring | usecharges: { value: 0 datatype: boolean} format: { value: ascii enumeration: ascii:html datatype: int} useimplicith: { value: 0 datatype: boolean} usequeryatoms: { value: 0 datatype: boolean} |
Compiled C module | R_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_QUERY A_ISOTOPE A_FORMAL_CHARGE | atomchange atom | mod_r_formula.so | |||
| R_FUSED_RING_COUNT | int | Number of rings this ring is fused to (fused means that two rings share a common bond) | Compiled C module | R_TYPE | atomchange bondchange atom bond | mod_r_fused_ring_count.so | ||||
| R_HASHGROUP_COUNT | intvector | Ring-oriented population of basic atom hash groups | Compiled C module | A_EXTENDED_RINGHASH A_RINGSYSTEM_NUMBER | atomchange bondchange merge hadd ring | mod_r_hashgroup_count.so | ||||
| R_HCOUNT | short | Number of hydrogen ligands on ring | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange hadd atom bond ring | mod_r_hcount.so | ||||
| R_HETEROATOM_COUNT | byte | Number of hetero atoms in the ring | (builtin) | E_NRINGS A_ELEMENT A_TYPE | atomchange bondchange ring | |||||
| R_HETERO_SUBSTITUENT_COUNT | short | Number of non-hydrogen, non-carbon substituents outside ring bonded via valence or complex bond | Compiled C module | A_TYPE B_TYPE A_ELEMENT | atomchange bondchange atom bond ring | mod_r_hetero_substituent_count.so | ||||
| R_LABEL | int | Arbitrary ring label | (builtin) | atomchange bondchange | ||||||
| R_MOL_NUMBER | short | Number of molecule ring belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge ring | |||||
| R_NAME | string | Free-form user-defined ring name | atomchange bondchange stereochange ring | |||||||
| R_PI_ELECTRON_COUNT | short | Number of pi electrons in ring | Compiled C module | A_FREE_ELECTRONS A_TYPE B_TYPE B_ORDER B_ISAROMATIC | ring | mod_r_pi_electron_count.so | ||||
| R_QUERY | compound | Query attributes for matched substructure rings | ^none:aromatic:aliphatic:saturated:unsaturated,insaturated:carbocyclic:heterocyclic:monocyclic:polycyclic |
flags bitset formula formulamatch substituentcount bitset valencecount bitset neighborcount bitset hydrogencount bitset heterosubstituentcount bitset ringbondcount bitset pielectroncount bitset query querytree alphaformula formulamatch |
atomchange bondchange atom bond | |||||
| R_SIZE | short | Sizes of rings | (builtin) | atomchange bondchange ring | ||||||
| R_SUBSTITUENT_COUNT | short | Number of non-hydrogen substituents outside ring bonded via valence or complex bond | Compiled C module | A_TYPE B_TYPE A_ELEMENT | atomchange bondchange atom bond ring | mod_r_substituent_count.so | ||||
| R_SYSTEM | short | Number of ring system the ring is part of, beginning with 1 | (builtin) | R_TYPE | atomchange bondchange ring | |||||
| R_TYPE | bitset | Ring classification | ^none:sssr:esssr,triple:k,usssr:envelope |
(builtin) | atomchange bondchange ring | |||||
| R_UNSATURATED | short | Number of classical multiple bonds in the ring | (builtin) | B_TYPE B_ORDER | atomchange bondchange ring | |||||
| R_UNSATURATION | short | Overall unsaturation of ring (every non-aromatic multiple bond counts as n-1) | countarobonds: { value: 0 description: If set, aro bonds are counted with their Kekule bond order datatype: boolean}
|
Compiled C module | B_TYPE B_ORDER B_ARORING_COUNT | atomchange bondchange atom bond ring | mod_r_unsaturation.so | |||
| R_VB_NEIGHBOR_COUNT | short | Number of ligands on ring | Compiled C module | B_TYPE A_TYPE | atomchange bondchange atom bond ring | mod_r_vb_neighbor_count.so | ||||
| S_LABEL | int | Arbitrary sigma system label | (builtin) | never | ||||||
| S_MOL_NUMBER | short | Number of molecule (A_MOL_NUMBER) sigma system belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge sigma | |||||
| T_AID | int | PubChem AID assay identifier | Tcl script | never | t_aid.xpd | |||||
| T_ANNOTATED_MAP | diskfile (switchable between string blob diskfile url) |
Image where data in table has been plotted into | imagefile: { value: kinmap1.png datatype: diskfile constraints: readable} imagewidth: { value: 1275 datatype: int} imageheight: { value: 1650 datatype: int} coordsfile: { value: kinmap.tab datatype: diskfile constraints: readable} xfactor: { value: 0.735 datatype: double} yfactor: { value: -0.735 datatype: double} xoffset: { value: 115 datatype: double} yoffset: { value: 1550 datatype: double} annotationfontsize: { value: 10 datatype: double} annotationfont: { value: Arial datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} tagcolumn: { value: {} datatype: string} namecolumn: { value: {} datatype: string} shapecolumn: { value: {} datatype: string} sizecolumn: { value: {} datatype: string} outlinecolorcolumn: { value: {} datatype: string} fillcolorcolumn: { value: {} datatype: string} textcolorcolumn: { value: {} datatype: string} headercolumn: { value: {} datatype: string} footercolumn: { value: {} datatype: string} datacolumn1: { value: {} datatype: string} datacolumn2: { value: {} datatype: string} datacolumn3: { value: {} datatype: string} datacolumn4: { value: {} datatype: string} datacolumn5: { value: {} datatype: string} httpheader: { value: 0 datatype: int} id: { value: {} datatype: string} onmouseover: { value: {} datatype: string} onmouseout: { value: {} datatype: string} onclick: { value: {} datatype: string} taglocations: { value: 0 datatype: boolean} markedtaglocations: { value: {} datatype: string constraints: list} markedtagcolor: { value: orange datatype: color} markedtaglocations2: { value: {} datatype: string constraints: list} markedtagcolor2: { value: red datatype: color} imgonmousedown: { value: {} datatype: string} imgonmouseup: { value: {} datatype: string} imgonmousemove: { value: {} datatype: string} taglocationonclick: { value: {} datatype: string} dragobj: { value: 0 datatype: boolean} shownamelegend: { value: 0 datatype: boolean} showsizelegend: { value: 0 datatype: boolean} tagsizelegend: { value: 25 5 50 10 75 15 100 20 comment: value/tagsize combos for legend datatype: string} |
Tcl script | atomchange bondchange stereochange atom bond | t_annotated_map.xpd | ||||
| T_AUTHOR | compound | Table author data, computation copies these from the internal object author fields | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
Tcl script | never | t_author.xpd | ||||
| T_COMMENT | stringvector | FCree-form table comment strings | never | |||||||
| T_DIVERSITY_SET | table | Select a diverse subset from the source dataset. | property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property} structurecolumn: { value: -1 description: Column with decodable structure data or a structure cell object which is used to perform the structure filter query on, or to compute the similarity bitvector if it is not taken from a table column. Value -1 uses the row ensemble. datatype: int} query: { value: all description: Structure filter query expression datatype: string} size: { value: 50 description: Target size minvalue: 1 datatype: int} startrow: { value: -1 description: First structure source row, -1 is random datatype: int} minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int} |
Tcl script | atomchange bondchange atom bond | t_diversity_set.xpd | ||||
| T_EXTJS_VISUALIZATION | blob (switchable between blob diskfile) |
