RDKit::MolShapes Namespace Reference

Functions
RDKIT_SHAPEHELPERS_EXPORT void	EncodeShape (const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId=-1, const RDGeom::Transform3D *trans=nullptr, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
	Encode the shape of a molecule on to a grid.
RDKIT_SHAPEHELPERS_EXPORT void	EncodeShape (const Conformer &conf, RDGeom::UniformGrid3D &grid, const RDGeom::Transform3D *trans=nullptr, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
	Emcode the shape of a conformer on to a grid.
RDKIT_SHAPEHELPERS_EXPORT void	computeConfDimsAndOffset (const Conformer &conf, RDGeom::Point3D &dims, RDGeom::Point3D &offSet, const RDGeom::Transform3D *trans=nullptr, double padding=2.5)
RDKIT_SHAPEHELPERS_EXPORT void	computeConfBox (const Conformer &conf, RDGeom::Point3D &leftBottom, RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans=nullptr, double padding=2.5)
	Compute the box that will fit the conformer.
RDKIT_SHAPEHELPERS_EXPORT void	computeUnionBox (const RDGeom::Point3D &leftBottom1, const RDGeom::Point3D &rightTop1, const RDGeom::Point3D &leftBottom2, const RDGeom::Point3D &rightTop2, RDGeom::Point3D &uLeftBottom, RDGeom::Point3D &uRightTop)
	Compute the union of two boxes.
RDKIT_SHAPEHELPERS_EXPORT std::vector< double >	getConfDimensions (const Conformer &conf, double padding=2.5, const RDGeom::Point3D *center=nullptr, bool ignoreHs=true)
	Compute dimensions of a conformer.
RDKIT_SHAPEHELPERS_EXPORT double	tverskyIndex (const ROMol &mol1, const ROMol &mol2, double alpha, double beta, int confId1=-1, int confId2=-1, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
RDKIT_SHAPEHELPERS_EXPORT double	tverskyIndex (const Conformer &conf1, const Conformer &conf2, double alpha, double beta, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
RDKIT_SHAPEHELPERS_EXPORT double	tanimotoDistance (const ROMol &mol1, const ROMol &mol2, int confId1=-1, int confId2=-1, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
RDKIT_SHAPEHELPERS_EXPORT double	tanimotoDistance (const Conformer &conf1, const Conformer &conf2, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
RDKIT_SHAPEHELPERS_EXPORT double	protrudeDistance (const ROMol &mol1, const ROMol &mol2, int confId1=-1, int confId2=-1, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true, bool allowReordering=true)
RDKIT_SHAPEHELPERS_EXPORT double	protrudeDistance (const Conformer &conf1, const Conformer &conf2, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true, bool allowReordering=true)

Function Documentation

computeConfBox()

RDKIT_SHAPEHELPERS_EXPORT void RDKit::MolShapes::computeConfBox	(	const Conformer &	conf,
		RDGeom::Point3D &	leftBottom,
		RDGeom::Point3D &	rightTop,
		const RDGeom::Transform3D *	trans = nullptr,
		double	padding = 2.5 )

Compute the box that will fit the conformer.

Parameters

conf	The conformer of interest
leftBottom	Storage for one extremity of the box
rightTop	Storage for other extremity of the box
trans	Optional transformation to be applied to the atom coordinates
padding	Padding added on the sides around the conformer

computeConfDimsAndOffset()

RDKIT_SHAPEHELPERS_EXPORT void RDKit::MolShapes::computeConfDimsAndOffset	(	const Conformer &	conf,
		RDGeom::Point3D &	dims,
		RDGeom::Point3D &	offSet,
		const RDGeom::Transform3D *	trans = nullptr,
		double	padding = 2.5 )

Compute the size of the box that can fit the conformation, and offset of the box from the origin

computeUnionBox()

RDKIT_SHAPEHELPERS_EXPORT void RDKit::MolShapes::computeUnionBox	(	const RDGeom::Point3D &	leftBottom1,
		const RDGeom::Point3D &	rightTop1,
		const RDGeom::Point3D &	leftBottom2,
		const RDGeom::Point3D &	rightTop2,
		RDGeom::Point3D &	uLeftBottom,
		RDGeom::Point3D &	uRightTop )

Compute the union of two boxes.

EncodeShape() [1/2]

RDKIT_SHAPEHELPERS_EXPORT void RDKit::MolShapes::EncodeShape	(	const Conformer &	conf,
		RDGeom::UniformGrid3D &	grid,
		const RDGeom::Transform3D *	trans = nullptr,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true )

Emcode the shape of a conformer on to a grid.

Parameters

conf	The conformer of interest
grid	Grid onto which the molecule is encoded
trans	Optional 3D transform to be applied to this conformation
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the layers outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process

EncodeShape() [2/2]

RDKIT_SHAPEHELPERS_EXPORT void RDKit::MolShapes::EncodeShape	(	const ROMol &	mol,
		RDGeom::UniformGrid3D &	grid,
		int	confId = -1,
		const RDGeom::Transform3D *	trans = nullptr,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true )

Encode the shape of a molecule on to a grid.

