sigma append

sigma append ehandle label ?property value?...

s.append({?property:value,?...})

s.append(?property,value,?...)

Standard data manipulation command for appending property data. It is explained in more detail in the section about setting property data.

sigma atoms

sigma atoms ehandle label ?filterset? ?filtermode?

s.atoms(?filters=?,?mode=?)

Standard cross-referencing command to obtain the labels or references of the atoms in the σ system. This is explained in more detail in the section about object cross-references.

sigma bonds

sigma bonds ehandle label ?filterset? ?filtermode?

s.bonds(?filters=?,?mode=?)

Standard cross-referencing command to obtain the labels or references of the bonds between the atoms associated with a σ system. This is explained in more detail in the section about object cross-references.

sigma create

sigma create ehandle ?atom/atomlist?...

Sigma(eref,?aref/arefsequence/alabel?,...)

Sigma(aref,...)

Sigma.Create(eref,?aref/arefsequence/alabel?,...)

Sigma.Create(aref,...)

Define a new σ system from an atom set, which may be empty. A new system is always created, even if one with the same atoms already exists. Before the command is executed, the default π system set is automatically instantiated if it was not yet computed. Adding a new system invalidates properties which are sensitive to σ set changes.

The command returns the label or reference of the new σ system.

sigma defined

sigma defined ehandle label property

s.defined(property)

This command checks whether a property is defined for the σ system. This is explained in more detail in the section about property validity checking. Note that this is not a check for the presence of property data! The ens valid command is used for this purpose.

sigma delete

sigma delete ehandle ?label?...

sigma delete ehandle all

s.delete()

Sigma.Delete(eref,?sref/slabel/srefsequence?,...)

Sigma.Delete(sref,...)

Sigma.Delete(eref,“all”)

This command deletes specific or all σ systems from the ensemble. A sigma property invalidation event is generated and thus the command may indirectly change the ensemble data.

The command returns the number of deleted items.

sigma dget

sigma dget ehandle label propertylist ?filterset? ?parameterdict?

s.dget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the sigma get command. The difference between sigma get and sigma dget is that the latter does not attempt computation of property data, but rather initializes the property values to the default and returns that default if the data is not yet available. For data already present, sigma get and sigma dget are equivalent.

sigma ens

s.ens()

Python -only method to get the ensemble reference from a σ reference.

sigma exists

sigma exists ehandle label ?filterlist?

s.exists(?filters=?)

Sigma.Exists(eref,label,?filters=?)

Check whether this σ system exists. Optionally, a filter list can be supplied to check for the presence of specific features. The command returns 0 if the system does not exist, or fails the filter, and 1 in case of successful testing.

sigma expr

sigma expr ehandle label expression

s.expr(expression)

Compute a standard SQL -style property expression for the σ system. This is explained in detail in the chapter on property expressions.

sigma fill

sigma fill ehandle label ?property value?...

s.fill({property:value,...})

s.fill(?property,value?,...)

Standard data manipulation command for setting data, ignoring possible mismatches between the lengths of the lists of objects associated with the property and the value list. It is explained in more detail in the section about setting property data.

The command returns the first fill value.

sigma filter

sigma filter ehandle label filterlist

s.filter(filters)

Check whether a σ system passes a filter list. The return value is boolean 1 for success and 0 for failure.

sigma get

sigma get ehandle label propertylist ?filterset? ?parameterdict?

s.get(property=,?filters=?,?parameters=?)

s[property]

s.property

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

sigma groups

sigma groups ehandle label ?filterset? ?filtermode?

s.groups(?filters=?,?groups=?)

Standard cross-referencing command to obtain the labels or references of the groups the σ system overlaps with. This is explained in more detail in the section about object cross-references. An overlap between a σ system and a group is established when there are common atoms which are contained in both objects.

Example:

sigma groups $ehandle 1

sigma index

sigma index ehandle label

s.index()

Get the index of the σ system. The index is the position in the σ set of the ensemble. The first position is index 0.

Example:

sigma index $ehandle 99

sigma jget

sigma jget ehandle label propertylist ?filterset? ?parameterdict?

s.jget(property=,?filters=?,?parameters=?)

This is a variant of sigma get which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

sigma jnew

sigma jnew ehandle label propertylist ?filterset? ?parameterdict?

s.jnew(property=,?filters=?,?parameters=?)

This is a variant of sigma new which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

sigma jshow

sigma jshow ehandle label propertylist ?filterset? ?parameterdict?

s.jshow(property=,?filters=?,?parameters=?)