Interface to standard Web visualizations using the ExtJS JavaScript library | style: { value: barchart description: Graphics style enumeration: barchart datatype: int} height: { value: 300 description: Canvas width minvalue: 50 maxvalue: 5000 datatype: int} width: { value: 400 description: Canvas height minvalue: 50 maxvalue: 5000 datatype: string} xcolumn: { value: 0 datatype: string} ycolumn: { value: 1 datatype: string} font: { value: sans-serif datatype: string} fontsize: { value: 10 minvalue: 5 maxvalue: 32 datatype: int} barcolor: { value: #4682B4 datatype: string} margin: { value: 25 minvalue: 0 maxvalue: 100 datatype: int} ylabel: { value: {} datatype: string} xlabel: { value: {} datatype: string} filename: { value: {} datatype: string} htmlpage: { value: 0 description: If set, write complete HTML page, otherwise write only ExtJS generator statements. datatype: boolean} title: { value: {} description: Graph title datatype: string} rendertarget: { value: {} description: DOM id of object to render to (empty is default body) datatype: string} extjspath: { value: . description: path to ExtJS installation datatype: string} graphvar: { value: graph description: JavaScript variable to hold the graph root object reference. If empty, do not set a var. datatype: string} valuelabels: { value: 1 description: if set, add point/bar value labels datatype: boolean} |
Tcl script | atomchange bondchange atom bond | t_extjs_visualization.xpd | ||||
| T_HISTOGRAM | blob (switchable between blob diskfile) |
Histogram plot of a table column as a GIF or PNG image. Also computes image map T_HISTOGRAM_IMAGE_MAP for Web applications. | width: { value: 200 datatype: int} height: { value: 200 datatype: int} nbins: { value: 5 datatype: int} datacolumn: { value: 0 datatype: string} bgcolor: { value: white datatype: color} barcolor1: { value: grey datatype: color} barcolor2: { value: black datatype: color} format: { value: png enumeration: gif:png,png24:png8 datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} axiscolor: { value: black datatype: color} border: { value: 5 datatype: int} spacing: { value: 3 datatype: int} axisfont: { value: arialn datatype: string} axisfontsize: { value: 8 datatype: double} tickwidth: { value: 3 datatype: int} nticks: { value: 5 datatype: int} showxname: { value: 1 datatype: boolean} showxrange: { value: 1 datatype: boolean} |
Tcl script | never | t_histogram.xpd | ||||
| T_HISTOGRAM_IMAGEMAP | string | Image map associated with table column histogram T_HISTOGRAM | name: { value: {} datatype: string} target: { value: {} datatype: string} url: { value: {} datatype: url} title: { value: {} datatype: string} mapcolumn: { value: {} datatype: string} |
T_HISTOGRAM | never | |||||
| T_HISTORY | compoundvector | Table data record processing history | program string version string patchlevel string pgmdate date user string date date machine string |
never | ||||||
| T_IDENT | string | Table ID | Tcl script | atomchange bondchange atom bond | t_ident.xpd | |||||
| T_NAME | string | Table name | atomchange bondchange atom bond | |||||||
| T_NCBI_ASSAY_ANNOTATED_XREFS | compoundvector | NCBI annotated assay reference | {} {} undefined:pcit=1:pgene=2 |
xref choice comment string type int |
never | |||||
| T_NCBI_ASSAY_CONCENTRATION | compound | NCBI assay concentration item | 0 {mm=4:um=5:nm=6:pm=7:fm=8:mgml=9:ugml=10:ngml=11:pgml=12:fgml=13:m=14:unspecified=254} -1 |
concentration double unit int dr-id int |
never | |||||
| T_NCBI_ASSAY_COUNTS | intvector | Activity counts for a PubChem assay | sid_total int sid_active int sid_inactive int sid_inconclusive int sid_unspecified int sid_probe int cid_total int cid_active int cid_inactive int cid_inconclusive int cid_unspecified int cid_probe int |
Compiled C module | never | mod_t_ncbi_assay_counts.so | ||||
| T_NCBI_ASSAY_DESCRIPTION | compound | NCBI assay description data | {} {} {} {} {} {} {} {} {} {} {} other:screening:confirmatory:summary {} smallmolecule=1:nucleotide=2:other=255 {} mlscn=1:mlpcn=2:mlscn-ap=3:mlpcn-ap=4:journal-article=5:assay-vendor=6:literature-extracted=7:literature-author=8:literature-publisher=9:rnaigi=10:other=255 |
aid compound source choice name string description stringvector protocol stringvector comment stringvector xrefs compoundvector results compoundvector pub choicevector revision int targets compoundvector activity-outcome-method int doseresponses compoundvector substance-type int grant-number stringvector project-category int is-panel boolean assay-group stringvector panel-info compound is-mlp-late-stage boolean categorized-comment dictionary |
Compiled C module | never | mod_t_ncbi_assay_description.so | |||
| T_NCBI_ASSAY_DOSE_RESPONSE_ATTRIBUTIONS | compoundvector | NCBI assay dose/response attribution | id int description string dn string rn string type int |
never | ||||||
| T_NCBI_ASSAY_ID | compound | NCBI assay identifier | aid int version int |
Tcl script | never | t_ncbi_assay_id.xpd | ||||
| T_NCBI_ASSAY_PANEL | compound | Info on assay panels (combined assays) | name string description string members compoundvector |
never | ||||||
| T_NCBI_ASSAY_PANEL_MEMBERS | compoundvector | Info on assay panel members | {} {} {} {} {} {} {} other:screening:confirmatory:summary |
mid int name string description string protocol stringvector comment stringvector targets compoundvector xrefs compoundvector activity-outcome-method int doseresponses compoundvector categorized-comment dictionary |
never | |||||
| T_NCBI_ASSAY_PANEL_TEST_RESULT | intpair | Assay panel test result data | {} regular=1:outcome=2:score=3:ac=4 |
never | ||||||
| T_NCBI_ASSAY_RESULT_CONSTRAINTS | choice | NCBI assay result column constraints | fset floatvector fmin double fmax double frange floatpair iset intvector imin int imax int irange intpair sset stringvector |
never | ||||||
| T_NCBI_ASSAY_RESULT_TYPES | compoundvector | NCBI assay result (column) definitions | {} {} {} float=1:int=2:bool=3:string=4 {} ppt=1:ppm=2:ppb=3:mm=4:um=5:nm=6:pm=7:fm=8:mg/ml,mgml=9:ug/ml,ugml=10:ng/ml,ngml=11:pg/ml,pgml=12:fm/ml,fmml=13:m=14:percent=15:ratio=16:sec=17:rsec=18:min=19:rmin=20:day=21:rday=22:ml/min/kg,ml-min-kg,mlminkg=23:l/kg,l-kg,lkg=24:hr*ng/ml,hr-ng-ml,hrngml=25:cm/sec,cm-sec,cmsec=26:mg/kg,mg-kg,mgkg=27:none=254:unspecified=255 {} linear=1:ln=2:log=3:reciprocal=4:negative=5:nlog=6:nln=7 {} {} {} {} none:pmid:mmdb:url:protein-gi:nucleotide-gi:taxonomy:mim:gene:probe:aid:sid:cid:protein-target-gi:nucleotide-target-gi:target-name:target-descr:target-tax-id:gene-target-id |
tid int name string description stringvector type int constraints choice unit int sunit string transform int stransform string tc compound ac boolean panelinfo intpair annotation int |
never | |||||
| T_NCBI_ASSAY_SUBMIT | choice | NCBI assay submission data | aid int source choice description compound aidversion intpair |
never | ||||||
| T_NCBI_ASSAY_TARGETS | compoundvector | NCBI assay target data | {} {} {unknown=0:protein=1:dna=2:rna=3:other-biopolymer=4} |
name string mol-id int molecule-type int organism compound description string comment stringvector |
never | |||||
| T_NCBI_ASSAY_XREF | choice | NCBI assay crossreference data | regid string rn string mesh string pmid int gi int mmdb int sid int cid int dburl url sburl url asurl url protein-gi int nucleotide-gi int taxonomy int aid int mim int gene int probe int biosystem int geogse int geogsm int patent string |
never | ||||||
| T_NCBI_BIBLIO_AFFILIATION | choice | NCBI author affiliation | str string std compound |
never | ||||||
| T_NCBI_BIBLIO_ARTICLE_FROM | choice | Article container reference | journal compound book compound proc compound |
never | ||||||
| T_NCBI_BIBLIO_ARTICLE_ID_SET | choicevector | Article reference ID set | pubmed int medline int doi string pii string pmcid int pmcpid string pmpid string other compound |
never | ||||||
| T_NCBI_BIBLIO_AUTHORS | choice | NCBI author reference | std compoundvector ml stringvector str stringvector |
