rdkit.Geometry.rdGeometry module

Module containing geometry objects like points, grids, etc

rdkit.Geometry.rdGeometry.ComputeDihedralAngle((Point3D)pt1, (Point3D)pt2, (Point3D)pt3, (Point3D)pt4) → float :

calculates the dihedral angle determined by four Point3D objects

C++ signature :

double ComputeDihedralAngle(RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D)

rdkit.Geometry.rdGeometry.ComputeGridCentroid((UniformGrid3D_)grid, (Point3D)pt, (float)windowRadius) → tuple :

Compute the grid point at the center of sphere around a Point3D

C++ signature :

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

rdkit.Geometry.rdGeometry.ComputeSignedDihedralAngle((Point3D)pt1, (Point3D)pt2, (Point3D)pt3, (Point3D)pt4) → float :

calculates the signed dihedral angle determined by four Point3D objects

C++ signature :

double ComputeSignedDihedralAngle(RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D,RDGeom::Point3D)

rdkit.Geometry.rdGeometry.FindGridTerminalPoints((UniformGrid3D_)grid, (float)windowRadius, (float)inclusionFraction) → tuple :

Find a grid’s terminal points (defined in the subshape algorithm).

C++ signature :

boost::python::tuple FindGridTerminalPoints(RDGeom::UniformGrid3D,double,double)

class rdkit.Geometry.rdGeometry.Point2D((object)self)

Bases: instance

A class to represent a two-dimensional point

Default Constructor

C++ signature :

void __init__(_object*)

__init__( (object)self, (float)xv, (float)yv) -> None :

C++ signature :

void __init__(_object*,double,double)

__init__( (object)self, (Point3D)other) -> None :

construct from a Point3D (ignoring the z component)

C++ signature :

void __init__(_object*,RDGeom::Point3D)

AngleTo((Point2D)self, (Point2D)other) → float :

determines the angle between a vector to this point (between 0 and PI)

C++ signature :

double AngleTo(RDGeom::Point2D {lvalue},RDGeom::Point2D)

DirectionVector((Point2D)self, (Point2D)other) → Point2D :

return a normalized direction vector from this point to another

C++ signature :

RDGeom::Point2D DirectionVector(RDGeom::Point2D {lvalue},RDGeom::Point2D)

DotProduct((Point2D)self, (Point2D)other) → float :

Dot product with another point

C++ signature :

double DotProduct(RDGeom::Point2D {lvalue},RDGeom::Point2D)

Length((Point2D)self) → float :

Length of the vector

C++ signature :

double Length(RDGeom::Point2D {lvalue})

LengthSq((Point2D)self) → float :

Square of the length

C++ signature :

double LengthSq(RDGeom::Point2D {lvalue})

Normalize((Point2D)self) → None :

Normalize the vector (using L2 norm)

C++ signature :

void Normalize(RDGeom::Point2D {lvalue})

SignedAngleTo((Point2D)self, (Point2D)other) → float :

determines the signed angle between a vector to this point (between 0 and 2*PI)

C++ signature :

double SignedAngleTo(RDGeom::Point2D {lvalue},RDGeom::Point2D)

property x

property y

class rdkit.Geometry.rdGeometry.Point3D((object)self)

Bases: instance

A class to represent a three-dimensional point The x, y, and z coordinates can be read and written using either attributes (i.e. pt.x = 4) or indexing (i.e. pt[0] = 4).

Default Constructor

C++ signature :

void __init__(_object*)

__init__( (object)self, (float)xv, (float)yv, (float)zv) -> None :

C++ signature :

void __init__(_object*,double,double,double)

AngleTo((Point3D)self, (Point3D)other) → float :

determines the angle between a vector to this point (between 0 and PI)

C++ signature :

double AngleTo(RDGeom::Point3D {lvalue},RDGeom::Point3D)

CrossProduct((Point3D)self, (Point3D)other) → Point3D :

Get the cross product between two points

C++ signature :

RDGeom::Point3D CrossProduct(RDGeom::Point3D {lvalue},RDGeom::Point3D)

