MolTransforms Namespace Reference

Functions
void	transformMolsAtoms (RDKit::ROMol *mol, RDGeom::Transform3D &tform)
void	transformAtom (RDKit::Atom *atom, RDGeom::Transform3D &tform)
RDGeom::Point3D	computeCentroid (const RDKit::Conformer &conf, bool ignoreHs=true)
	Compute the centroid of a conformer.
RDNumeric::DoubleSymmMatrix *	computeCovarianceMatrix (const RDKit::Conformer &conf, const RDGeom::Point3D &center, bool normalize=false, bool ignoreHs=true)
	Compute the covariance matrix for a conformer.
RDGeom::Transform3D *	computeCanonicalTransform (const RDKit::Conformer &conf, const RDGeom::Point3D *center=0, bool normalizeCovar=false, bool ignoreHs=true)
void	transformConformer (RDKit::Conformer &conf, const RDGeom::Transform3D &trans)
	Transform the conformation using the specified transformation.
void	canonicalizeConformer (RDKit::Conformer &conf, const RDGeom::Point3D *center=0, bool normalizeCovar=false, bool ignoreHs=true)
void	canonicalizeMol (RDKit::ROMol &mol, bool normalizeCovar=false, bool ignoreHs=true)
	Canonicalize all the conformations in a molecule.

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Function Documentation

void MolTransforms::canonicalizeConformer	(	RDKit::Conformer &	conf,
		const RDGeom::Point3D *	center = 0,
		bool	normalizeCovar = false,
		bool	ignoreHs = true
	)

Canonicalize the orientation of a conformer so that its principal axes around the specified center point coincide with the x, y, z axes

Parameters:

	conf	The conformer of interest
	center	Optional center point about which the principal axes are computed if not specified the centroid of the conformer will be used
	normalizeCovar	Optionally normalize the covariance matrix by the number of atoms
	ignoreHs	If true, ignore hydrogen atoms

void MolTransforms::canonicalizeMol	(	RDKit::ROMol &	mol,
		bool	normalizeCovar = false,
		bool	ignoreHs = true
	)

Canonicalize all the conformations in a molecule.

Parameters:

	mol	the molecule of interest
	normalizeCovar	Optionally normalize the covariance matrix by the number of atoms
	ignoreHs	If true, ignore hydrogens

RDGeom::Transform3D* MolTransforms::computeCanonicalTransform	(	const RDKit::Conformer &	conf,
		const RDGeom::Point3D *	center = 0,
		bool	normalizeCovar = false,
		bool	ignoreHs = true
	)

Compute the transformation require to orient the conformation along the principal axes about the center; i.e. center is made to coincide with the origin, the largest princiapl axis with the x-axis, the next largest with the y-axis and the smallest with the z-axis

If center is not specified the the centroid of the conformer will be used

Parameters:

	conf	Conformer of interest
	center	Center to be used for canonicalization, defaults to the centroid of the conformation
	normalizeCovar	Normalize the covariance matrix with the number of atoms
	ignoreHs	Optinally ignore hydrogens

RDGeom::Point3D MolTransforms::computeCentroid	(	const RDKit::Conformer &	conf,
		bool	ignoreHs = true
	)

Compute the centroid of a conformer.

This is simple the average of the heavy atom locations in the conformer, not attention is paid to hydrogens or the differences in atomic radii

Parameters:

	conf	Conformer of interest
	ignoreHs	If true, ignore hydrogen atoms

RDNumeric::DoubleSymmMatrix* MolTransforms::computeCovarianceMatrix	(	const RDKit::Conformer &	conf,
		const RDGeom::Point3D &	center,
		bool	normalize = false,
		bool	ignoreHs = true
	)

Compute the covariance matrix for a conformer.

Parameters:

	conf	Conformer of interest
	center	Center to be used for covariance matrix calculation
	normalize	If true, normalize the covariance matrix by the number of atoms
	ignoreHs	If true, ignore hydrogen atoms

void MolTransforms::transformAtom	(	RDKit::Atom *	atom,
		RDGeom::Transform3D &	tform
	)

void MolTransforms::transformConformer	(	RDKit::Conformer &	conf,
		const RDGeom::Transform3D &	trans
	)

Transform the conformation using the specified transformation.

void MolTransforms::transformMolsAtoms	(	RDKit::ROMol *	mol,
		RDGeom::Transform3D &	tform
	)