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 (const Point3D &pt1, const Point3D &pt2, const Point3D &pt3, const Point3D &pt4) |
| std::ostream & | operator<< (std::ostream &target, const RDGeom::Point &pt) |
| RDGeom::Point3D | operator+ (const RDGeom::Point3D &p1, const RDGeom::Point3D &p2) |
| RDGeom::Point3D | operator- (const RDGeom::Point3D &p1, const RDGeom::Point3D &p2) |
| RDGeom::Point3D | operator* (const RDGeom::Point3D &p1, double v) |
| RDGeom::Point3D | operator/ (const RDGeom::Point3D &p1, double v) |
| RDGeom::Point2D | operator+ (const RDGeom::Point2D &p1, const RDGeom::Point2D &p2) |
| RDGeom::Point2D | operator- (const RDGeom::Point2D &p1, const RDGeom::Point2D &p2) |
| RDGeom::Point2D | operator* (const RDGeom::Point2D &p1, double v) |
| RDGeom::Point2D | operator/ (const RDGeom::Point2D &p1, double v) |
| RDGeom::PointND | operator+ (const RDGeom::PointND &p1, const RDGeom::PointND &p2) |
| RDGeom::PointND | operator- (const RDGeom::PointND &p1, const RDGeom::PointND &p2) |
| RDGeom::PointND | operator* (const RDGeom::PointND &p1, double v) |
| RDGeom::PointND | operator/ (const RDGeom::PointND &p1, double v) |
| void | writeGridToStream (const UniformGrid3D &grid, std::ostream &outStrm) |
| | writes the contents of the grid to a stream
|
| void | writeGridToFile (const UniformGrid3D &grid, 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 |
| 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 49 of file Utils.h.
References RDGeom::Point3D::length(), RDGeom::Transform3D::SetRotation(), RDGeom::Transform3D::TransformPoint(), and X_Axis.