Parameters

mol	The molecule of interest
grid	Grid onto which the molecule is encoded
confId	Id of the conformation on the molecule to be encoded
trans	Optional 3D transform to be applied to this conformation
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the layers outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process

getConfDimensions()

RDKIT_SHAPEHELPERS_EXPORT std::vector< double > RDKit::MolShapes::getConfDimensions	(	const Conformer &	conf,
		double	padding = 2.5,
		const RDGeom::Point3D *	center = nullptr,
		bool	ignoreHs = true )

Compute dimensions of a conformer.

Parameters

conf	Conformer of interest
padding	Padding added to the atom coordinates on all sides
center	Optionally specify the center
ignoreHs	if true, ignore the hydrogen atoms in computing the centroid

protrudeDistance() [1/2]

RDKIT_SHAPEHELPERS_EXPORT double RDKit::MolShapes::protrudeDistance	(	const Conformer &	conf1,
		const Conformer &	conf2,
		double	gridSpacing = 0.5,
		DiscreteValueVect::DiscreteValueType	bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true,
		bool	allowReordering = true )

Compute the shape protrusion distance between two conformers based on a predefined alignment

Parameters

conf1	The first conformer of interest
conf2	The second conformer of interest
gridSpacing	resolution of the grid used to encode the molecular shapes
bitsPerPoint	number of bit used to encode the occupancy at each grid point
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process
allowReordering	if set the order will be automatically updated so that the value calculated is the protrusion of the smaller shape from the larger one.

protrudeDistance() [2/2]

RDKIT_SHAPEHELPERS_EXPORT double RDKit::MolShapes::protrudeDistance	(	const ROMol &	mol1,
		const ROMol &	mol2,
		int	confId1 = -1,
		int	confId2 = -1,
		double	gridSpacing = 0.5,
		DiscreteValueVect::DiscreteValueType	bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true,
		bool	allowReordering = true )

Compute the shape protrusion distance between two molecule based on a predefined alignment

Parameters

mol1	The first molecule of interest
mol2	The second molecule of interest
confId1	Conformer in the first molecule (defaults to first conformer)
confId2	Conformer in the second molecule (defaults to first conformer)
gridSpacing	resolution of the grid used to encode the molecular shapes
bitsPerPoint	number of bit used to encode the occupancy at each grid point defaults to two bits per grid point
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process
allowReordering	if set the order will be automatically updated so that the value calculated is the protrusion of the smaller shape from the larger one.

tanimotoDistance() [1/2]

RDKIT_SHAPEHELPERS_EXPORT double RDKit::MolShapes::tanimotoDistance	(	const Conformer &	conf1,
		const Conformer &	conf2,
		double	gridSpacing = 0.5,
		DiscreteValueVect::DiscreteValueType	bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true )

Compute the shape tanimoto distance between two conformers based on a predefined alignment

Parameters

conf1	The first conformer of interest
conf2	The second conformer of interest
gridSpacing	resolution of the grid used to encode the molecular shapes
bitsPerPoint	number of bit used to encode the occupancy at each grid point
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process

tanimotoDistance() [2/2]

RDKIT_SHAPEHELPERS_EXPORT double RDKit::MolShapes::tanimotoDistance	(	const ROMol &	mol1,
		const ROMol &	mol2,
		int	confId1 = -1,
		int	confId2 = -1,
		double	gridSpacing = 0.5,
		DiscreteValueVect::DiscreteValueType	bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true )

Compute the shape tanimoto distance between two molecule based on a predefined alignment

Parameters

mol1	The first molecule of interest
mol2	The second molecule of interest
confId1	Conformer in the first molecule (defaults to first conformer)
confId2	Conformer in the second molecule (defaults to first conformer)
gridSpacing	resolution of the grid used to encode the molecular shapes
bitsPerPoint	number of bit used to encode the occupancy at each grid point defaults to two bits per grid point
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process

tverskyIndex() [1/2]

RDKIT_SHAPEHELPERS_EXPORT double RDKit::MolShapes::tverskyIndex	(	const Conformer &	conf1,
		const Conformer &	conf2,
		double	alpha,
		double	beta,
		double	gridSpacing = 0.5,
		DiscreteValueVect::DiscreteValueType	bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true )

Compute the shape tversky index between two conformers based on a predefined alignment

Parameters

conf1	The first conformer of interest
conf2	The second conformer of interest
alpha
beta
gridSpacing	resolution of the grid used to encode the molecular shapes
bitsPerPoint	number of bit used to encode the occupancy at each grid point
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process

tverskyIndex() [2/2]

RDKIT_SHAPEHELPERS_EXPORT double RDKit::MolShapes::tverskyIndex	(	const ROMol &	mol1,
		const ROMol &	mol2,
		double	alpha,
		double	beta,
		int	confId1 = -1,
		int	confId2 = -1,
		double	gridSpacing = 0.5,
		DiscreteValueVect::DiscreteValueType	bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
		double	vdwScale = 0.8,
		double	stepSize = 0.25,
		int	maxLayers = -1,
		bool	ignoreHs = true )

Compute the shape tversky index between two molecule based on a predefined alignment

Parameters

mol1	The first molecule of interest
mol2	The second molecule of interest
alpha
beta
confId1	Conformer in the first molecule (defaults to first conformer)
confId2	Conformer in the second molecule (defaults to first conformer)
gridSpacing	resolution of the grid used to encode the molecular shapes
bitsPerPoint	number of bit used to encode the occupancy at each grid point defaults to two bits per grid point
vdwScale	Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy
stepSize	thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers	the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHs	if true, ignore the hydrogen atoms in the shape encoding process