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.
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.
void computeConfDimsAndOffset (const Conformer &conf, RDGeom::Point3D &dims, RDGeom::Point3D &offSet, const RDGeom::Transform3D *trans=0, double padding=2.5)
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.
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.
std::vector< double > getConfDimensions (const Conformer &conf, double padding=2.5, const RDGeom::Point3D *center=0, bool ignoreHs=true)
 Compute dimensions of a conformer.
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 predefined alignment.
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 predefined alignment.
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 predefined alignment.
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 predefined alignment.

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:
conf The conformer of interest
leftBottom Storage for one extremity of the box
rightTop Storage for other extremity of the box
trans Optional transformation to be applied to the atom coordinates
padding Padding 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 box 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 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:
conf The conformer of interest
grid Grid onto which the molecule is encoded
trans Optional 3D transform to be applied to this conformation
vdwScale Scaling 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
stepSize thickness of the layers outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers the 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
ignoreHs if true, ignore the hydrogen atoms in the shape encoding process

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:
mol The molecule of interest
grid Grid onto which the molecule is encoded
confId Id of the conformation on the molecule to be encoded
trans Optional 3D transform to be applied to this conformation
vdwScale Scaling 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
stepSize thickness of the layers outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers the 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
ignoreHs if 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:
conf Conformer of interest
padding Padding added to the atom coordinates on all sides
center Optionally specify the center
ignoreHs if true, ignore the hydrogen atoms in computing the centroid

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 predefined alignment.

Parameters:
conf1 The first conformer of interest
conf2 The second conformer of interest
gridSpacing resolution of the grid used to encode the molecular shapes
bitsPerPoint number of bit used to encode the occupancy at each grid point
vdwScale Scaling 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
stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers the 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
ignoreHs if true, ignore the hydrogen atoms in the shape encoding process
allowReordering if 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 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 predefined alignment.

Parameters:
mol1 The first molecule of interest
mol2 The second molecule of interest
confId1 Conformer in the first molecule (defaults to first conformer)
confId2 Conformer in the second molecule (defaults to first conformer)
gridSpacing resolution of the grid used to encode the molecular shapes
bitsPerPoint number of bit used to encode the occupancy at each grid point defaults to two bits per grid point
vdwScale Scaling 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
stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers the 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
ignoreHs if true, ignore the hydrogen atoms in the shape encoding process
allowReordering if 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 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 predefined alignment.

Parameters:
conf1 The first conformer of interest
conf2 The second conformer of interest
gridSpacing resolution of the grid used to encode the molecular shapes
bitsPerPoint number of bit used to encode the occupancy at each grid point
vdwScale Scaling 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
stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers the 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
ignoreHs if true, ignore the hydrogen atoms in the shape encoding process

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 predefined alignment.

Parameters:
mol1 The first molecule of interest
mol2 The second molecule of interest
confId1 Conformer in the first molecule (defaults to first conformer)
confId2 Conformer in the second molecule (defaults to first conformer)
gridSpacing resolution of the grid used to encode the molecular shapes
bitsPerPoint number of bit used to encode the occupancy at each grid point defaults to two bits per grid point
vdwScale Scaling 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
stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value
maxLayers the 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
ignoreHs if true, ignore the hydrogen atoms in the shape encoding process

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