RDKit
Open-source cheminformatics and machine learning.
RDKit::MolShapes Namespace Reference

Functions

void EncodeShape (const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId=-1, const RDGeom::Transform3D *trans=0, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
 Encode the shape of a molecule on to a grid. More...
 
void EncodeShape (const Conformer &conf, RDGeom::UniformGrid3D &grid, const RDGeom::Transform3D *trans=0, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
 Emcode the shape of a conformer on to a grid. More...
 
void computeConfDimsAndOffset (const Conformer &conf, RDGeom::Point3D &dims, RDGeom::Point3D &offSet, const RDGeom::Transform3D *trans=0, double padding=2.5)
 Compute the size of the box that can fit the conformation, and offset of the. More...
 
void computeConfBox (const Conformer &conf, RDGeom::Point3D &leftBottom, RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans=0, double padding=2.5)
 Compute the a box that will fit the confomer. More...
 
void computeUnionBox (const RDGeom::Point3D &leftBottom1, const RDGeom::Point3D &rightTop1, const RDGeom::Point3D &leftBottom2, const RDGeom::Point3D &rightTop2, RDGeom::Point3D &uLeftBottom, RDGeom::Point3D &uRightTop)
 Compute the union of two boxes. More...
 
std::vector< double > getConfDimensions (const Conformer &conf, double padding=2.5, const RDGeom::Point3D *center=0, bool ignoreHs=true)
 Compute dimensions of a conformer. More...
 
double tanimotoDistance (const ROMol &mol1, const ROMol &mol2, int confId1=-1, int confId2=-1, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
 Compute the shape tanimoto distance between two molecule based on a. More...
 
double tanimotoDistance (const Conformer &conf1, const Conformer &conf2, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
 Compute the shape tanimoto distance between two conformers based on a. More...
 
double protrudeDistance (const ROMol &mol1, const ROMol &mol2, int confId1=-1, int confId2=-1, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true, bool allowReordering=true)
 Compute the shape protrusion distance between two molecule based on a. More...
 
double protrudeDistance (const Conformer &conf1, const Conformer &conf2, double gridSpacing=0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true, bool allowReordering=true)
 Compute the shape protrusion distance between two conformers based on a. More...
 

Function Documentation

void RDKit::MolShapes::computeConfBox ( const Conformer conf,
RDGeom::Point3D leftBottom,
RDGeom::Point3D rightTop,
const RDGeom::Transform3D trans = 0,
double  padding = 2.5 
)

Compute the a box that will fit the confomer.

Parameters
confThe conformer of interest
leftBottomStorage for one extremity of the box
rightTopStorage for other extremity of the box
transOptional transformation to be applied to the atom coordinates
paddingPadding added on the sides around the conformer
void RDKit::MolShapes::computeConfDimsAndOffset ( const Conformer conf,
RDGeom::Point3D dims,
RDGeom::Point3D offSet,
const RDGeom::Transform3D trans = 0,
double  padding = 2.5 
)

Compute the size of the box that can fit the conformation, and offset of the.

from the origin

void RDKit::MolShapes::computeUnionBox ( const RDGeom::Point3D leftBottom1,
const RDGeom::Point3D rightTop1,
const RDGeom::Point3D leftBottom2,
const RDGeom::Point3D rightTop2,
RDGeom::Point3D uLeftBottom,
RDGeom::Point3D uRightTop 
)

Compute the union of two boxes.

void RDKit::MolShapes::EncodeShape ( const ROMol mol,
RDGeom::UniformGrid3D grid,
int  confId = -1,
const RDGeom::Transform3D trans = 0,
double  vdwScale = 0.8,
double  stepSize = 0.25,
int  maxLayers = -1,
bool  ignoreHs = true 
)

Encode the shape of a molecule on to a grid.

Parameters
molThe molecule of interest
gridGrid onto which the molecule is encoded
confIdId of the conformation on the molecule to be encoded
transOptional 3D transform to be applied to this conformation
vdwScaleScaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupany
stepSizethickness of the layers outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayersthe maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHsif true, ignore the hydrogen atoms in the shape encoding process
void RDKit::MolShapes::EncodeShape ( const Conformer conf,
RDGeom::UniformGrid3D grid,
const RDGeom::Transform3D trans = 0,
double  vdwScale = 0.8,
double  stepSize = 0.25,
int  maxLayers = -1,
bool  ignoreHs = true 
)

Emcode the shape of a conformer on to a grid.