DirectionVector((Point3D)self, (Point3D)other) → Point3D :

return a normalized direction vector from this point to another

C++ signature :

RDGeom::Point3D DirectionVector(RDGeom::Point3D {lvalue},RDGeom::Point3D)

Distance((Point3D)self, (Point3D)pt2) → float :

Distance from this point to another point

C++ signature :

double Distance(RDGeom::Point3D,RDGeom::Point3D)

DotProduct((Point3D)self, (Point3D)other) → float :

Dot product with another point

C++ signature :

double DotProduct(RDGeom::Point3D {lvalue},RDGeom::Point3D)

Length((Point3D)self) → float :

Length of the vector

C++ signature :

double Length(RDGeom::Point3D {lvalue})

LengthSq((Point3D)self) → float :

Square of the length

C++ signature :

double LengthSq(RDGeom::Point3D {lvalue})

Normalize((Point3D)self) → None :

Normalize the vector (using L2 norm)

C++ signature :

void Normalize(RDGeom::Point3D {lvalue})

SignedAngleTo((Point3D)self, (Point3D)other) → float :

determines the signed angle between a vector to this point (between 0 and 2*PI)

C++ signature :

double SignedAngleTo(RDGeom::Point3D {lvalue},RDGeom::Point3D)

property x

property y

property z

class rdkit.Geometry.rdGeometry.PointND((object)self, (int)dim)

Bases: instance

A class to represent an N-dimensional point

C++ signature :

void __init__(_object*,unsigned int)

AngleTo((PointND)self, (PointND)other) → float :

determines the angle between a vector to this point (between 0 and PI)

C++ signature :

double AngleTo(RDGeom::PointND {lvalue},RDGeom::PointND)

DirectionVector((PointND)self, (PointND)other) → PointND :

return a normalized direction vector from this point to another

C++ signature :

RDGeom::PointND DirectionVector(RDGeom::PointND {lvalue},RDGeom::PointND)

Distance((Point3D)self, (Point3D)pt2) → float :

Distance from this point to another point

C++ signature :

double Distance(RDGeom::Point3D,RDGeom::Point3D)

DotProduct((PointND)self, (PointND)other) → float :

Dot product with another point

C++ signature :

double DotProduct(RDGeom::PointND {lvalue},RDGeom::PointND)

Length((PointND)self) → float :

Length of the vector

C++ signature :

double Length(RDGeom::PointND {lvalue})

LengthSq((PointND)self) → float :

Square of the length

C++ signature :

double LengthSq(RDGeom::PointND {lvalue})

Normalize((PointND)self) → None :

Normalize the vector (using L2 norm)

C++ signature :

void Normalize(RDGeom::PointND {lvalue})

rdkit.Geometry.rdGeometry.ProtrudeDistance((UniformGrid3D_)grid1, (UniformGrid3D_)grid2) → float :

Compute the protrude distance between two grid objects

C++ signature :

double ProtrudeDistance(RDGeom::UniformGrid3D,RDGeom::UniformGrid3D)

rdkit.Geometry.rdGeometry.TanimotoDistance((UniformGrid3D_)grid1, (UniformGrid3D_)grid2) → float :

Compute the tanimoto distance between two grid objects

C++ signature :

double TanimotoDistance(RDGeom::UniformGrid3D,RDGeom::UniformGrid3D)

rdkit.Geometry.rdGeometry.TverskyIndex((UniformGrid3D_)grid1, (UniformGrid3D_)grid2, (float)alpha, (float)beta) → float :

Compute the tversky index between two grid objects

C++ signature :

double TverskyIndex(RDGeom::UniformGrid3D,RDGeom::UniformGrid3D,double,double)

rdkit.Geometry.rdGeometry.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]]])

class rdkit.Geometry.rdGeometry.UniformGrid3D_((object)self, (str)pkl)

Bases: instance

Class to represent a uniform three-dimensional cubic grid. Each grid point can store a poisitive integer value. For the sake of efficiency these value can either be binary, fit in 2, 4, 8 or 16 bits

pickle constructor

C++ signature :

void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

CompareParams((UniformGrid3D_)self, (UniformGrid3D_)other) → bool :

Compare the parameters between two grid object

C++ signature :

bool CompareParams(RDGeom::UniformGrid3D {lvalue},RDGeom::UniformGrid3D)

GetGridIndex((UniformGrid3D_)self, (int)xi, (int)yi, (int)zi) → int :

Get the index to the grid point with the three integer indices provided

C++ signature :

int GetGridIndex(RDGeom::UniformGrid3D {lvalue},unsigned int,unsigned int,unsigned int)

GetGridIndices((UniformGrid3D_)self, (int)idx) → tuple :

Returns the integer indices of the grid index provided.

