Classes
class	Grid3D
	Virtual base class for a grid object. More...

class	GridException

class	Point

class	Point2D

class	Point3D

class	PointND

class	Transform2D

class	Transform3D

class	UniformGrid3D

Typedefs
typedef std::vector< RDGeom::Point * >	PointPtrVect

typedef PointPtrVect::iterator	PointPtrVect_I

typedef PointPtrVect::const_iterator	PointPtrVect_CI

typedef std::vector< RDGeom::Point3D * >	Point3DPtrVect

typedef std::vector< RDGeom::Point2D * >	Point2DPtrVect

typedef Point3DPtrVect::iterator	Point3DPtrVect_I

typedef Point3DPtrVect::const_iterator	Point3DPtrVect_CI

typedef Point2DPtrVect::iterator	Point2DPtrVect_I

typedef Point2DPtrVect::const_iterator	Point2DPtrVect_CI

typedef std::vector< const RDGeom::Point3D * >	Point3DConstPtrVect

typedef Point3DConstPtrVect::iterator	Point3DConstPtrVect_I

typedef Point3DConstPtrVect::const_iterator	Point3DConstPtrVect_CI

typedef std::vector< Point3D >	POINT3D_VECT

typedef std::vector< Point3D >::iterator	POINT3D_VECT_I

typedef std::vector< Point3D >::const_iterator	POINT3D_VECT_CI

typedef std::map< int, Point2D >	INT_POINT2D_MAP

typedef INT_POINT2D_MAP::iterator	INT_POINT2D_MAP_I

typedef INT_POINT2D_MAP::const_iterator	INT_POINT2D_MAP_CI

Enumerations
enum	AxisType { X_Axis , Y_Axis , Z_Axis }

Functions
template<class GRIDTYPE >
RDKIT_RDGEOMETRYLIB_EXPORT double	tverskyIndex (const GRIDTYPE &grid1, const GRIDTYPE &grid2, double alpha, double beta)
	calculate the tversky index between the shapes encoded on two grids

template<class GRIDTYPE >
RDKIT_RDGEOMETRYLIB_EXPORT double	tanimotoDistance (const GRIDTYPE &grid1, const GRIDTYPE &grid2)
	calculate the tanimoto distance between the shapes encoded on two grids

template<class GRIDTYPE >
RDKIT_RDGEOMETRYLIB_EXPORT double	protrudeDistance (const GRIDTYPE &grid1, const GRIDTYPE &grid2)
	calculate the protrude distance between the shapes encoded on two grids

RDKIT_RDGEOMETRYLIB_EXPORT Point3D	computeGridCentroid (const UniformGrid3D &grid, const Point3D &pt, double windowRadius, double &weightSum)
	calculate the grid centroid within a window of a point

RDKIT_RDGEOMETRYLIB_EXPORT std::vector< Point3D >	findGridTerminalPoints (const UniformGrid3D &grid, double windowRadius, double inclusionFraction)

RDKIT_RDGEOMETRYLIB_EXPORT double	computeDihedralAngle (const Point3D &pt1, const Point3D &pt2, const Point3D &pt3, const Point3D &pt4)

RDKIT_RDGEOMETRYLIB_EXPORT double	computeSignedDihedralAngle (const Point3D &pt1, const Point3D &pt2, const Point3D &pt3, const Point3D &pt4)

RDKIT_RDGEOMETRYLIB_EXPORT std::ostream &	operator<< (std::ostream &target, const RDGeom::Point &pt)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D	operator+ (const RDGeom::Point3D &p1, const RDGeom::Point3D &p2)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D	operator- (const RDGeom::Point3D &p1, const RDGeom::Point3D &p2)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D	operator* (const RDGeom::Point3D &p1, double v)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D	operator/ (const RDGeom::Point3D &p1, double v)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D	operator+ (const RDGeom::Point2D &p1, const RDGeom::Point2D &p2)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D	operator- (const RDGeom::Point2D &p1, const RDGeom::Point2D &p2)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D	operator* (const RDGeom::Point2D &p1, double v)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D	operator/ (const RDGeom::Point2D &p1, double v)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND	operator+ (const RDGeom::PointND &p1, const RDGeom::PointND &p2)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND	operator- (const RDGeom::PointND &p1, const RDGeom::PointND &p2)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND	operator* (const RDGeom::PointND &p1, double v)

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND	operator/ (const RDGeom::PointND &p1, double v)