never | ||||||
| T_NCBI_BIBLIO_AUTHOR_LIST | compound | NCBI author reference | names choice affil choice |
never | ||||||
| T_NCBI_BIBLIO_FULL_AUTHOR_SET | compoundvector | NCBI author reference | {} primary=1:secondary=2 compiler=1:editor=2:patent-assignee=3:translator=4 |
name choice level int role int affil choice is-corr boolean |
never | |||||
| T_NCBI_BIBLIO_IMPRINT | compound | Document imprint data | {} {} {} {} {} {} {} {} {} published:submitted:in-press:other=255 {} {} none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255 |
date date volume string issue string pages string section string pub choice cprt date part-sup string language string prepub int part-supi string retract compound pubstatus int history compoundvector |
never | |||||
| T_NCBI_BIBLIO_MEETING | compound | Meeting reference | number string date date place choice |
never | ||||||
| T_NCBI_BIBLIO_PATENT_ID | choice | Patent ID reference | number string app-number string |
never | ||||||
| T_NCBI_BIBLIO_PATENT_PRIORITY | compoundvector | Patent priorities | country string number string date date |
never | ||||||
| T_NCBI_BIBLIO_PUBSTATUS_HISTORY | compoundvector | Publication status history | none:received:accepted:epublish:ppublish:revised:pmc:pmcr:pubmed:pubmedr:aheadofprint:premedline:medline:other=255 |
pubstatus int date date |
never | |||||
| T_NCBI_BIBLIO_RETRACTION | compound | Document retraction information | none:retracted:notice:in-error:erratum |
type int exp string |
never | |||||
| T_NCBI_BIBLIO_STD_AFFILIATION | compound | NCBI structured affiliation | affil string div string city string sub string country string street string email string fax string phone string postal-code string |
never | ||||||
| T_NCBI_BIBLIO_TITLE | choicevector | NCBI bibliographic title reference | name string tsub string trans string jta string iso-jta string ml-jta string coden string issn string abr string isdn string |
never | ||||||
| T_NCBI_BIOSOURCE | compound | NCBI assay target organism | {unknown:genomic:chloroplast:chromoplast:kinetoplast:mitochondrion:plastid:macronuclear:extrachrom:plasmid:transposon:insertion-seq:cyanelle:proviral:virion:nucleomorph:apicoplast:leucoplast:proplastid:endogenous-virus:hydrogenosome:chromosome} {unknown:natural:natmut:mut:artificial:synthetic:other=255} |
genome int origin int organism compound |
never | |||||
| T_NCBI_DBTAG | compound | Structured data to identify a database entry | db string tag string |
never | ||||||
| T_NCBI_DBTAGS | compoundvector | Structured data to identify a database entry | db string tag string |
never | ||||||
| T_NCBI_DBTRACKING | compound | NCBI assy db source data | name string source-id string date date description string pub choice |
never | ||||||
| T_NCBI_MMDB | compound | MMDB source information | mmdb-id int molecule-id int molecule-name stringvector residue-id int residue-name string atom-id int atom-name string |
never | ||||||
| T_NCBI_ORGANISM | compound | NCBI organism descriptor | taxname string common string mod stringvector db compoundvector syn stringvector |
never | ||||||
| T_NCBI_PERSON_ID | choice | NCBI person reference | dbtag compound name compound str string consortium string |
never | ||||||
| T_NCBI_PUBLICATION | choice | Publication in PubMed style | gen compound sub compound medline compound muid int article compound journal compound book compound proc compound patent compound pat-id compound man compound equiv choicevector pmid int |
never | ||||||
| T_NCBI_PUBLICATION_ARTICLE | compound | Article reference | title choicevector authors compound from choice ids choicevector |
never | ||||||
| T_NCBI_PUBLICATION_BOOK | compound | Book reference | title choicevector coll choicevector authors compound imp compound |
never | ||||||
| T_NCBI_PUBLICATION_GENERAL | compound | General publication reference | cit string authors compound muid int journal choicevector volume string issue string pages string date date serial-number int title string pmid int |
never | ||||||
| T_NCBI_PUBLICATION_JOURNAL | compound | Journal reference | title choicevector imp compound |
never | ||||||
| T_NCBI_PUBLICATION_MANUSCRIPT | compound | Manuscript reference | {} {} unknown:manuscript:letter:thesis |
cit compound man-id string type int |
never | |||||
| T_NCBI_PUBLICATION_MEDLINE | compound | Medline reference | {} {} {} {} {} {} {} {} {} {} {} {} publisher:premedline:medline |
uid int em date cit compound abstract string mesh compoundvector substance compoundvector xref compoundvector idnum stringvector gene stringvector pmid int pub-type stringvector mlfield compoundvector status int |
never | |||||
| T_NCBI_PUBLICATION_MEDLINE_FIELD_DOCREF_SET | compoundvector | Docrefs of NCBI medline field of publication | none:medline:pubmed:ncbigi |
type int uid int |
never | |||||
| T_NCBI_PUBLICATION_MEDLINE_FIELD_SET | compoundvector | NCBI medline field of publication | other:comment:erratum |
type int str string ids compoundvector |
never | |||||
| T_NCBI_PUBLICATION_MEDLINE_MESH_QUALIFIER_SET | compoundvector | Medline mesh term qualifiers | mp boolean subh string |
never | ||||||
| T_NCBI_PUBLICATION_MEDLINE_MESH_SET | compoundvector | Medline mesh references | mp boolean term string qual compoundvector |
never | ||||||
| T_NCBI_PUBLICATION_MEDLINE_RN_SET | compoundvector | Medline substance references | nameonly:cas:rc |
type int cit string name string |
never | |||||
| T_NCBI_PUBLICATION_MEDLINE_SI_SET | compoundvector | Medline crossreferences | none:ddbj:carbbank:embl:hdb:genbank:hgml:mim:msd:pdb:pir:prfseqdb:psd:swissprot:gdb |
type int cit string |
never | |||||
| T_NCBI_PUBLICATION_PATENT | compound | Patent reference | title string authors compound country string doc-type string number string date-issue date class stringvector app-number string app-date date applicants compound assignees compound priority compoundvector abstract string |
never | ||||||
| T_NCBI_PUBLICATION_PATENT_ID | compound | Patent ID reference | country string id choice doc-type string |
never | ||||||
| T_NCBI_PUBLICATION_PROCEEDINGS | compound | Proceedings reference | book compound meeting compound |
never | ||||||
| T_NCBI_PUBLICATION_SET | choicevector | Publication in PubMed style | gen compound sub compound medline compound muid int article compound journal compound book compound proc compound patent compound pat-id compound man compound equiv string pmid int |
never | ||||||
| T_NCBI_PUBLICATION_SUBMISSION | compound | Submission reference | {} {} unknown:paper:tape:floppy:email:other=255 |
authors compound imp compound medium int date date descr string |
never | |||||
| T_NCBI_SOURCE | choice | NCBI assay source data | individual choice db compound mmdb compound |
Tcl script | never | t_ncbi_source.xpd | ||||
| T_NCBI_STD_NAME | compound | NCBI standardized name reference | last string first string middle string full string initials string suffix string title string |
never | ||||||
| T_PUBCHEM_URL | url | PubChem assay id data display URL | Tcl script | T_AID | atomchange bondchange stereochange merge | t_pubchem_url.xpd | ||||
| T_QUERY | compound | Structured information about query used to generate this table. | ens,structure:enslist,elist,structures:record,rec:recordlist,reclist:bitvector,bit:count,cnt:delete,del:property,prop:propertylist,proplist:file,molfile:filelist:table,qtable,hitlist:reaction:reactionlist,xlist,reactions:array,tclarray,pythonarray:vrecord,vrec:vrecordlist,vreclist:custom:customlist:ensblob:reactionblob:exists:tablecollection:vertex:vertexlist:row,index:rowlist,indexlist |