C++ signature :

boost::python::tuple GetGridIndices(RDGeom::UniformGrid3D,unsigned int)

GetGridPointIndex((UniformGrid3D_)self, (Point3D)point) → int :

Get the index to the grid point closest to the specified point

C++ signature :

int GetGridPointIndex(RDGeom::UniformGrid3D {lvalue},RDGeom::Point3D)

GetGridPointLoc((UniformGrid3D_)self, (int)pointId) → Point3D :

Get the location of the specified grid point

C++ signature :

RDGeom::Point3D GetGridPointLoc(RDGeom::UniformGrid3D {lvalue},unsigned int)

GetNumX((UniformGrid3D_)self) → int :

Get the number of grid points along x-axis

C++ signature :

unsigned int GetNumX(RDGeom::UniformGrid3D {lvalue})

GetNumY((UniformGrid3D_)self) → int :

Get the number of grid points along y-axis

C++ signature :

unsigned int GetNumY(RDGeom::UniformGrid3D {lvalue})

GetNumZ((UniformGrid3D_)self) → int :

Get the number of grid points along z-axis

C++ signature :

unsigned int GetNumZ(RDGeom::UniformGrid3D {lvalue})

GetOccupancyVect((UniformGrid3D_)self) → DiscreteValueVect :

Get the occupancy vector for the grid

C++ signature :

RDKit::DiscreteValueVect const* GetOccupancyVect(RDGeom::UniformGrid3D {lvalue})

GetOffset((UniformGrid3D_)self) → Point3D :

Get the location of the center of the grid

C++ signature :

RDGeom::Point3D GetOffset(RDGeom::UniformGrid3D {lvalue})

GetSize((UniformGrid3D_)self) → int :

Get the size of the grid (number of grid points)

C++ signature :

unsigned int GetSize(RDGeom::UniformGrid3D {lvalue})

GetSpacing((UniformGrid3D_)self) → float :

Get the grid spacing

C++ signature :

double GetSpacing(RDGeom::UniformGrid3D {lvalue})

GetVal((UniformGrid3D_)self, (int)id) → int :

Get the value at the specified grid point

C++ signature :

int GetVal(RDGeom::UniformGrid3D,unsigned int)

GetValPoint((UniformGrid3D_)self, (Point3D)pt) → int :

Get the value at the closest grid point

C++ signature :

int GetValPoint(RDGeom::UniformGrid3D,RDGeom::Point3D)

SetSphereOccupancy((UniformGrid3D_)self, (Point3D)center, (float)radius, (float)stepSize[, (int)maxLayers=-1[, (bool)ignoreOutOfBound=True]]) → None :

Set the occupancy on the grid for a sphere or specified radius

and multiple layers around this sphere, with decreasing values of

occupancy

C++ signature :

void SetSphereOccupancy(RDGeom::UniformGrid3D {lvalue},RDGeom::Point3D,double,double [,int=-1 [,bool=True]])

SetVal((UniformGrid3D_)self, (int)id, (int)val) → None :

Set the value at the specified grid point

C++ signature :

void SetVal(RDGeom::UniformGrid3D {lvalue},unsigned int,unsigned int)

SetValPoint((UniformGrid3D_)self, (Point3D)pt, (int)val) → None :

Set the value at grid point closest to the specified point

C++ signature :

void SetValPoint(RDGeom::UniformGrid3D {lvalue},RDGeom::Point3D,unsigned int)

rdkit.Geometry.rdGeometry.WriteGridToFile((UniformGrid3D_)grid, (str)filename) → 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> >)