RDKit::MolAlign Namespace Reference

Classes
class	MolAlignException
Functions
double	getAlignmentTransform (const ROMol &prbMol, const ROMol &refMol, RDGeom::Transform3D &trans, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50)
	Alignment functions.
double	alignMol (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50)
	Optimally (minimum RMSD) align a molecule to another molecule.
void	alignMolConformers (ROMol &mol, const std::vector< unsigned int > *atomIds=0, const std::vector< unsigned int > *confIds=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50)
	Align the conformations of a molecule using a common set of atoms.

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Function Documentation

double RDKit::MolAlign::alignMol	(	ROMol &	prbMol,
		const ROMol &	refMol,
		int	prbCid = -1,
		int	refCid = -1,
		const MatchVectType *	atomMap = 0,
		const RDNumeric::DoubleVector *	weights = 0,
		bool	reflect = false,
		unsigned int	maxIters = 50
	)

Optimally (minimum RMSD) align a molecule to another molecule.

The 3D transformation required to align the specied conformation in the probe molecule to a specified conformation in the reference molecule is computed so that the root mean squared distance between a specified set of atoms is minimized. This transforms is them applied to the specified conformation in the probe molecule

Parameters:

	prbMol	molecule that is to be aligned
	refMol	molecule used as the reference for the alignment
	prbCid	ID of the conformation in the probe to be used for the alignment (defaults to first conformation)
	refCid	ID of the conformation in the ref molecule to which the alignment is computed (defaults to first conformation)
	atomMap	a vector of pairs of atom IDs (probe AtomId, ref AtomId) used to compute the alignments. If this mapping is not specified an attempt is made to generate on by substructure matching
	weights	Optionally specify weights for each of the atom pairs
	reflect	if true reflect the conformation of the probe molecule
	maxIters	maximum number of iteration used in mimizing the RMSD

Returns RMSD value

void RDKit::MolAlign::alignMolConformers	(	ROMol &	mol,
		const std::vector< unsigned int > *	atomIds = 0,
		const std::vector< unsigned int > *	confIds = 0,
		const RDNumeric::DoubleVector *	weights = 0,
		bool	reflect = false,
		unsigned int	maxIters = 50
	)

Align the conformations of a molecule using a common set of atoms.

Parameters:

	mol	The molecule of interest
	atomIds	vector of atoms to be used to generate the alignment. All atoms will be used is not specified
	confIds	vector of conformations to align - defaults to all
	weights	vector of weights to applied to particular atom pairs defaults to all weights = 1
	reflect	toggles reflecting (about the origin) the alignment
	maxIters	the maximum number of iterations to attempt

double RDKit::MolAlign::getAlignmentTransform	(	const ROMol &	prbMol,
		const ROMol &	refMol,
		RDGeom::Transform3D &	trans,
		int	prbCid = -1,
		int	refCid = -1,
		const MatchVectType *	atomMap = 0,
		const RDNumeric::DoubleVector *	weights = 0,
		bool	reflect = false,
		unsigned int	maxIters = 50
	)

Alignment functions.

Compute the transformation required to align a molecule

The 3D transformation required to align the specied conformation in the probe molecule to a specified conformation in the reference molecule is computed so that the root mean squared distance between a specified set of atoms is minimized

Parameters:

	prbMol	molecule that is to be aligned
	refMol	molecule used as the reference for the alignment
	trans	storage for the computed transform
	prbCid	ID of the conformation in the probe to be used for the alignment (defaults to first conformation)
	refCid	ID of the conformation in the ref molecule to which the alignment is computed (defaults to first conformation)
	atomMap	a vector of pairs of atom IDs (probe AtomId, ref AtomId) used to compute the alignments. If this mapping is not specified an attempt is made to generate on by substructure matching
	weights	Optionally specify weights for each of the atom pairs
	reflect	if true reflect the conformation of the probe molecule
	maxIters	maximum number of iteration used in mimizing the RMSD

Returns RMSD value