mode int query string retrieve string timeout int maxhits int date datetime startpos int endpos int nhits int nexamined int querytime int eof boolean comment string displayquery string file string parameters string webenv string extid int extdb string |
never | |||||
| T_QUERY_GIF | diskfile (switchable between string blob diskfile url) |
Depiction of query used to generate a table | width: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int} height: { value: 300 minvalue: 1 maxvalue: 2048 datatype: int} bgcolor: { value: transparent datatype: color} suppressnodes: { value: E_LIVE_IN_ENTREZ datatype: string} frame: { value: 0 datatype: int} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int} crop: { value: 2 minvalue: -1 datatype: int} format: { value: gif datatype: string} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} fixiepngsize: { value: 1 datatype: boolean} molimgwidth: { value: 75 minvalue: 25 maxvalue: 500 datatype: int} molimgheight: { value: 75 minvalue: 25 maxvalue: 500 datatype: int} font: { value: arialn datatype: string} fontsize: { value: 8 datatype: string} interlace: { value: 1 datatype: string} suppressedproperties: { value: {} datatype: string constraints: propertylist} downloadfilename: { value: {} datatype: string} |
Compiled C module | T_QUERY | never | mod_t_query_gif.so | |||
| T_TIMESTAMP | datetime | Table timestamp | Tcl script | never | t_timestamp.xpd | |||||
| T_XYPLOT | blob (switchable between blob diskfile) |
XY plot of two table columns | width: { value: 200 datatype: int} height: { value: 200 datatype: int} xdatacolumn: { value: 0 datatype: string} ydatacolumn: { value: 1 datatype: string} bgcolor: { value: white datatype: color} format: { value: gif datatype: string} filename: { value: {} datatype: string constraints: writeable} axiscolor: { value: black datatype: color} border: { value: 5 datatype: int} spacing: { value: 3 datatype: int} axisfont: { value: arialn datatype: string} axisfontsize: { value: 8 datatype: int} tickwidth: { value: 3 datatype: int} xnticks: { value: 5 datatype: int} ynticks: { value: 5 datatype: int} markercolor: { value: black datatype: color} markerstyle: { value: cross enumeration: cross:box:diamond:circle:dot datatype: string} markersize: { value: 5 datatype: int} showxname: { value: 1 datatype: boolean} showyname: { value: 1 datatype: boolean} xaxisstart: { value: auto datatype: string} yaxisstart: { value: auto datatype: string} |
Tcl script | never | t_xyplot.xpd | ||||
| T_XYPLOT_IMAGEMAP | string | Image map associated with xyplot | name: { value: {} datatype: string} target: { value: {} datatype: string} url: { value: {} datatype: string} title: { value: {} datatype: string} mapcolumn: { value: {} datatype: string} |
T_XYPLOT | never | |||||
| U_LABEL | int | Arbitrary label for torsion objects | (builtin) | never | ||||||
| U_MOL_NUMBER | short | Number of molecule (A_MOL_NUMBER) torsion belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge torsion | |||||
| V_COMMENT | string | Vertex (node) comment in free format | never | |||||||
| V_GRAPHICS | compoundvector | Vertex (node) graphics | none:arc:bitmap:image:line:oval,ellipse,ellipsis:polygon:rectangle,rect:text:box:circle:rhombus,diamond:ver_ellipsis:hor_ellipsis:triangle:pentagon:hexagon:octagon:roundedrectangle,roundrectangle,roundrect,roundedrect |
type int attributes dictionary |
imgproperty: { value: E_GIF description: Property to use as image data datatype: string constraints: property} directory: { value: img description: Image directory datatype: string constraints: directory} imgparameters: { value: crop 4 bonds 6 frame 0 bgcolor white height 120 width 120 bondcolor black atomcolor black asymbol xsymbol description: Override attributes for the image computation datatype: dictionary} |
Tcl script | V_STRUCTURE | never | v_graphics.xpd | |
| V_HASHY | uint64 | Vertex node structure hash, without stereochemistry or isotope labelling (usually copied from E_HASHY structure values) | atomchange bondchange atom bond | |||||||
| V_IDENT | string | Vertex ident string | Compiled C module | never | mod_v_ident.so | |||||
| V_LABEL | int | Vertex (node) label in network objects | Compiled C module | never | mod_v_label.so | |||||
| V_LABELSET | intvector | Vertex (node) full label set (primary and alternative). This is for example used in the OBO network format I/O module. | never | |||||||
| V_LABEL_GRAPHICS | compound | Vertex (node) label graphics | none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon |
type int attributes dictionary |
never | |||||
| V_LEVEL | short | Distance of vertex to root | Compiled C module | never | mod_v_level.so | |||||
| V_NAME | string | Vertex (node) name in free format | never | |||||||
| V_ONTOLOGY_DBXREFS | compoundvector | Ontology database cross references | db string record string description string |
never | ||||||
| V_ONTOLOGY_TERM | compound | Ontology term. Used for example in the OBO network data I/O module | id string name string definition compound synonyms compoundvector dbxrefs compoundvector substructure structure structurehash uint64 altids stringvector obsolete boolean comment string |
never | ||||||
| V_ONTOLOGY_TERM_DEFINITION | compound | Ontology term definition with references to database entries defining these | definition string dbxrefs compoundvector |
never | ||||||
| V_ONTOLOGY_TERM_SYNONYMS | compoundvector | Ontology term synonyms, with classification of the synonym relationship and database references thereof | {} default:exact:broad:narrow:related |
text string scope int type string dbxrefs compoundvector |
never | |||||
| V_PARTITION | int | Partition code for vertices (nodes). If a symbolic name is available, I/O modules modify the enumeration field of the property. | atomchange bondchange atom bond | |||||||
| V_RECORD | int | Reference record number (1-based) for a vertex data item | atomchange bondchange atom bond | |||||||
| V_SMALLWORLD_DATA | compound | Vertex data for a fragment network modelled after R. Sayles SmallWorld approach | record int smiles string count int |
atomchange bondchange atom bond | ||||||
| V_STRUCTURE | structure | A structure associated with a network vertex/node | never | |||||||
| V_TEXT | string | Vertex (node) text label | never | |||||||
| V_TYPE | string | Vertex type identifier (free form) | atomchange bondchange atom bond | |||||||
| V_URL | url | Vertex reference URL | atomchange bondchange atom bond | |||||||
| V_WEIGHT | double | Graph vertex (node) weight | Compiled C module | never | mod_v_weight.so | |||||
| V_XY | floatpair | Vertex (node) graph coordinates | x float y float |
layouter: { value: neato enumeration: dot:neato:twopi:circle:fdp:sfdp:patchwork datatype: string}
|
Compiled C module | never | mod_v_xy.so | |||
| X_ANNOTATION | choicevector | Graphical annotation objects for reaction renderings. This is a choice vector type, the structure of every supported annotation type is defined by its own X_xxx_ANNOTATION property- | text compound rectangle compound ellipse compound roundedrectangle compound polyline compound bracket compound |
A_XY | never | |||||
| X_ARROW | compound | Reaction arrow style | none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow |
style byte overtext stringvector undertext stringvector p1 floatpair p2 floatpair |
never | |||||
| X_ASCII_IMAGE | string (switchable between string unicode) |
Ascii (or Unicode) rendering of a reaction. Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the last line. |
headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} header: { value: {} datatype: string} footer: { value: {} datatype: string} showreagent: { value: 1 datatype: boolean} showproduct: { value: 1 datatype: boolean} showintermediate: { value: 1 datatype: boolean} |
Compiled C module | E_ASCII_IMAGE E_REACTION_ROLE | atomchange bondchange stereochange merge mol atom bond | mod_x_ascii_image.so | |||
| X_ATOM_ECONOMY | double | Sum of the molecular weight of the products divided by the sum of the molecular weight of the reagents | Tcl script | atomchange bondchange atom bond | x_atom_economy.xpd | |||||
| X_AUTHOR | compound | Information about the original author of a reaction or related document | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
never | ||||||
| X_BRACKET_ANNOTATION | compound | Bracket annotation for reaction renderings. This is a choice vector branch of property X_ANNOTATION. | {} {} {} ROUND:SQUARE:BRACES:CHEVRONS SINGLE:DOUBLE |
coords floatvector linecolor color linewidth float type int orientation int |
A_XY | never | ||||
| X_CGR | structure | Condensed graph representation of the reaction. This format includes a superset of all atoms and bonds (marked in B_REACTION_CENTER) which participate in the reaction. The result pseudo structure usually violates valence bond rules. | Hoonakker, F.; Lachiche, N.; Varnek, A. Condensed Graph of Reaction: Considas one single pseudo molecule. Int. J. Artif. Intell. Tools 2011, 20, 253–270. | Tcl script | atomchange bondchange atom bond pi reaction ringsystem | x_cgr.xpd | ||||
| X_CLASS | string | Free-form reaction classification | atomchange bondchange stereochange atom bond | |||||||
| X_CML_STRING | string | CML reaction encoding as a string | pedantic: { value: 1 datatype: boolean}
|
Tcl script | never | x_cml_string.xpd | ||||
| X_COLOR | color | Background color to use in plots | never | |||||||
| X_COMMENT | stringvector | Free form comment for reaction | never | |||||||
| X_CONVENTION | string | Free-form textual description of reaction encoding convention | never | |||||||
| X_DELTA_ALIRING_COUNT | int | Change in number of aliphatic ESSSR rings in the reaction | Tcl script | E_ALIRING_COUNT | atomchange bondchange atom bond | x_delta_aliring_count.xpd | ||||
| X_DELTA_ARORING_COUNT | int | Change in number of aromatic ESSSR rings in the reaction | Tcl script | E_ARORING_COUNT | atomchange bondchange atom bond | x_delta_aroring_count.xpd | ||||
| X_DELTA_RING_COUNT | int | Change in number of ESSSR rings in the reaction | Tcl script | E_NESSSR | atomchange bondchange atom bond | x_delta_ring_count.xpd | ||||
| X_DIRECTION | byte | Reaction direction encoding | undefined:forward:equilibrium,both:backward,reverse |
atomchange bondchange stereochange atom bond | ||||||
| X_ELLIPSE_ANNOTATION | compound | Ellipse or circle annotation for reaction renderings. This is a choice vector branch of property X_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float bgcolor color style bitset |
A_XY | never | ||||
| X_EMF_IMAGE | diskfile (switchable between blob diskfile url) |
EMF/WMF reaction depiction | hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} height: { value: 180 datatype: int} width: { value: 400 datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} crop: { value: -1 datatype: int} header: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} footer: { value: {} datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} border: { value: 12 datatype: int} bgcolor: { value: transparent datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: X_NAME datatype: string} reaction: { value: none datatype: string} metadata: { value: 1 datatype: boolean} format: { value: emf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int} arrowsize: { value: 35 datatype: int} bonds: { value: 8 datatype: int} arrowcolor: { value: black datatype: color} showsolvent: { value: 1 datatype: boolean} annotationfontsize: { value: -1 datatype: double} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} solventcolor: { value: blue datatype: color} reagentcolor: { value: blue datatype: color} framecolor: { value: black datatype: color} suppressedfragmentsfile: { value: reagents.tbin datatype: diskfile constraints: readable} showplus: { value: 1 datatype: boolean} arrowtext_over: { value: {} datatype: string} arrowtext_under: { value: {} datatype: string} showempty: { value: 1 datatype: boolean} font: { value: arialn datatype: string} showmapping: { value: 0 datatype: boolean} frame: { value: 1 datatype: boolean} colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int} usesubscripts: { value: 1 datatype: boolean} arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int} compact: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} usereagenttable: { value: 0 datatype: boolean} showintermediate: { value: 0 datatype: boolean} |
Compiled C module | M_EMF_IMAGE | atomchange bondchange stereochange merge mol atom bond | mod_x_emf_image.so | |||
| X_ENZYMES | stringvector | IDs of enzymes participating in the reaction | atomchange bondchange stereochange atom bond | |||||||
| X_FILE | compound | Info about the file the reaction was read from | filename string startrecord int endrecord int line int format string offset int64 length int |
atomchange bondchange stereochange merge | ||||||
| X_GIF | diskfile (switchable between string blob diskfile url) |
GIF/PNG reaction depiction | height: { value: 180 datatype: int} width: { value: 400 datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 datatype: int} crop: { value: -1 datatype: int} header: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} footer: { value: {} datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: color constraints: property} border: { value: 12 datatype: int} bgcolor: { value: white datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: X_NAME datatype: string} reaction: { value: none enumeration: none:cactvs,blob:rxnfile:rdfile datatype: int} metadata: { value: 1 datatype: boolean} format: { value: gif enumeration: png,png24:png8:gif datatype: string} arrowsize: { value: 35 datatype: int} bonds: { value: 8 datatype: double} arrowcolor: { value: black datatype: color} showsolvent: { value: 1 datatype: boolean} showcatalyst: { value: 1 datatype: boolean} annotationfontsize: { value: -1 datatype: double} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} solventcolor: { value: blue datatype: color} framecolor: { value: black datatype: color} antialiasing: { value: 3 datatype: int} suppressedfragmentsfile: { value: reagents.tbin datatype: diskfile constraints: readable} showplus: { value: 1 datatype: boolean} arrowtext_over: { value: {} datatype: string} arrowtext_under: { value: {} datatype: string} showempty: { value: 1 datatype: boolean} font: { value: dejavusans datatype: string} showmapping: { value: 0 datatype: boolean} usesubscripts: { value: 1 datatype: boolean} frame: { value: 0 datatype: boolean} arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int} compact: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} showintermediate: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} invert: { value: 0 description: If set, reverse drawing of reaction direction datatype: boolean} interlace: { value: 1 datatype: boolean} usereagenttable: { value: 0 datatype: boolean} |
Compiled C module | M_GIF E_REACTION_ROLE X_XYEXTENT | atomchange bondchange stereochange atom bond | mod_x_gif.so | |||
| X_HASH | uint64 | Reaction hashcode, without stereochemistry and isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_HASHY E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_hash.so | |||
