OEStructuralSuperposition

Warning

This is a deprecated API. Please use OESuperpose class instead.

Attention

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

class OEStructuralSuperposition

This class represents OEStructuralSuperposition that performs a structural superposition on fit protein to a reference protein, using a superposition method given as an optional parameter.

See also

• OESuperpositionOptions class

• OESecondaryStructureSuperposition class

Constructors

OEStructuralSuperposition(argRefMol: Union[OEGraphMol,OEMol,OEQMol],
                          argFitMol: Union[OEGraphMol,OEMol,OEQMol],
                          argOpts: OESuperpositionOptions = OESuperpositionOptions()) -> OEStructuralSuperposition

Constructor that superimposes the argFitMol to the argRefMol. If no OESuperpositionOptions are passed in as argOpts, then the default behavior of using a superposition to all globally matched atoms will be used.

Both argRefMol and argFitMol must have 3D coordinates assigned.

OEStructuralSuperposition(rhs: OEStructuralSuperposition) -> OEStructuralSuperposition

Copy constructor.

operator bool

IsValid() -> bool

Returns whether the OEStructuralSuperposition object is valid.

ConstraintsMet

ConstraintsMet() -> bool

Returns whether or not the constraints were met.

GetFitChains

GetFitChains() -> OEStringVector

Returns 1-letter code of all names of fit protein chains.

See also

• OEStructuralSuperposition.GetRefChains method

GetRMSD

GetRMSD() -> float

Returns the RMSD of the structural superposition.

GetRefChains

GetRefChains() -> OEStringVector

Returns 1-letter code of all names of reference protein chains.

See also

• OEStructuralSuperposition.GetFitChains method

GetRegion

GetRegion() -> OEIntVector

Returns the index of all residues involved in the alignment.

GetRotMatrix

GetRotMatrix(rmat: OEDoubleArray) -> None

Returns by reference the rotation matrix of the superposition.

GetScore

GetScore() -> int

Returns the sequence alignment score for the structural superposition.

GetTranslation

GetTranslation(trans: OEDoubleArray) -> None

Returns by reference the translation vector of the superposition.

Transform

Transform(mol: Union[OEGraphMol,OEMol,OEQMol]) -> None

Transforms the input molecule using the stored rotation matrix and translation vector from the superposition.