Package rdkit :: Package Geometry :: Module rdGeometry

Module rdGeometry

Module containing geometry objects like points, grids etc

Classes

[hide private]

Point2D
A class to represent a two-dimensional point

Point3D
A class to represent a three-dimensional point The x, y, and z coordinates can be read and written using either attributes (i.e.

PointND
A class to represent an N-dimensional point

UniformGrid3D_
Class to represent a uniform three-dimensional cubic grid.

Functions

[hide private]

ComputeDihedralAngle(...)
ComputeDihedralAngle( (Point3D)arg1, (Point3D)arg2, (Point3D)arg3, (Point3D)arg4) -> float : calculates the dihedral angle determined by four Point3D objects

ComputeGridCentroid(...)
ComputeGridCentroid( (UniformGrid3D_)arg1, (Point3D)arg2, (float)arg3) -> tuple : Compute the grid point at the center of sphere around a Point3D

ComputeSignedDihedralAngle(...)
ComputeSignedDihedralAngle( (Point3D)arg1, (Point3D)arg2, (Point3D)arg3, (Point3D)arg4) -> float : calculates the signed dihedral angle determined by four Point3D objects

FindGridTerminalPoints(...)
FindGridTerminalPoints( (UniformGrid3D_)arg1, (float)arg2, (float)arg3) -> tuple : Find a grid's terminal points (defined in the subshape algorithm).

ProtrudeDistance(...)
ProtrudeDistance( (UniformGrid3D_)arg1, (UniformGrid3D_)arg2) -> float : Compute the protrude distance between two grid objects

TanimotoDistance(...)
TanimotoDistance( (UniformGrid3D_)arg1, (UniformGrid3D_)arg2) -> float : Compute the tanimoto distance between two grid objects

UniformGrid3D(...)
UniformGrid3D( (float)dimX, (float)dimY, (float)dimZ [, (float)spacing=0.5 [, (DiscreteValueType)valType=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (Point3D)offSet=None]]]) -> UniformGrid3D_ : Faking the constructor

WriteGridToFile(...)
WriteGridToFile( (UniformGrid3D_)arg1, (str)arg2) -> None : Write the grid to a grid file

Variables

[hide private]

__package__ = None

Function Details

[hide private]

ComputeDihedralAngle(...)


ComputeDihedralAngle( (Point3D)arg1, (Point3D)arg2, (Point3D)arg3, (Point3D)arg4) -> float :
    calculates the dihedral angle determined by four Point3D objects

    C++ signature :
        double ComputeDihedralAngle(RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D)

ComputeGridCentroid(...)


ComputeGridCentroid( (UniformGrid3D_)arg1, (Point3D)arg2, (float)arg3) -> tuple :
    Compute the grid point at the center of sphere around a Point3D

    C++ signature :
        boost::python::tuple ComputeGridCentroid(RDGeom::UniformGrid3D,RDGeom::Point3D,double)

ComputeSignedDihedralAngle(...)


ComputeSignedDihedralAngle( (Point3D)arg1, (Point3D)arg2, (Point3D)arg3, (Point3D)arg4) -> float :
    calculates the signed dihedral angle determined by four Point3D objects

    C++ signature :
        double ComputeSignedDihedralAngle(RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D)

FindGridTerminalPoints(...)


FindGridTerminalPoints( (UniformGrid3D_)arg1, (float)arg2, (float)arg3) -> tuple :
    Find a grid's terminal points (defined in the subshape algorithm).

    C++ signature :
        boost::python::tuple FindGridTerminalPoints(RDGeom::UniformGrid3D,double,double)

ProtrudeDistance(...)


ProtrudeDistance( (UniformGrid3D_)arg1, (UniformGrid3D_)arg2) -> float :
    Compute the protrude distance between two grid objects

    C++ signature :
        double ProtrudeDistance(RDGeom::UniformGrid3D,RDGeom::UniformGrid3D)

TanimotoDistance(...)


TanimotoDistance( (UniformGrid3D_)arg1, (UniformGrid3D_)arg2) -> float :
    Compute the tanimoto distance between two grid objects

    C++ signature :
        double TanimotoDistance(RDGeom::UniformGrid3D,RDGeom::UniformGrid3D)

UniformGrid3D(...)


UniformGrid3D( (float)dimX, (float)dimY, (float)dimZ [, (float)spacing=0.5 [, (DiscreteValueType)valType=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (Point3D)offSet=None]]]) -> UniformGrid3D_ :
    Faking the constructor

    C++ signature :
        RDGeom::UniformGrid3D* UniformGrid3D(double,double,double [,double=0.5 [,RDKit::DiscreteValueVect::DiscreteValueType=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [,RDGeom::Point3D const*=None]]])

WriteGridToFile(...)


WriteGridToFile( (UniformGrid3D_)arg1, (str)arg2) -> None :
    Write the grid to a grid file

    C++ signature :
        void WriteGridToFile(RDGeom::UniformGrid3D,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)