| X_HASH128 | uint128 | 128 bit reaction hashcode, without stereochemistry and isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_HASH128 E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_hash128.so | |||
| X_HISTORY | compoundvector | Reaction data record processing history | program string version string patchlevel string pgmdate date user string date date machine string |
never | ||||||
| X_IDENT | string | Free-form Reaction ID | Tcl script | never | ||||||
| X_INCHI | string | RInChI string of reaction | prefix: { value: 1 description: Wether to include the RInChI= prefix datatype: boolean}
|
Compiled C module | X_DIRECTION X_RDF_STRING E_REACTION_ROLE | atomchange bondchange stereochange atom bond | mod_x_inchi.so | |||
| X_INCHI_AUXINFO | string | Auxinfo part of reaction InChI (RINCHI) | atomchange bondchange stereochange atom bond | |||||||
| X_ISOTOPE_HASH | uint64 | Reaction hashcode, without stereochemistry and with isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_HASHIY E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_isotope_hash.so | |||
| X_ISOTOPE_HASH128 | uint128 | 128 bit reaction hashcode, without stereochemistry but with isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_ISOTOPE_HASH128 E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_isotope_hash128.so | |||
| X_ISOTOPE_STEREO_HASH | uint64 | Reaction hashcode, with stereochemistry and isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_HASHISY E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_isotope_stereo_hash.so | |||
| X_ISOTOPE_STEREO_HASH128 | uint128 | 128 bit reaction hashcode, with stereochemistry and isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_ISOTOPE_STEREO_HASH128 E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_isotope_stereo_hash128.so | |||
| X_KEGG_ID | string | Reaction KEGG ID (www.genome.jp) | atomchange bondchange stereochange merge | |||||||
| X_LEVEL | int | Reaction level | never | |||||||
| X_LHASA_GIF | diskfile (switchable between blob diskfile url) |
GIF/PNG rendering of a Lhasa transform result (from X_LHASA_SCORE data) | format: { value: png enumeration: png,png24:png8:gif datatype: int} height: { value: 220 datatype: int} width: { value: 500 datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 datatype: int} reaction: { value: none enumeration: none:cactvs,blob:rxnfile:rdfile datatype: int} antialiasing: { value: 3 datatype: int} downloadfilename: { value: {} datatype: string} bgcolor: { value: transparent datatype: color} font: { value: dejavusans datatype: string} border: { value: 12 datatype: int} interlace: { value: 1 datatype: boolean} arrowsize: { value: 35 datatype: int} arrowcolor: { value: black datatype: color} bonds: { value: 8 datatype: double} showintermediate: { value: 1 datatype: boolean} showattackpoints: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset} showlocants: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset} locants: { value: 0 datatype: string constraints: list} annotationfontsize: { value: -1 datatype: double} showplus: { value: 1 datatype: boolean} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} showpath: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset} showbondchanges: { value: 0 enumeration: ^none:reagent:product:intermediates datatype: bitset} arrowtext_over: { value: {} datatype: string} arrowtext_under: { value: {} datatype: string} arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int} asymbol: { value: symbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: color constraints: property} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} |
Compiled C module | X_LHASA_SCORE X_XYEXTENT M_GIF E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_lhasa_gif.so | |||
| X_LHASA_LOCANTS | compoundvector | Atom and bond locant set used by the Lhasa engine, describing a set of atoms and/or bonds which participated in a score, Contains atoms and/or bond labels. | atomset intvector bondset intvector |
atomchange bondchange stereochange mol atom bond ring | ||||||
| X_LHASA_REPORT | diskfile (switchable between blob diskfile url) |
HTML-formatted report on a scored Lhasa reaction | templatefile: { value: report.htpl datatype: diskfile constraints: readable} filename: { value: {} datatype: diskfile constraints: writeable} pagewrapper: { value: 1 datatype: boolean} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: string} |
Tcl script | X_LHASA_SCORE X_LHASA_GIF | atomchange bondchange atom bond | x_lhasa_report.xpd | |||
| X_LHASA_SCORE | compound | Retroreaction scores, ratings and reaction conditions computed via a Lhasa CHMTRN rule. | {} {} {} {} {} {} {} {} {} {} {} {} {} {^none:protected:interfering:participating} {} {} {} {} {} {} {} {} {} {} {} |
ident int name string url url authorlitref string score int basescore int ratings dictionary conditions stringvector conditioncodes intvector descriptiveconditions stringvector actualconditions stringvector warnings stringvector warningcodes intvector atommarks int variables dictionary pathatoms intvector pathbondatoms intpairvector brokenbondatoms intpairvector changedbondatoms intpairvector newbondatoms intpairvector scorefactors compoundvector genericlitrefs stringvector optlitrefs stringvector title string |
atomchange bondchange stereochange atom bond | |||||
| X_LHASA_SCORE_FACTORS | compoundvector | Registered atom and bond configurations which influenced the Lhasa score for this retroreaction. | undefined,undef,none:reagent,educt,reactant:product:solvent:catalyst:intermediate:impurity:byproduct:agent:waste:precursor:altreagent |
reactionstep int locants compoundvector condition dictionary |
atomchange bondchange stereochange mol atom bond ring | |||||
| X_LONG_INCHIKEY | string | Long reaction InChI (RINCHI) key variant | Compiled C module | X_INCHI | atomchange bondchange stereochange atom bond | mod_x_long_inchikey.so | ||||
| X_METADATA | dictionary | Dublin Core metadata on this reaction | never | |||||||
| X_MINIMOL | blob | Minimol representation of a reaction | Compiled C module | atomchange bondchange stereochange merge 3dabsolute atom bond | mod_x_minimol.so | |||||
| X_MRV_STRING | string | MRV reaction reacord encoding as a string (with newlines) | Tcl script | never | x_mrv_string.xpd | |||||
| X_NAME | string | Long reaction identification string | Tcl script | never | ||||||
| X_NUMBER | int | Reaction number intended to be used as identifier | never | |||||||
| X_POLYLINE_ANNOTATION | compound | Polyline as reaction drawing annotation. This is one of the choice variants of property X_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float style bitset headskip double tailskip double headwidth double tailwidth double headlength double taillength double headflags bitset tailflags bitset arcangle double curved boolean |
A_XY | never | ||||
| X_PRODUCT_NUMBERS | shortvector | ID number of reaction products | never | |||||||
| X_RDF_STRING | string | RDF reaction record encoded as a string | reverse: { value: 0 description: if set, reverse direction of reaction datatype: boolean}
|
Tcl script | E_REACTION_ROLE | atomchange bondchange stereochange merge hadd atom bond | x_rdf_string.xpd | |||
| X_REACTION_TEMPLATE | reaction | Reaction template extracted from full reaction | Coley, Connor, JCIM 2019 | Tcl script | A_MAPPING | atomchange bondchange stereochange atom bond | x_reaction_template.xpd | |||
| X_REAGENT_NUMBERS | shortvector | ID number of reaction reagents | never | |||||||
| X_RECTANGLE_ANNOTATION | compound | Rectangular annotation object for reaction renderings. This is a choice vector branch of property X_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float bgcolor color style bitset |
