OEMolComplexCategorizer¶

class OEMolComplexCategorizer : public OEMolComplexCategorizerBase

Concrete class functor used by OESplitMolComplex and OEGetMolComplexComponents to assign functional roles to molecular fragments. The OESplitMolComplexOptions class holds a OEMolComplexCategorizer object by default.

The following methods are publicly inherited from OEMolComplexCategorizerBase:

`operator()`	`GetBundleCofactors`
`CreateCopy`	`UsingExplicitLigandName`
`GetResidueCategoryData`

Constructors¶

OEMolComplexCategorizer(const OEMolComplexCategorizer &rhs)
OEMolComplexCategorizer(const std::string &ligName=std::string())

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

See also

OEMolComplexCategorizer::AddLigandName

operator=¶

OEMolComplexCategorizer &operator=(const OEMolComplexCategorizer &rhs)

Assignment operator.

operator()¶

std::string operator()(OESystem::OERoleSet &roles,
                       std::map<std::string, unsigned> &counts,
                       const OEChem::OEAtomBondSet& frag,
                       bool isCovalent = false) const

Method to examine the OEAtomBondSet frag and return three things required by OESplitMolComplex and OEGetMolComplexComponents to process the component:

a new title string
a OERoleSet containing the functional roles associated with this fragment (see OEMolComplexFilterCategory)
an updated map of how many times a residue has been seen to date

If isCovalent is true, additional tests may be performed to determine whether the fragment might be considered a (covalent) ligand which is indicated with the OEMolComplexFilterCategory::Ligand OERole in roles.

AddLigandName¶

void AddLigandName(const std::string &ligName)

Store an additional ligand name in the OEResidueCategoryData associated with this object. Method UsingExplicitLigandName will return true and components will be recognized as ligands if and only if they have a residue name string matching one of the OEResidueDatabaseCategory::Ligand entries.

See also

OEMolComplexCategorizer::Constructors
OEMolComplexCategorizer::SetResidueCategoryData

ClearLigandSubSearch¶

void ClearLigandSubSearch()

Clear any ligand subsearch pattern.

See also

OEMolComplexCategorizer::GetLigandSubSearch
OEMolComplexCategorizer::SetLigandSubSearch

CreateCopy¶

OEMolComplexCategorizerBase *CreateCopy() const

CreateCopy method.

GetBundleCofactors¶

bool GetBundleCofactors() const

Returns true if cofactors (other than metals) are associated with the category OEMolComplexFilterCategory::ProtComplex.

GetLigandSubSearch¶

OEChem::OESubSearch GetLigandSubSearch() const

Return the subsearch pattern used to identify the ligand by graph.

See also

Substructure Search section
OEMolComplexCategorizer::SetLigandSubSearch
OEMolComplexCategorizer::ClearLigandSubSearch

GetMaxLigAtoms¶

unsigned GetMaxLigAtoms() const

Return the maximum number of non-hydrogen atoms in a ligand.

See also

OEMolComplexCategorizer::SetMaxLigAtoms

GetMaxLigResidues¶

unsigned GetMaxLigResidues() const

See also

OEMolComplexCategorizer::SetMaxLigResidues

Return the maximum number of residues in a ligand.

GetMaxPeptideResidues¶

unsigned GetMaxPeptideResidues() const

Return the maximum number of residues in a peptide.

GetMaxProteinAtoms¶

unsigned GetMaxProteinAtoms() const

Return the maximum number of non-hydrogen atoms in a protein.

GetMinLigAtoms¶

unsigned GetMinLigAtoms() const

Return the minimum number of non-hydrogen atoms in a ligand.

See also

OEMolComplexCategorizer::SetMinLigAtoms

GetResidueCategoryData¶

OEResidueCategoryData *GetResidueCategoryData() const

Return a new copy of the OEResidueCategoryData object used to define all the molecular components that are not ligands.

To avoid a memory leak in C++, the returned pointer should be stored in a variable of the OEOwnedPtr template class or deallocated with the delete operator.

OEResidueCategoryData& GetResidueCategoryData()

Returns a reference to the OEResidueCategoryData object used to define all the molecular components that are not ligands.

SetBundleCofactors¶

void SetBundleCofactors(bool bundle=true)

Controls whether cofactors (other than metals) should be associated with the category OEMolComplexFilterCategory::ProtComplex.

SetLigandSubSearch¶

void SetLigandSubSearch(const char *smarts)
void SetLigandSubSearch(const OEChem::OESubSearch &ss)

Define a subsearch pattern used to identify the ligand by graph.

See also

Substructure Search section
OEMolComplexCategorizer::GetLigandSubSearch
OEMolComplexCategorizer::ClearLigandSubSearch

SetMaxLigAtoms¶

void SetMaxLigAtoms(unsigned n)

Set the maximum number of non-hydrogen atoms in a ligand. Default = 70.

Note

When no ligand is found, other molecules such as peptides, nucleic acids, or sugars may be treated as ligands. If this occurs, this restriction will not apply.

SetMaxLigResidues¶

void SetMaxLigResidues(unsigned n)

Set the maximum number of residues in a ligand. Default = 3.

Note

When no ligand is found, other molecules such as peptides, nucleic acids, or sugars may be treated as ligands. If this occurs, this restriction will not apply.

SetMaxPeptideResidues¶

void SetMaxPeptideResidues(unsigned n)

Set the maximum number of residues to be considered a peptide. Default = 49.

SetMaxProteinAtoms¶

void SetMaxProteinAtoms(unsigned n)

Set the maximum number of non-hydrogen atoms in a protein. Default = 0, meaning unlimited.

SetMinLigAtoms¶

void SetMinLigAtoms(unsigned n)

Set the minimum number of non-hydrogen atoms in a ligand. Default = 4.

Note

When no ligand is found, other molecules such as peptides, nucleic acids, or sugars may be treated as ligands. If this occurs, this restriction will not apply.

SetResidueCategoryData¶

void SetResidueCategoryData(const OEResidueCategoryData &db)

Set the OEResidueCategoryData object used to define all the molecular components that are not ligands.

UsingExplicitLigandName¶

bool UsingExplicitLigandName() const

Returns true if an explicit ligand residue name is being used to identify the ligand.