OESuperposeOptions

Attention

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

class OESuperposeOptions

This class represents OESuperposeOptions that sets the optional parameters for structural superposition using the OESuperpose class.

Code Example

Constructors

OESuperposeOptions(const unsigned method = OESuperposeMethod::Default)

Default constructor.

OESuperposeOptions(const OESuperposeOptions &rhs)

Copy constructor.

operator=

OESuperposeOptions &operator=(const OESuperposeOptions &argOpts)

Assignment operator.

GetMethod

unsigned GetMethod() const

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

SetMethod

bool SetMethod(unsigned value)

Sets the type of superposition to be performed. Types are taken from the constants given in OESuperposeMethod.

GetUseConstraints

unsigned GetUseConstraints() const

Returns whether or not ligand or site-residue constraints should be used to validate the superposition.

SetUseConstraints

bool SetUseConstraints(unsigned value)

Sets whether or not ligand or site-residue constraints should be used to validate the superposition.

GetValidRMSD

double GetValidRMSD() const

Returns the RMSD threshold for validating the superposition of the reference and fit molecules. OESuperposeResults::IsValid returns false if the RMSD of the superposed molecules exceeds this threshold. The default value is 10.0 Angstroms for sequence-based methods and -1.0 for shape-based methods (RMSD calculation is only applicable to sequence-based methods).

SetValidRMSD

bool SetValidRMSD(double value)

Sets the RMSD threshold for validating the superposition of the reference and fit molecules.

Warning

RMSD calculation is only applicable to sequence-based methods. Please avoid using this function when running shape-based superposition.

GetValidTanimoto

double GetValidTanimoto() const

Returns the Tanimoto threshold for validating the superposition of the reference and fit molecules. OESuperposeResults::IsValid returns false if the Tanimoto of the superposed molecules is smaller than this threshold. The default value is 0.0 for shape-based methods and -1.0 for sequence-based methods (Tanimoto calculation is only applicable to shape-based methods).

SetValidTanimoto

bool SetValidTanimoto(double value)

Sets the Tanimoto threshold for validating the superposition of the reference and fit molecules.

Warning

Tanimoto calculation is only applicable to shape-based methods. Please avoid using this function when running sequence-based superposition.

GetValidSeqScore

int GetValidSeqScore() const

Returns the sequence alignment score threshold for validating the superposition of the reference and fit molecules. OESuperposeResults::IsValid returns false if the sequence alignment score of the superposed molecules is smaller than this threshold. The default value is 200 for sequence-based methods and -1000 for shape-based methods (sequence alignment score is only applicable to sequence-based methods).

SetValidSeqScore

bool SetValidSeqScore(int value)

Sets the sequence alignment score threshold for validating the superposition of the reference and fit molecules.

Warning

sequence alignment score is only applicable to sequence-based methods. Please avoid using this function when running shape-based superposition.