RDKIT_RDGEOMETRYLIB_EXPORT void	writeGridToStream (const UniformGrid3D &grid, std::ostream &outStrm)
	writes the contents of the grid to a stream

RDKIT_RDGEOMETRYLIB_EXPORT void	writeGridToFile (const UniformGrid3D &grid, const std::string &filename)
	writes the contents of the grid to a named file

double	compute13Dist (double d1, double d2, double angle)
	Compute the 13 distance between points give the 12 distances and the angle between the axes.

double	compute14Dist3D (double d1, double d2, double d3, double ang12, double ang23, double torAng)
	Compute the 14 distances give the 12 distance and the angles.

double	compute14DistCis (double d1, double d2, double d3, double ang12, double ang23)
	Compute the 14 distances give the 12 distance and bond angle for cis configuration.

double	compute14DistTrans (double d1, double d2, double d3, double ang12, double ang23)
	Compute the 14 distances give the 12 distance and bond angle for trans configuration.

Variables
const unsigned int	DIM_2D = 3

const unsigned int	DIM_3D = 4

Typedef Documentation

◆ INT_POINT2D_MAP

typedef std::map<int, Point2D> RDGeom::INT_POINT2D_MAP

Definition at line 561 of file point.h.

◆ INT_POINT2D_MAP_CI

typedef INT_POINT2D_MAP::const_iterator RDGeom::INT_POINT2D_MAP_CI

Definition at line 563 of file point.h.

◆ INT_POINT2D_MAP_I

typedef INT_POINT2D_MAP::iterator RDGeom::INT_POINT2D_MAP_I

Definition at line 562 of file point.h.

◆ Point2DPtrVect

typedef std::vector<RDGeom::Point2D *> RDGeom::Point2DPtrVect

Definition at line 547 of file point.h.

◆ Point2DPtrVect_CI

typedef Point2DPtrVect::const_iterator RDGeom::Point2DPtrVect_CI

Definition at line 551 of file point.h.

◆ Point2DPtrVect_I

typedef Point2DPtrVect::iterator RDGeom::Point2DPtrVect_I

Definition at line 550 of file point.h.

◆ POINT3D_VECT

typedef std::vector<Point3D> RDGeom::POINT3D_VECT

Definition at line 557 of file point.h.

◆ POINT3D_VECT_CI

typedef std::vector<Point3D>::const_iterator RDGeom::POINT3D_VECT_CI

Definition at line 559 of file point.h.

◆ POINT3D_VECT_I

typedef std::vector<Point3D>::iterator RDGeom::POINT3D_VECT_I

Definition at line 558 of file point.h.

◆ Point3DConstPtrVect

typedef std::vector<const RDGeom::Point3D *> RDGeom::Point3DConstPtrVect

Definition at line 553 of file point.h.

◆ Point3DConstPtrVect_CI

typedef Point3DConstPtrVect::const_iterator RDGeom::Point3DConstPtrVect_CI

Definition at line 555 of file point.h.

◆ Point3DConstPtrVect_I

typedef Point3DConstPtrVect::iterator RDGeom::Point3DConstPtrVect_I

Definition at line 554 of file point.h.

◆ Point3DPtrVect

typedef std::vector<RDGeom::Point3D *> RDGeom::Point3DPtrVect

Definition at line 546 of file point.h.

◆ Point3DPtrVect_CI

typedef Point3DPtrVect::const_iterator RDGeom::Point3DPtrVect_CI

Definition at line 549 of file point.h.

◆ Point3DPtrVect_I

typedef Point3DPtrVect::iterator RDGeom::Point3DPtrVect_I

Definition at line 548 of file point.h.

◆ PointPtrVect

typedef std::vector<RDGeom::Point *> RDGeom::PointPtrVect

Definition at line 542 of file point.h.

◆ PointPtrVect_CI

typedef PointPtrVect::const_iterator RDGeom::PointPtrVect_CI

Definition at line 544 of file point.h.

◆ PointPtrVect_I

typedef PointPtrVect::iterator RDGeom::PointPtrVect_I

Definition at line 543 of file point.h.

Enumeration Type Documentation

◆ AxisType

enum RDGeom::AxisType

Enumerator
X_Axis
Y_Axis
Z_Axis

Definition at line 16 of file Transform.h.

Function Documentation

◆ compute13Dist()

double RDGeom::compute13Dist	(	double	d1,
		double	d2,
		double	angle
	)

inline

Compute the 13 distance between points give the 12 distances and the angle between the axes.

Definition at line 24 of file Geometry/Utils.h.