A_XY | never | ||||
| X_REREG | string | MDL external registry number | never | |||||||
| X_REVERSE_REACTION | reaction | Reverse reaction, i.e. with swapped reagent and product, other reaction roles unchanged | Tcl script | E_REACTION_ROLE | never | x_reverse_reaction.xpd | ||||
| X_RHEA_ID | string | Reaction registration ID in the RHEA database (https://www.rhea-db.org/) | atomchange bondchange atom bond | |||||||
| X_RHEA_URL | url | Display URL for a reaction the RHEA database (https://www.rhea-db.org) | Tcl script | atomchange bondchange atom bond | x_rhea_url.xpd | |||||
| X_RIREG | string | MDL internal registry number | never | |||||||
| X_ROUNDED_RECTANGLE_ANNOTATION | compound | Rounded rectangle annotation for reaction renderings. This is a choice vector branch of property X_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float bgcolor color style bitset arcwidth float archeight float |
A_XY | never | ||||
| X_RULE_NUMBER | short | Reaction rule number | never | |||||||
| X_RXN_STRING | string | RXN reaction record encoded as a string | reverse: { value: 0 description: if set, reverse direction of reaction datatype: boolean}
|
Tcl script | E_REACTION_ROLE | atomchange bondchange stereochange merge hadd atom bond | x_rxn_string.xpd | |||
| X_SCREEN | bitvector | Screen bits for reacting bonds, used to filter reaction queries | Tcl script | B_TYPE A_ELEMENT B_ORDER A_TYPE | atomchange bondchange atom bond | |||||
| X_SHORT_INCHIKEY | string | Short reaction InChI (RINCHI) key variant | prefix: { value: 1 description: Flag whether to include RInChIKey= prefix datatype: boolean}
|
Compiled C module | X_INCHI | atomchange bondchange stereochange atom bond | mod_x_short_inchikey.so | |||
| X_SMILES | string | Reaction SMIRKS (SMILES) string | usearo: { value: 0 datatype: boolean} unique: { value: 0 datatype: boolean} usestereo: { value: 1 datatype: boolean} usesuperatom: { value: 0 datatype: boolean} useisotope: { value: 1 datatype: boolean} usemapping: { value: 1 datatype: boolean} smarts: { value: 0 datatype: boolean} usehcount: { value: 1 datatype: boolean} useexplicith: { value: 0 datatype: boolean} |
Tcl script | E_REACTION_ROLE E_SMILES | atomchange bondchange stereochange merge hadd | ||||
| X_SMIRKS | string | Transform for a reaction in Daylight SMIRKS notation. Computation function for this property is limited, it performs a simple topological change and reaction MCSS analysis. | debug: { value: 0 datatype: boolean} useoldmapping: { value: 0 datatype: boolean} |
Tcl script | atomchange bondchange stereochange merge | |||||
| X_STEREO_HASH | uint64 | Reaction hashcode, with stereochemistry and without isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_HASHSY E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_stereo_hash.so | |||
| X_STEREO_HASH128 | uint128 | 128 bit reaction hashcode, with stereochemistry but without isotope labelling | usedirection: { value: 1 description: if not set, reagent/product sides are exchangeable datatype: boolean} useagents: { value: 0 description: if set, also mix in other agents (solvent, catalyst, etc.) into hash datatype: boolean} |
Compiled C module | E_STEREO_HASH128 E_REACTION_ROLE | atomchange bondchange atom bond | mod_x_stereo_hash128.so | |||
| X_SVG_IMAGE | diskfile (switchable between blob diskfile url) |
SVG reaction depiction | hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} height: { value: 180 datatype: int} width: { value: 400 datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} header: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} footer: { value: {} datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} border: { value: 12 datatype: int} bgcolor: { value: transparent datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: X_NAME datatype: string} metadata: { value: 1 datatype: boolean} arrowsize: { value: 35 datatype: int} bonds: { value: 8 datatype: int} arrowcolor: { value: black datatype: color} showsolvent: { value: 1 datatype: boolean} annotationfontsize: { value: -1 datatype: double} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} solventcolor: { value: blue datatype: color} framecolor: { value: black datatype: color} reagentcolor: { value: blue datatype: color} suppressedfragmentsfile: { value: reagents.tbin datatype: diskfile constraints: readable} showplus: { value: 1 datatype: boolean} arrowtext_over: { value: {} datatype: string} arrowtext_under: { value: {} datatype: string} showempty: { value: 1 datatype: boolean} font: { value: arialn datatype: string} showmapping: { value: 0 datatype: boolean} frame: { value: 1 datatype: boolean} usesubscripts: { value: 1 datatype: boolean} uselinecaps: { value: 1 datatype: boolean} arrowstyle: { value: right enumeration: none:left:right:equilibrium,bidirectional,both:resonance:retro,retrosynthetic:hollow:undefined datatype: int} compact: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} usereagenttable: { value: 0 datatype: boolean} showintermediate: { value: 0 datatype: boolean} usewebfont: { value: 0 datatype: boolean} id: { value: {} datatype: string} title: { value: {} datatype: string} standalone: { value: 1 datatype: boolean} xmlheader: { value: 1 datatype: boolean} |
Compiled C module | M_SVG_IMAGE | atomchange bondchange stereochange merge mol atom bond | mod_x_svg_image.so | |||
| X_TEXT_ANNOTATION | compound | Annotation string for reaction renderings. This is a choice vector branch of property X_ANNOTATION. | {} {} {} center:left:right center:top:bottom {} {} ^none:bold:italic:underline:outline:shadow:subscript:superscript:formula |
coords floatpair text stringvector color color align int valign int font string fontsize float style bitset charset string width double height double |
A_XY | never | ||||
| X_TITLE | string | Reaction title string | never | |||||||
| X_URL | url | URL of molecular data file | never | |||||||
| X_WEB_INCHIKEY | string | Web reaction InChI (RINCHI) key variant | prefix: { value: 1 description: Flag whether to include RInChIKey= prefix datatype: boolean}
|
Compiled C module | X_INCHI | atomchange bondchange stereochange atom bond | mod_x_web_inchikey.so | |||
| X_XYEXTENT | floatvector | Reaction plot coordinate rectangles. This is computed from the complete reaction with the combined bounds of reagents and products, but without tsking the coordinates of other reaction components into account. Coordinates of those two ensembles are standardized to a common bond length, an moved so that the bounding boxes are a adjustable multiple of the standard bond length apart, and vertically centered. The result vector contains four bounding boxes in xmin,xmax,ymin,ymax order: The outer bounding box, the reagent bounding box and the product bounding box. |
xmin float xmax float ymim float ymax float rxmin float rxmax float rymin float rymax float pxmin float pxmax float pymin float pymax float |
arrowgap: { value: 3 description: in standard bond lengths datatype: double}
|
Compiled C module | A_XY | merge | mod_x_xyextent.so | ||
| X_YIELD | float | Reaction yield in percents | atomchange bondchange stereochange 3drelative atom bond | |||||||
| Y_ALIRING_COUNT | short | Number of aliphatic rings the ringsystem contains | Compiled C module | R_AROMATIC R_TYPE Y_LABEL R_SYSTEM | atomchange bondchange ring | mod_y_aliring_count.so | ||||
| Y_AROMATIC | short | Ringsystem aromaticity status, indicating whether none, some or all rings in the system are aromatic. | no,none:some,partially:full,all |