Parameters
confThe conformer of interest
gridGrid onto which the molecule is encoded
transOptional 3D transform to be applied to this conformation
vdwScaleScaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupany
stepSizethickness of the layers outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayersthe maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHsif true, ignore the hydrogen atoms in the shape encoding process
std::vector<double> RDKit::MolShapes::getConfDimensions ( const Conformer conf,
double  padding = 2.5,
const RDGeom::Point3D center = 0,
bool  ignoreHs = true 
)

Compute dimensions of a conformer.

Parameters
confConformer of interest
paddingPadding added to the atom coordinates on all sides
centerOptionally specify the center
ignoreHsif true, ignore the hydrogen atoms in computing the centroid
double RDKit::MolShapes::protrudeDistance ( const ROMol mol1,
const ROMol mol2,
int  confId1 = -1,
int  confId2 = -1,
double  gridSpacing = 0.5,
DiscreteValueVect::DiscreteValueType  bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
double  vdwScale = 0.8,
double  stepSize = 0.25,
int  maxLayers = -1,
bool  ignoreHs = true,
bool  allowReordering = true 
)

Compute the shape protrusion distance between two molecule based on a.

Parameters
mol1The first molecule of interest
mol2The second molecule of interest
confId1Conformer in the first molecule (defaults to first conformer)
confId2Conformer in the second molecule (defaults to first conformer)
gridSpacingresolution of the grid used to encode the molecular shapes
bitsPerPointnumber of bit used to encode the occupancy at each grid point defaults to two bits per grid point
vdwScaleScaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupany
stepSizethickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayersthe maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHsif true, ignore the hydrogen atoms in the shape encoding process
allowReorderingif set the order will be automatically updated so that the value calculated is the protrusion of the smaller shape from the larger one.
double RDKit::MolShapes::protrudeDistance ( const Conformer conf1,
const Conformer conf2,
double  gridSpacing = 0.5,
DiscreteValueVect::DiscreteValueType  bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
double  vdwScale = 0.8,
double  stepSize = 0.25,
int  maxLayers = -1,
bool  ignoreHs = true,
bool  allowReordering = true 
)

Compute the shape protrusion distance between two conformers based on a.

Parameters
conf1The first conformer of interest
conf2The second conformer of interest
gridSpacingresolution of the grid used to encode the molecular shapes
bitsPerPointnumber of bit used to encode the occupancy at each grid point
vdwScaleScaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupany
stepSizethickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayersthe maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHsif true, ignore the hydrogen atoms in the shape encoding process
allowReorderingif set the order will be automatically updated so that the value calculated is the protrusion of the smaller shape from the larger one.
double RDKit::MolShapes::tanimotoDistance ( const ROMol mol1,
const ROMol mol2,
int  confId1 = -1,
int  confId2 = -1,
double  gridSpacing = 0.5,
DiscreteValueVect::DiscreteValueType  bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
double  vdwScale = 0.8,
double  stepSize = 0.25,
int  maxLayers = -1,
bool  ignoreHs = true 
)

Compute the shape tanimoto distance between two molecule based on a.

Parameters
mol1The first molecule of interest
mol2The second molecule of interest
confId1Conformer in the first molecule (defaults to first conformer)
confId2Conformer in the second molecule (defaults to first conformer)
gridSpacingresolution of the grid used to encode the molecular shapes
bitsPerPointnumber of bit used to encode the occupancy at each grid point defaults to two bits per grid point
vdwScaleScaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupany
stepSizethickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayersthe maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHsif true, ignore the hydrogen atoms in the shape encoding process
double RDKit::MolShapes::tanimotoDistance ( const Conformer conf1,
const Conformer conf2,
double  gridSpacing = 0.5,
DiscreteValueVect::DiscreteValueType  bitsPerPoint = DiscreteValueVect::TWOBITVALUE,
double  vdwScale = 0.8,
double  stepSize = 0.25,
int  maxLayers = -1,
bool  ignoreHs = true 
)

Compute the shape tanimoto distance between two conformers based on a.

Parameters
conf1The first conformer of interest
conf2The second conformer of interest
gridSpacingresolution of the grid used to encode the molecular shapes
bitsPerPointnumber of bit used to encode the occupancy at each grid point
vdwScaleScaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupany
stepSizethickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayersthe maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers
ignoreHsif true, ignore the hydrogen atoms in the shape encoding process