OESuperpositionOptions¶

Attention

This API is currently available in C++ and Python.

class OESuperpositionOptions

This class represents OESuperpositionOptions that sets the optional parameters for structural superposition using the OEStructuralSuperposition class.

See also

OEStructuralSuperposition class
OESecondaryStructureSuperposition class

Constructors¶

OESuperpositionOptions()

Default constructor.

OESuperpositionOptions(const OESuperpositionOptions &rhs)

Copy constructor.

operator=¶

OESuperpositionOptions &operator=(const OESuperpositionOptions &argOpts)

Assignment operator.

AddSiteResidue¶

void AddSiteResidue(const std::string &argSiteResidue)

Add a single site residue for OESuperpositionType::Site -based superpositions based on a site-specific string that takes the form: <residue name>:<residue number>:<insertion code>:<chain id>.

See also

OESuperpositionOptions::SetSiteResidues method
OESuperpositionOptions::GetSiteResidues method
OESuperpositionOptions::ClearSiteResidues method

ClearLigandConstraints¶

void ClearLigandConstraints()

Clear the stored ligand constraints, if they exist.

See also

OESuperpositionOptions::SetLigandConstraints method
OESuperpositionOptions::GetLigandConstraints method
OESuperpositionOptions::HasLigandConstraints method

ClearSiteResidues¶

void ClearSiteResidues()

Remove any existing site residues from the OESuperpositionOptions object that would be used in the OESuperpositionType::Site -based superposition calculations.

See also

OESuperpositionOptions::AddSiteResidue method
OESuperpositionOptions::SetSiteResidues method
OESuperpositionOptions::GetSiteResidues method

GetDist¶

double GetDist() const

Get the cutoff distance used in the nearest neighbors calculation for the site residue constraints (default = 5.0 Angstroms) for OESuperpositionType::Site -based superpositions.

GetLigandConstraints¶

void GetLigandConstraints(OEChem::OEMolBase& refLig, OEChem::OEMolBase& fitLig) const

Returns by reference the reference and fit ligand constraints that are stored.

See also

OESuperpositionOptions::SetLigandConstraints method
OESuperpositionOptions::HasLigandConstraints method
OESuperpositionOptions::ClearLigandConstraints method

GetSiteResidues¶

std::vector<std::string> GetSiteResidues() const

Get the site residues used in the OESuperpositionType::Site -based calculation.

GetSuperpositionType¶

unsigned GetSuperpositionType() const

Get the type of superposition to be performed. Types are given from the constants given in OESuperpositionType. The default type is OESuperpositionType::Default.

HasLigandConstraints¶

bool HasLigandConstraints() const

Returns whether or not ligand constraints have been set.

See also

OESuperpositionOptions::SetLigandConstraints method
OESuperpositionOptions::GetLigandConstraints method
OESuperpositionOptions::ClearLigandConstraints method

SetDist¶

void SetDist(double argDist)

Set the cutoff distance used in the nearest neighbors calculation for the site residue constraints for OESuperpositionType::Site -based superpositions.

SetLigandConstraints¶

void SetLigandConstraints(const OEChem::OEMolBase& refLig, const OEChem::OEMolBase& fitLig)

Sets the ligand constraints that will be used for the superposition.

See also

OESuperpositionOptions::GetLigandConstraints method
OESuperpositionOptions::HasLigandConstraints method
OESuperpositionOptions::ClearLigandConstraints method

SetSiteResidues¶

void SetSiteResidues(const std::vector<std::string> &argSiteResidues)

Set all site residues at once for OESuperpositionType::Site -based superpositions using a string vector, where each string takes the form <residue name>:<residue number>:<insertion code>:<chain id>.

See also

OESuperpositionOptions::AddSiteResidue method
OESuperpositionOptions::GetSiteResidues method
OESuperpositionOptions::ClearSiteResidues method

SetSuperpositionType¶

bool SetSuperpositionType(unsigned type)

Set the type of superposition to be performed. Types are taken from the constants given in OESuperpositionType.