OESplitMolComplexOptions

class OESplitMolComplexOptions

The OESplitMolComplexOptions class encapsulates properties and resources that determine how OESplitMolComplex and OEGetMolComplexComponents operate. For examples detailing how to modify and/or operate different filters see Splitting Macromolecular Complexes.

Constructors

OESplitMolComplexOptions(ligName: str = str()) -> OESplitMolComplexOptions
OESplitMolComplexOptions(rhs: OESplitMolComplexOptions) -> OESplitMolComplexOptions

Constructor and copy constructor. If ligName is specified in the call to the constructor, components will be recognized as ligands if and only if they have a matching residue name string.

See also

GetAddRGroup

GetAddRGroup() -> bool

Returns true if “R groups” are to be added when covalent bonds are broken.

GetAdjustHCount

GetAdjustHCount() -> bool

Returns true if the implicit hydrogen count is to be adjusted when covalent bonds are broken.

GetAssumptions

GetAssumptions() -> int

Return assumptions about molecular perception.

See also

GetCategorizer

GetCategorizer() -> OEMolComplexCategorizerBase

Return a new copy of the OEMolComplexCategorizerBase object used to categorize molecular components.

GetCollectProteinByChain

GetCollectProteinByChain() -> bool

Returns true if fragmented protein chains be associated with the same the same site.

GetCombinedFilter

GetCombinedFilter() -> OEUnaryRoleSetPred

Returns a new copy of the filter that matches the ligand or protein or water filters.

See also

GetLigandFilter

GetLigandFilter() -> OEUnaryRoleSetPred

Returns a new copy of the ligand filter.

GetMaxBindingSiteDist

GetMaxBindingSiteDist() -> float

Return the maximum distance from the ligand to be associated with a binding site. Can not be less than 1.0 Å.

GetMaxSurfaceWaterDist

GetMaxSurfaceWaterDist() -> float

Return the maximum distance from the protein to be considered a surface water. Can not be less than 1.0 Å.

GetOtherFilter

GetOtherFilter() -> OEUnaryRoleSetPred

Returns a new copy of the filter that matches everything that does not match the combined filter.

See also

GetPromoteUnknowns

GetPromoteUnknowns() -> bool

Returns true if components classified as OEMolComplexFilterCategory_Unknown should be considered the ligand if no others ligand is found.

GetProteinFilter

GetProteinFilter() -> OEUnaryRoleSetPred

Returns a new copy of the protein filter.

GetSeparateResidues

GetSeparateResidues() -> bool

Returns true if proteins are to be separated into individual residues before selection. Separating into residues can be used to extract binding site residues.

GetSplitCovalent

GetSplitCovalent() -> bool

Returns true if covalent ligands are to be searched for and split out as separate components.

GetSplitCovalentCofactors

GetSplitCovalentCofactors() -> bool

Returns true if covalent cofactors are to be searched for and split out as separate components.

GetWarnNoLigand

GetWarnNoLigand() -> bool

Returns true if a verbose level warning will be generated when a ligand is not found.

GetWaterFilter

GetWaterFilter() -> OEUnaryRoleSetPred

Returns a new copy of the water filter.

ResetFilters

ResetFilters(site: int = 1, surfaceWaters: bool = False,
             ligCategory: int, protCategory: int,
             waterCategory: int, modelNo: int = 1) -> None

Regenerate filters based on parameters. Can be overridden by methods to set individual filters. Site 0 means all sites. ModelNo 0 means all models.

Note

It may be necessary to remove the input flavor OEIFlavor_PDB_ENDM to read all models (see the splitmolcomplex example for how to do this). In most situations, the modelNo parameter should be set to either 0 or 1 (the default). The reason for this is that the site counter, which the site parameter selects based on, does not reset for each model and therefore site and model are not independent. A good example of where this can be used is with a PDB biological assembly file: setting the modelNo parameter to 0 (use all models), allows a binding site spanning symmetry related proteins marked as different models to be recognized.

See also

SetAddRGroup

SetAddRGroup(addR: bool = True) -> None

Set whether “R groups” are to be added when covalent bonds are broken.

SetAdjustHCount

SetAdjustHCount(adjust: bool = True) -> None

Set whether the implicit hydrogen count is to be adjusted when covalent bonds are broken.

SetAssumptions

SetAssumptions(assume: int) -> None

Set assumptions about molecular perception. Default = OEAssumption_ResPerceived

SetCategorizer

SetCategorizer(cat: OEMolComplexCategorizerBase) -> None

Set the OEMolComplexCategorizerBase object used to categorize molecular components.

SetCollectProteinByChain

SetCollectProteinByChain(collect: bool = True) -> None

Set whether fragmented protein chains should be collected into the same site. Default = true

SetLigandFilter

SetLigandFilter(f: OEUnaryRoleSetPred) -> None

Set the ligand filter. Default is an OEMolComplexFilterFactory created with OEMolComplexFilterCategory_Ligand

See also

SetMaxBindingSiteDist

SetMaxBindingSiteDist(dist: float) -> None

Set the maximum distance from the ligand to be associated with a binding site. Default = 8.0 Å

SetMaxSurfaceWaterDist

SetMaxSurfaceWaterDist(dist: float) -> None

Set the maximum distance from the protein to be considered a surface water. Default = 5.0 Å

SetPromoteUnknowns

SetPromoteUnknowns(promote: bool = True) -> None

Set whether components classified as OEMolComplexFilterCategory_Unknown should be considered the ligand if no others ligand is found. Default = true

SetProteinFilter

SetProteinFilter(f: OEUnaryRoleSetPred) -> None

Set the protein filter. Default is an OEMolComplexFilterFactory created with OEMolComplexFilterCategory_ProtComplex

See also

SetSeparateResidues

SetSeparateResidues(separate: bool = True) -> None

Set whether to separate proteins into individual residues before selection. Can be used to identify binding site residues. Default = false

SetSplitCovalent

SetSplitCovalent(split: bool = True) -> None

Set whether covalent ligands are to be searched for and split out as separate components. Default = false

SetSplitCovalentCofactors

SetSplitCovalentCofactors(split: bool = True) -> None

Set whether covalent cofactors are to be searched for and split out as separate components. Default = false

SetWarnNoLigand

SetWarnNoLigand(warn: bool = True) -> None

Set whether to send out a verbose level warning if a ligand is not found. Default = true

SetWaterFilter

SetWaterFilter(f: OEUnaryRoleSetPred) -> None

Set the water filter. Default is an OEMolComplexFilterFactory created with OEMolComplexFilterCategory_Water

See also