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

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

RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Point3D	computeCentroid (const RDKit::Conformer &conf, bool ignoreHs=true, const std::vector< double > *weights=nullptr)
	Compute the centroid of a conformer.

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

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

RDKIT_MOLTRANSFORMS_EXPORT void	transformMolSubstanceGroups (RDKit::ROMol &mol, const RDGeom::Transform3D &trans)
	Transforms coordinates in a molecule's substance groups.

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

RDKIT_MOLTRANSFORMS_EXPORT void	canonicalizeMol (RDKit::ROMol &mol, bool normalizeCovar=false, bool ignoreHs=true)
	Canonicalize all the conformations in a molecule.

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

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

RDKIT_MOLTRANSFORMS_EXPORT 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.

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.

RDKIT_MOLTRANSFORMS_EXPORT 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)

RDKIT_MOLTRANSFORMS_EXPORT 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.

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.

RDKIT_MOLTRANSFORMS_EXPORT 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()

RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::canonicalizeConformer	(	RDKit::Conformer &	conf,
		const RDGeom::Point3D *	center = nullptr,
		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()

RDKIT_MOLTRANSFORMS_EXPORT 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()

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

Compute the transformation required to orient the conformation along the principal axes about the center; i.e. center is made to coincide with the origin, the largest principal 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 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	Optionally ignore hydrogens

◆ computeCentroid()

RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Point3D MolTransforms::computeCentroid	(	const RDKit::Conformer &	conf,
		bool	ignoreHs = true,
		const std::vector< double > *	weights = nullptr )

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
weights	If present, used to weigh the atomic coordinates

◆ 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 173 of file MolTransforms.h.

References getAngleRad(), and M_PI.

◆ getAngleRad()

RDKIT_MOLTRANSFORMS_EXPORT 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()

RDKIT_MOLTRANSFORMS_EXPORT 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 201 of file MolTransforms.h.

References getDihedralRad(), and M_PI.

◆ getDihedralRad()

RDKIT_MOLTRANSFORMS_EXPORT 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().

◆ 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 187 of file MolTransforms.h.

References M_PI, and setAngleRad().

◆ setAngleRad()

RDKIT_MOLTRANSFORMS_EXPORT 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 setAngleDeg().

◆ setBondLength()

RDKIT_MOLTRANSFORMS_EXPORT 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 216 of file MolTransforms.h.

References M_PI, and setDihedralRad().

◆ setDihedralRad()

RDKIT_MOLTRANSFORMS_EXPORT 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 setDihedralDeg().

◆ transformAtom()

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

◆ transformConformer()

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

Transform the conformation using the specified transformation.

◆ transformMolsAtoms()

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

◆ transformMolSubstanceGroups()

RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::transformMolSubstanceGroups	(	RDKit::ROMol &	mol,
		const RDGeom::Transform3D &	trans )

Transforms coordinates in a molecule's substance groups.

Functions

Function Documentation

◆ canonicalizeConformer()

◆ canonicalizeMol()

◆ computeCanonicalTransform()

◆ computeCentroid()

◆ getAngleDeg()

◆ getAngleRad()

◆ getBondLength()

◆ getDihedralDeg()

◆ getDihedralRad()

◆ setAngleDeg()

◆ setAngleRad()

◆ setBondLength()

◆ setDihedralDeg()

◆ setDihedralRad()

◆ transformAtom()

◆ transformConformer()

◆ transformMolsAtoms()

◆ transformMolSubstanceGroups()