◆ compute14Dist3D()

double RDGeom::compute14Dist3D	(	double	d1,
		double	d2,
		double	d3,
		double	ang12,
		double	ang23,
		double	torAng
	)

inline

Compute the 14 distances give the 12 distance and the angles.

This is computed by aligning the d2 axis with the x-axis (with atom 2 at the origin. Atom 1 is made to lie int he xy-plane with a +ve y-coordinate and finally the coordinates for atom 4 are computed.

ARGUMENTS: d1 - distance between atoms 1 and 2 d2 - distance between atoms 2 and 3 d3 - distance between atoms 3 and 4 ang12 - angle between the axes d1 and d2 ang23 - angle between the axes d2 and d3 torAng - torsional agnle of the axis d2

NOTE: we are specifically calling this function compute14Dist3D because we assume the torsional angle can take any value including 0 and 180 deg. However, if using either 0 or 180 as the torsional angle (which is often the case) the user is recommended to use the specialized functions below instead of this function; they will be speedier.

Definition at line 50 of file Geometry/Utils.h.

References RDGeom::Point3D::length(), RDGeom::Transform3D::SetRotation(), RDGeom::Transform3D::TransformPoint(), and X_Axis.

◆ compute14DistCis()

double RDGeom::compute14DistCis	(	double	d1,
		double	d2,
		double	d3,
		double	ang12,
		double	ang23
	)

inline

Compute the 14 distances give the 12 distance and bond angle for cis configuration.

This is simply a special case of the above function compute14Dist3D; with torsion angle set to 0. However, this function should be speedier

Definition at line 74 of file Geometry/Utils.h.

◆ compute14DistTrans()

double RDGeom::compute14DistTrans	(	double	d1,
		double	d2,
		double	d3,
		double	ang12,
		double	ang23
	)

inline

Compute the 14 distances give the 12 distance and bond angle for trans configuration.

This is simply a special case of the above function compute14Dist3D; with torsion angle set to 180. However, this function should be speedier

Definition at line 88 of file Geometry/Utils.h.

◆ computeDihedralAngle()

RDKIT_RDGEOMETRYLIB_EXPORT double RDGeom::computeDihedralAngle	(	const Point3D &	pt1,
		const Point3D &	pt2,
		const Point3D &	pt3,
		const Point3D &	pt4
	)

◆ computeGridCentroid()

RDKIT_RDGEOMETRYLIB_EXPORT Point3D RDGeom::computeGridCentroid	(	const UniformGrid3D &	grid,
		const Point3D &	pt,
		double	windowRadius,
		double &	weightSum
	)

calculate the grid centroid within a window of a point

◆ computeSignedDihedralAngle()

RDKIT_RDGEOMETRYLIB_EXPORT double RDGeom::computeSignedDihedralAngle	(	const Point3D &	pt1,
		const Point3D &	pt2,
		const Point3D &	pt3,
		const Point3D &	pt4
	)

◆ findGridTerminalPoints()

RDKIT_RDGEOMETRYLIB_EXPORT std::vector< Point3D > RDGeom::findGridTerminalPoints	(	const UniformGrid3D &	grid,
		double	windowRadius,
		double	inclusionFraction
	)

find terminal points of a shape encoded on a grid this is part of the subshape implementation

◆ operator*() [1/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D RDGeom::operator*	(	const RDGeom::Point2D &	p1,
		double	v
	)

◆ operator*() [2/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D RDGeom::operator*	(	const RDGeom::Point3D &	p1,
		double	v
	)

◆ operator*() [3/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND RDGeom::operator*	(	const RDGeom::PointND &	p1,
		double	v
	)

◆ operator+() [1/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D RDGeom::operator+	(	const RDGeom::Point2D &	p1,
		const RDGeom::Point2D &	p2
	)

◆ operator+() [2/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D RDGeom::operator+	(	const RDGeom::Point3D &	p1,
		const RDGeom::Point3D &	p2
	)

◆ operator+() [3/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND RDGeom::operator+	(	const RDGeom::PointND &	p1,
		const RDGeom::PointND &	p2
	)

◆ operator-() [1/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D RDGeom::operator-	(	const RDGeom::Point2D &	p1,
		const RDGeom::Point2D &	p2
	)

◆ operator-() [2/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D RDGeom::operator-	(	const RDGeom::Point3D &	p1,
		const RDGeom::Point3D &	p2
	)

◆ operator-() [3/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND RDGeom::operator-	(	const RDGeom::PointND &	p1,
		const RDGeom::PointND &	p2
	)

