OESuperpositionOptions

Attention

This is a preliminary API until Fall 2020 and may be improved based on user feedback. It 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

Code Example

• Calculating simple superposition example

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.