RDGeom Namespace Reference

Classes
class	GridException
class	Grid3D
	Virtual base class for a grid object. More...
class	Point
class	Point3D
class	Point2D
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>
double	tanimotoDistance (const GRIDTYPE &grid1, const GRIDTYPE &grid2)
	calculate the tanimoto distance between the shapes encoded on two grids
template<class GRIDTYPE>
double	protrudeDistance (const GRIDTYPE &grid1, const GRIDTYPE &grid2)
	calculate the protrude distance between the shapes encoded on two grids
Point3D	computeGridCentroid (const UniformGrid3D &grid, const Point3D &pt, double windowRadius, double &weightSum)
	calculate the grid centroid within a window of a point
std::vector< Point3D >	findGridTerminalPoints (const UniformGrid3D &grid, double windowRadius, double inclusionFraction)
double	computeDihedralAngle (Point3D pt1, Point3D pt2, Point3D pt3, Point3D pt4)
void	writeGridToStream (const UniformGrid3D &grid, std::ostream &outStrm)
void	writeGridToFile (const UniformGrid3D &grid, std::string filename)
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

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Typedef Documentation

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

Definition at line 530 of file point.h.

typedef INT_POINT2D_MAP::const_iterator RDGeom::INT_POINT2D_MAP_CI

Definition at line 532 of file point.h.

typedef INT_POINT2D_MAP::iterator RDGeom::INT_POINT2D_MAP_I

Definition at line 531 of file point.h.

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

Definition at line 516 of file point.h.

typedef Point2DPtrVect::const_iterator RDGeom::Point2DPtrVect_CI

Definition at line 520 of file point.h.

typedef Point2DPtrVect::iterator RDGeom::Point2DPtrVect_I

Definition at line 519 of file point.h.

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

Definition at line 526 of file point.h.

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

Definition at line 528 of file point.h.

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

Definition at line 527 of file point.h.

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

Definition at line 522 of file point.h.

typedef Point3DConstPtrVect::const_iterator RDGeom::Point3DConstPtrVect_CI

Definition at line 524 of file point.h.

typedef Point3DConstPtrVect::iterator RDGeom::Point3DConstPtrVect_I

Definition at line 523 of file point.h.

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

Definition at line 515 of file point.h.

typedef Point3DPtrVect::const_iterator RDGeom::Point3DPtrVect_CI

Definition at line 518 of file point.h.

typedef Point3DPtrVect::iterator RDGeom::Point3DPtrVect_I

Definition at line 517 of file point.h.

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

Definition at line 511 of file point.h.

typedef PointPtrVect::const_iterator RDGeom::PointPtrVect_CI

Definition at line 513 of file point.h.

typedef PointPtrVect::iterator RDGeom::PointPtrVect_I

Definition at line 512 of file point.h.

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Enumeration Type Documentation

enum RDGeom::AxisType

Enumerator:

X_Axis
Y_Axis
Z_Axis

Definition at line 11 of file Transform.h.

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Function Documentation

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 19 of file Utils.h.

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 45 of file Utils.h.

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

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 69 of file Utils.h.

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 84 of file Utils.h.

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

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

calculate the grid centroid within a window of a point

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

template<class GRIDTYPE>

double RDGeom::protrudeDistance	(	const GRIDTYPE &	grid1,
		const GRIDTYPE &	grid2
	)			[inline]

calculate the protrude distance between the shapes encoded on two grids

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

template<class GRIDTYPE>

double RDGeom::tanimotoDistance	(	const GRIDTYPE &	grid1,
		const GRIDTYPE &	grid2
	)			[inline]

calculate the tanimoto distance between the shapes encoded on two grids

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

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

writes the contents of the grid to a named file

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

writes the contents of the grid to a stream

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Variable Documentation

const unsigned int RDGeom::DIM_2D = 3

Definition at line 14 of file Transform2D.h.

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

const unsigned int RDGeom::DIM_3D = 4

Definition at line 15 of file Transform3D.h.

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

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