Compiled C module | B_ISAROMATIC B_TYPE | atomchange bondchange atom bond ring | mod_y_aromatic.so | |||
| Y_ARORING_COUNT | int | Number of aromatic ESSR rings in ringsystem | Compiled C module | R_SYSTEM R_TYPE Y_LABEL R_AROMATIC | atomchange bondchange ring | mod_y_aroring_count.so | ||||
| Y_DAYLIGHT_ARORING_COUNT | int | Number of aromatic ESSR rings in ringsystem, using alswys Daylight aromaticity definition | Compiled C module | R_SYSTEM R_TYPE Y_LABEL R_DAYLIGHT_AROMATIC | atomchange bondchange ring | mod_y_daylight_aroring_count.so | ||||
| Y_ELEMENT_COUNT | shortvector | Count of element types of atoms of ringsystem | ? short h short he short li short be short b short c short n short o short f short ne short na short mg short al short si short p short s short cl short ar short k short ca short sc short ti short v short cr short mn short fe short co short ni short cu short zn short ga short ge short as short se short br short kr short rb short sr short y short zr short nb short mo short tc short ru short rh short pd short ag short cd short in short sn short sb short te short i short xe short cs short ba short la short ce short pr short nd short pm short sm short eu short gd short tb short dy short ho short er short tm short yb short lu short hf short ta short w short re short os short ir short pt short au short hg short tl short pb short bi short po short at short rn short fr short ra short ac short th short pa short u short np short pu short am short cm short bk short cf short es short fm short md short no short lr short rf short db short sg short bh short hs short mt short ds short |
Compiled C module | A_ELEMENT A_TYPE | atomchange merge hadd | mod_y_element_count.so | |||
| Y_FORMULA | string | Elemental formula of the ringsystem | usecharges: { value: 0 datatype: boolean} format: { value: ascii enumeration: ascii:html datatype: int} useimplicith: { value: 0 datatype: boolean} usequeryatoms: { value: 0 datatype: boolean} |
Compiled C module | Y_ELEMENT_COUNT A_TYPE A_ELEMENT A_HYDROGENS_NEEDED A_QUERY A_ISOTOPE A_FORMAL_CHARGE | atomchange atom | mod_y_formula.so | |||
| Y_FUSION | byte | Maximum fusion state of ring system. 0:isolated ring, 1:spiro (one common atom), 2:annealed/fused (two common atoms), 3: cage (more than two common atoms between any two ringsystem rings). | isolated,isolatedring:spiro:annealed,fusion,fused:cage |
Compiled C module | R_TYPE A_RINGSYSTEM_NUMBER | atomchange bondchange atom bond ring | mod_y_fusion.so | |||
| Y_HASHGROUP_COUNT | intvector | Ringsystem-oriented population of basic atom hash groups | Compiled C module | A_EXTENDED_RINGHASH A_RINGSYSTEM_NUMBER | atomchange bondchange merge hadd ring | mod_y_hashgroup_count.so | ||||
| Y_HASHY | uint64 | Perturbed ringsystem hashcode | usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string} usesubstitution: { value: none description: none: pure ring system, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string} |
Compiled C module | A_RINGSYSTEM_NUMBER A_EXTENDED_RINGHASH A_EXTENDED_RINGHASH_GROUP B_TYPE A_LABEL Y_HASHGROUP_COUNT | atomchange bondchange hadd atom bond ring | mod_y_hashy.so | |||
| Y_HCOUNT | short | Number of hydrogen ligands on ringsystem | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange hadd atom bond ring | mod_y_hcount.so | ||||
| Y_HETEROATOM_COUNT | int | Number of hetero (not C or H) atoms in the ringsystems | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_y_heteroatom_count.so | ||||
| Y_HETERO_SUBSTITUENT_COUNT | short | Number of non-hydrogen, non-carbon substituents outside ring system bonded via valence or complex bond | Compiled C module | A_TYPE B_TYPE A_ELEMENT | atomchange bondchange atom bond ring | mod_y_hetero_substituent_count.so | ||||
| Y_LABEL | int | Arbitrary ringsystem label | (builtin) | never | ||||||
| Y_MOL_NUMBER | int | (builtin) | A_MOL_NUMBER | atomchange bondchange merge ring | ||||||
| Y_NAME | string | Ringsystem name | R_TYPE | atomchange bondchange stereochange ring | ||||||
| Y_NATOMS | int | Number of atoms in ring system | Compiled C module | ring | mod_y_natoms.so | |||||
| Y_PI_ELECTRON_COUNT | short | Number of pi electrons in ring system | Compiled C module | A_FREE_ELECTRONS A_TYPE B_TYPE B_ORDER B_ISAROMATIC | ring | mod_y_pi_electron_count.so | ||||
| Y_QUERY | compound | Query attributes for matched substructure ringsystems | ^none:aromatic,fullyaromatic:aliphatic,fullyaromatic:saturated:unsaturated,insaturated:carbocyclic:heterocyclic:monocyclic:polycyclic:mixed,mixedaromaticaliphatic:partiallyaromatic:partiallyaliphatic |
flags bitset formula formulamatch substituentcount bitset valencecount bitset neighborcount bitset hydrogencount bitset heterosubstituentcount bitset ringbondcount bitset pielectroncount bitset query querytree alphaformula formulamatch |
atomchange bondchange atom bond | |||||
| Y_RING_CONTRACTION_HASH | uint64vector | Hashcodes of the various pseudo structures generated by eliminating all different sequences of connected unsubstituted ring atoms. | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange merge shuffle hadd ring | mod_y_ring_contraction_hash.so | ||||
| Y_RING_COUNT | int | Number of ESSR rings in ringsystem | Compiled C module | R_SYSTEM R_TYPE Y_LABEL | atomchange bondchange ring | mod_y_ring_count.so | ||||
| Y_RING_SIZE_BITS | bitset | Bits set for rings of size n the ringsystem contains | Compiled C module | R_SYSTEM Y_LABEL | atomchange bondchange atom bond ring | mod_y_ring_size_bits.so | ||||
| Y_SMILES | string | SMILES of the ring systems | usearo: { value: 0 datatype: boolean} unique: { value: 0 datatype: boolean} usestereo: { value: 1 datatype: boolean} usesuperatom: { value: 0 datatype: boolean} useisotope: { value: 1 datatype: boolean} usemapping: { value: 1 datatype: boolean} smarts: { value: 0 datatype: boolean} usehcount: { value: 1 datatype: boolean} useexplicith: { value: 0 datatype: boolean} |
Tcl script | atomchange bondchange stereochange merge hadd ringsystem | y_smiles.xpd | ||||
| Y_STRONGLY_FUSED_RING_COUNT | int | Number of ESSSR rings in the ringsystem which are fused to another ring in the ring system by more than one bond | Compiled C module | R_SYSTEM R_TYPE Y_LABEL | atomchange bondchange atom bond ring | mod_y_strongly_fused_ring_count.so | ||||
| Y_SUBSTITUENT_COUNT | short | Number of non-hydrogen substituents outside ring system bonded via valence or complex bond | Compiled C module | A_TYPE B_TYPE A_ELEMENT | atomchange bondchange atom bond ring | mod_y_substituent_count.so | ||||
| Y_SUBSTITUENT_HASH | uint64 | Generalized molecule hash (of class M_HASHY) where all atoms in the ringsystem are set to a generic pseudo atom, and all ring hydrogens are ignored. | Compiled C module | M_HASHY | atomchange bondchange atom bond ring | mod_y_substituent_hash.so | ||||
| Y_UNSATURATION | short | Overall unsaturation of ring system (every non-aromatic multiple bond counts as n-1) | countarobonds: { value: 0 description: If set, aro bonds are counted with their Kekule bond order datatype: boolean}
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Compiled C module | B_TYPE B_ORDER B_ARORING_COUNT | atomchange bondchange atom bond ring | mod_y_unsaturation.so | |||
| Y_VB_NEIGHBOR_COUNT | short | Number of ligands on ringsystem | Compiled C module | A_TYPE B_TYPE | atomchange bondchange hadd atom bond ring | mod_y_vb_neighbor_count.so | ||||
| Z_ISOTOPE_DATA | compoundvector | Isotope information structure | isotope int weight double abundance double halflife double |
never |
Generated Thu Oct 06 19:46:02 CEST 2022 for toolkit version 3.4.8.22