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. More...

RDNumeric::DoubleSymmMatrix *	computeCovarianceMatrix (const RDKit::Conformer &conf, const RDGeom::Point3D &center, bool normalize=false, bool ignoreHs=true)
	Compute the covariance matrix for a conformer. More...

RDGeom::Transform3D *	computeCanonicalTransform (const RDKit::Conformer &conf, const RDGeom::Point3D *center=0, bool normalizeCovar=false, bool ignoreHs=true)
	origin, the largest princiapl axis with the x-axis, the next largest with More...

void	transformConformer (RDKit::Conformer &conf, const RDGeom::Transform3D &trans)
	Transform the conformation using the specified transformation. More...

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. More...

double	getBondLength (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId)
	Get the bond length between the specified atoms i, j. More...

void	setBondLength (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, double value)

double	getAngleRad (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId)
	Get the angle in radians among the specified atoms i, j, k. More...

double	getAngleDeg (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId)
	Get the angle in degrees among the specified atoms i, j, k. More...

void	setAngleRad (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, double value)

void	setAngleDeg (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, double value)

double	getDihedralRad (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId)
	Get the dihedral angle in radians among the specified atoms i, j, k, l. More...

double	getDihedralDeg (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId)
	Get the dihedral angle in degrees among the specified atoms i, j, k, l. More...

void	setDihedralRad (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId, double value)

void	setDihedralDeg (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId, double value)

Function Documentation

◆ canonicalizeConformer()

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

◆ canonicalizeMol()

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

◆ computeCanonicalTransform()

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

origin, the largest princiapl axis with the x-axis, the next largest with

Compute the transformation require to orient the conformation along the principal axes about the center; i.e. center is made to coincideand 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

◆ computeCentroid()

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

◆ computeCovarianceMatrix()

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

◆ getAngleDeg()

double MolTransforms::getAngleDeg	(	const RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId
	)

inline

Get the angle in degrees among the specified atoms i, j, k.

Definition at line 118 of file MolTransforms.h.

References getAngleRad(), M_PI, and setAngleRad().

◆ getAngleRad()

double MolTransforms::getAngleRad	(	const RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId
	)

Get the angle in radians among the specified atoms i, j, k.

Referenced by getAngleDeg().

◆ getBondLength()

double MolTransforms::getBondLength	(	const RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId
	)

Get the bond length between the specified atoms i, j.

◆ getDihedralDeg()

double MolTransforms::getDihedralDeg	(	const RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId,
		unsigned int	lAtomId
	)

inline

Get the dihedral angle in degrees among the specified atoms i, j, k, l.

Definition at line 142 of file MolTransforms.h.

References getDihedralRad(), M_PI, and setDihedralRad().

◆ getDihedralRad()

double MolTransforms::getDihedralRad	(	const RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId,
		unsigned int	lAtomId
	)

Get the dihedral angle in radians among the specified atoms i, j, k, l.

Referenced by getDihedralDeg(), and setAngleDeg().

◆ setAngleDeg()

void MolTransforms::setAngleDeg	(	RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId,
		double	value
	)

inline

Set the angle in degrees among the specified atoms i, j, k (all atoms bonded to atom k are moved)

Definition at line 130 of file MolTransforms.h.

References getDihedralRad(), M_PI, and setAngleRad().

◆ setAngleRad()

void MolTransforms::setAngleRad	(	RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId,
		double	value
	)

Set the angle in radians among the specified atoms i, j, k (all atoms bonded to atom k are moved)

Referenced by getAngleDeg(), and setAngleDeg().

◆ setBondLength()

void MolTransforms::setBondLength	(	RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		double	value
	)

Set the bond length between the specified atoms i, j (all atoms bonded to atom j are moved)

◆ setDihedralDeg()

void MolTransforms::setDihedralDeg	(	RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId,
		unsigned int	lAtomId,
		double	value
	)

inline

Set the dihedral angle in degrees among the specified atoms i, j, k, l (all atoms bonded to atom l are moved)

Definition at line 157 of file MolTransforms.h.

References M_PI, and setDihedralRad().

◆ setDihedralRad()

void MolTransforms::setDihedralRad	(	RDKit::Conformer &	conf,
		unsigned int	iAtomId,
		unsigned int	jAtomId,
		unsigned int	kAtomId,
		unsigned int	lAtomId,
		double	value
	)

Set the dihedral angle in radians among the specified atoms i, j, k, l (all atoms bonded to atom l are moved)

Referenced by getDihedralDeg(), and setDihedralDeg().

◆ transformAtom()

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

◆ transformConformer()

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

Transform the conformation using the specified transformation.

◆ transformMolsAtoms()

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

Functions

Function Documentation

◆ canonicalizeConformer()

◆ canonicalizeMol()

◆ computeCanonicalTransform()

◆ computeCentroid()

◆ computeCovarianceMatrix()

◆ getAngleDeg()

◆ getAngleRad()

◆ getBondLength()

◆ getDihedralDeg()

◆ getDihedralRad()

◆ setAngleDeg()

◆ setAngleRad()

◆ setBondLength()

◆ setDihedralDeg()

◆ setDihedralRad()

◆ transformAtom()

◆ transformConformer()

◆ transformMolsAtoms()