◆ operator/() [1/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point2D RDGeom::operator/	(	const RDGeom::Point2D &	p1,
		double	v
	)

◆ operator/() [2/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D RDGeom::operator/	(	const RDGeom::Point3D &	p1,
		double	v
	)

◆ operator/() [3/3]

RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::PointND RDGeom::operator/	(	const RDGeom::PointND &	p1,
		double	v
	)

◆ operator<<()

RDKIT_RDGEOMETRYLIB_EXPORT std::ostream & RDGeom::operator<<	(	std::ostream &	target,
		const RDGeom::Point &	pt
	)

◆ protrudeDistance()

template<class GRIDTYPE >

RDKIT_RDGEOMETRYLIB_EXPORT double RDGeom::protrudeDistance	(	const GRIDTYPE &	grid1,
		const GRIDTYPE &	grid2
	)

calculate the protrude distance between the shapes encoded on two grids

protrude(S1,S2) = ( | S1|S2 | - | S1&S2 | ) / | S1 |

◆ tanimotoDistance()

template<class GRIDTYPE >

RDKIT_RDGEOMETRYLIB_EXPORT double RDGeom::tanimotoDistance	(	const GRIDTYPE &	grid1,
		const GRIDTYPE &	grid2
	)

calculate the tanimoto distance between the shapes encoded on two grids

tanimoto(S1,S2) = 1 - ( | S1&S2 | / | S1|S2 | )

◆ tverskyIndex()

template<class GRIDTYPE >

RDKIT_RDGEOMETRYLIB_EXPORT double RDGeom::tverskyIndex	(	const GRIDTYPE &	grid1,
		const GRIDTYPE &	grid2,
		double	alpha,
		double	beta
	)

calculate the tversky index between the shapes encoded on two grids

tversky(S1,S2) = | S1&S2 | / ( alpha * ( | S1 | - | S1&S2 | ) + beta * ( | S2 | - | S1&S2 | ) + | S1&S2 | )

◆ writeGridToFile()

RDKIT_RDGEOMETRYLIB_EXPORT void RDGeom::writeGridToFile	(	const UniformGrid3D &	grid,
		const std::string &	filename
	)

writes the contents of the grid to a named file

◆ writeGridToStream()

RDKIT_RDGEOMETRYLIB_EXPORT void RDGeom::writeGridToStream	(	const UniformGrid3D &	grid,
		std::ostream &	outStrm
	)

writes the contents of the grid to a stream

Variable Documentation

◆ DIM_2D

const unsigned int RDGeom::DIM_2D = 3

Definition at line 19 of file Transform2D.h.

Referenced by RDGeom::Transform2D::Transform2D().

◆ DIM_3D

const unsigned int RDGeom::DIM_3D = 4

Definition at line 20 of file Transform3D.h.

Referenced by RDGeom::Transform3D::Transform3D().

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ INT_POINT2D_MAP

◆ INT_POINT2D_MAP_CI

◆ INT_POINT2D_MAP_I

◆ Point2DPtrVect

◆ Point2DPtrVect_CI

◆ Point2DPtrVect_I

◆ POINT3D_VECT

◆ POINT3D_VECT_CI

◆ POINT3D_VECT_I

◆ Point3DConstPtrVect

◆ Point3DConstPtrVect_CI

◆ Point3DConstPtrVect_I

◆ Point3DPtrVect

◆ Point3DPtrVect_CI

◆ Point3DPtrVect_I

◆ PointPtrVect

◆ PointPtrVect_CI

◆ PointPtrVect_I

Enumeration Type Documentation

◆ AxisType

Function Documentation

◆ compute13Dist()

◆ compute14Dist3D()

◆ compute14DistCis()

◆ compute14DistTrans()

◆ computeDihedralAngle()

◆ computeGridCentroid()

◆ computeSignedDihedralAngle()

◆ findGridTerminalPoints()

◆ operator*() [1/3]

◆ operator*() [2/3]

◆ operator*() [3/3]

◆ operator+() [1/3]

◆ operator+() [2/3]

◆ operator+() [3/3]

◆ operator-() [1/3]

◆ operator-() [2/3]

◆ operator-() [3/3]

◆ operator/() [1/3]

◆ operator/() [2/3]

◆ operator/() [3/3]

◆ operator<<()

◆ protrudeDistance()

◆ tanimotoDistance()

◆ tverskyIndex()

◆ writeGridToFile()

◆ writeGridToStream()

Variable Documentation

◆ DIM_2D

◆ DIM_3D