This is a variant of sigma show which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

sigma local

sigma local ehandle label propertylist ?filterset? ?parameterdict?

s.local(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading and recalculating object data. It is explained in more detail in the section about retrieving property data.

sigma mol

sigma mol ehandle label ?filterset? ?filtermode?

s.mol(?filters=?,?mode=?)

Standard cross-referencing command to obtain the label or reference of the molecule a σ system is part of. This is explained in more detail in the section about object cross-references.

sigma new

sigma new ehandle label propertylist ?filterset? ?parameterdict?

s.new(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

The difference between sigma get and sigma new is that the latter forces the re-computation of the property data, regardless whether it is present and valid, or not.

sigma nget

sigma nget ehandle label propertylist ?filterset? ?parameterdict?

s.nget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the sigma get command. The difference between sigma get and sigma nget is that the latter always returns numeric data, even if symbolic names for the values are available.

sigma pis

sigma pis ehandle label ?filterset? ?filtermode?

s.pis(?filter=?,?mode=?)

Standard cross-referencing command to obtain the labels or references of the π systems the σ system overlaps with. This is explained in more detail in the section about object cross-references.

Examples:

sigma pis $ehandle 1

sigma ref

Sigma.Ref(eref,identifier)

Python only method to get a σ reference. See sigma sigma command.

sigma rings

sigma rings ehandle label ?filterset? ?filtermode?

s.rings(?filters=?,?mode=?)

Standard cross-referencing command to obtain the labels or references of the rings the σ system is associated with. This is explained in more detail in the section about object cross-references. Rings which only partially overlap with the sigma system are included.

sigma ringsystems

sigma ringsystems ehandle label ?filterset? ?filtermode?

s.ringsystems(?filters=?,?mode=?)

Standard cross-referencing command to obtain the labels or references of the ring systems the σ system overlaps with. This is explained in more detail in the section about object cross-references.

sigma set

sigma set ehandle label ?property value?...

s.set(?property,value?,...)

s.set({property:value,...})

s.property = value

s[property] = value

Standard data manipulation command. It is explained in more detail in the section about setting property data.

sigma show

sigma show ehandle label propertylist ?filterset? ?parameterdict?

s.show(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the sigma get command. The difference between sigma get and sigma show is that the latter does not attempt computation of property data, but raises an error if the data is not present and valid. For data already present, sigma get and sigma show are equivalent.

sigma sigma

sigma sigma ehandle label

Sigma.Ref(eref,identifier)

Standard cross-referencing command to obtain the label or reference of the σ system as stored in property S_LABEL . This is explained in more detail in the section about object cross-references.

Example:

sigma sigma $ehandle #0

returns the label of the first σ system of the ensemble σ set.

sigma sqldget

sigma sqldget ehandle label propertylist ?filterset? ?parameterdict?

s.sqldget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the sigma get command. The differences between sigma get and sigma sqldget are that the latter does not attempt computation of property data, but initializes the property value to the default and returns that default, if the data is not present and valid; and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

sigma sqlget

sigma sqlget ehandle label propertylist ?filterset? ?parameterdict?

s.sqlget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the sigma get command. The difference between sigma get and sigma sqlget is that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

sigma sqlnew

sigma sqlnew ehandle label propertylist ?filterset? ?parameterdict?

s.sqlnew(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the sigma get command. The differences between sigma get and sigma sqlnew are that the latter forces re-computation of the property data, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

sigma sqlshow

sigma sqlshow ehandle label propertylist ?filterset? ?parameterdict?

s.sqlshow(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the sigma get command. The differences between sigma get and sigma sqlshow are that the latter does not attempt computation of property data, but raises an error if the data is not present and valid, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

sigma subcommands

sigma subcommands

dir(Sigma)

Lists all subcommands of the sigma command. Note that this command does not require an ensemble handle, nor a sigma label.

sigma surfaces

sigma surfaces ehandle label ?filterset? ?filtermode?

s.surfaces(?filters=?,?mode=?)

Standard cross-referencing command to obtain the labels of the surface patches the σ system is associated with. This is explained in more detail in the section about object cross-references.

sigma xbonds

sigma xbonds ehandle label ?filterset? ?filtermode?

s.xbonds(?filters=?,?mode=?)

Get labels or references of crossing bonds which are not contained in the σ system (defined as all bonds between the registered atoms in the system), but have one atom in the σ system.