Package rdkit :: Package Chem :: Module rdShapeHelpers
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Module rdShapeHelpers

Module containing functions to encode and compare the shapes of molecules

Functions [hide private]
 
ComputeConfBox(...)
ComputeConfBox( (Conformer)conf [, (AtomPairsParameters)trans=None [, (float)padding=2.0]]) -> tuple : Compute the lower and upper corners of a cuboid that will fit the conformer
 
ComputeConfDimsAndOffset(...)
ComputeConfDimsAndOffset( (Conformer)conf [, (AtomPairsParameters)trans=None [, (float)padding=2.0]]) -> tuple : Compute the size of the box that can fit the conformations, and offset of the box from the origin
 
ComputeUnionBox(...)
ComputeUnionBox( (tuple)arg1, (tuple)arg2) -> tuple : Compute the union of two boxes, so that all the points in both boxes are contained in the new box
 
EncodeShape(...)
EncodeShape( (Mol)mol, (UniformGrid3D_)grid [, (int)confId=-1 [, (AtomPairsParameters)trans=None [, (float)vdwScale=0.8 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True]]]]]]) -> None : Encode the shape of a molecule (one of its conformer) onto a grid
 
ShapeProtrudeDist(...)
ShapeProtrudeDist( (Mol)mol1, (Mol)mol2 [, (int)confId1=-1 [, (int)confId2=-1 [, (float)gridSpacing=0.5 [, (DiscreteValueType)bitsPerPoint=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (float)vdwScale=0.8 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True [, (bool)allowReordering=True]]]]]]]]]) -> float : Compute the shape protrude distance between two molecule based on a predefined alignment
 
ShapeTanimotoDist(...)
ShapeTanimotoDist( (Mol)mol1, (Mol)mol2 [, (int)confId1=-1 [, (int)confId2=-1 [, (float)gridSpacing=0.5 [, (DiscreteValueType)bitsPerPoint=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (float)vdwScale=0.8 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True]]]]]]]]) -> float : Compute the shape tanimoto distance between two molecule based on a predefined alignment
Variables [hide private]
  __package__ = None
hash(x)
Function Details [hide private]

ComputeConfBox(...)

 

ComputeConfBox( (Conformer)conf [, (AtomPairsParameters)trans=None [, (float)padding=2.0]]) -> tuple :
    Compute the lower and upper corners of a cuboid that will fit the conformer

    C++ signature :
        boost::python::tuple ComputeConfBox(RDKit::Conformer [,boost::python::api::object=None [,double=2.0]])

ComputeConfDimsAndOffset(...)

 

ComputeConfDimsAndOffset( (Conformer)conf [, (AtomPairsParameters)trans=None [, (float)padding=2.0]]) -> tuple :
    Compute the size of the box that can fit the conformations, and offset 
       of the box from the origin
    

    C++ signature :
        boost::python::tuple ComputeConfDimsAndOffset(RDKit::Conformer [,boost::python::api::object=None [,double=2.0]])

ComputeUnionBox(...)

 

ComputeUnionBox( (tuple)arg1, (tuple)arg2) -> tuple :
    Compute the union of two boxes, so that all the points in both boxes are 
        contained in the new box

    C++ signature :
        boost::python::tuple ComputeUnionBox(boost::python::tuple,boost::python::tuple)

EncodeShape(...)

 

EncodeShape( (Mol)mol, (UniformGrid3D_)grid [, (int)confId=-1 [, (AtomPairsParameters)trans=None [, (float)vdwScale=0.8 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True]]]]]]) -> None :
    Encode the shape of a molecule (one of its conformer) onto a grid
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - grid : grid onto which the encoding is written 
        - confId : id of the conformation of interest on mol (defaults to the first one) 
        - trans : any transformation that needs to be used to encode onto the grid (note the molecule remains unchanged) 
        - 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 occupancy 
        - setpSize : 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 of bits 
                      used per grid point - e.g. two bits per grid point will allow 3 layers
        - ignoreHs : when set, the contribution of Hs to the shape will be ignored
    

    C++ signature :
        void EncodeShape(RDKit::ROMol,RDGeom::UniformGrid3D {lvalue} [,int=-1 [,boost::python::api::object=None [,double=0.8 [,double=0.25 [,int=-1 [,bool=True]]]]]])

ShapeProtrudeDist(...)

 

ShapeProtrudeDist( (Mol)mol1, (Mol)mol2 [, (int)confId1=-1 [, (int)confId2=-1 [, (float)gridSpacing=0.5 [, (DiscreteValueType)bitsPerPoint=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (float)vdwScale=0.8 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True [, (bool)allowReordering=True]]]]]]]]]) -> float :
    Compute the shape protrude distance between two molecule based on a predefined alignment
      
      ARGUMENTS:
        - 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 occupancy 
        - 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 of bits 
                      used per grid point - e.g. two bits per grid point will allow 3 layers 
        - ignoreHs : when set, the contribution of Hs to the shape will be ignored
        - allowReordering : when set, the order will be automatically updated so that the value calculated
                            is the protrusion of the smaller shape from the larger one.
    

    C++ signature :
        double ShapeProtrudeDist(RDKit::ROMol,RDKit::ROMol [,int=-1 [,int=-1 [,double=0.5 [,RDKit::DiscreteValueVect::DiscreteValueType=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [,double=0.8 [,double=0.25 [,int=-1 [,bool=True [,bool=True]]]]]]]]])

ShapeTanimotoDist(...)

 

ShapeTanimotoDist( (Mol)mol1, (Mol)mol2 [, (int)confId1=-1 [, (int)confId2=-1 [, (float)gridSpacing=0.5 [, (DiscreteValueType)bitsPerPoint=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (float)vdwScale=0.8 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True]]]]]]]]) -> float :
    Compute the shape tanimoto distance between two molecule based on a predefined alignment
      
      ARGUMENTS:
        - 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 bits 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 occupancy 
        - 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 of bits 
                      used per grid point - e.g. two bits per grid point will allow 3 layers 
        - ignoreHs : when set, the contribution of Hs to the shape will be ignored
    

    C++ signature :
        double ShapeTanimotoDist(RDKit::ROMol,RDKit::ROMol [,int=-1 [,int=-1 [,double=0.5 [,RDKit::DiscreteValueVect::DiscreteValueType=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [,double=0.8 [,double=0.25 [,int=-1 [,bool=True]]]]]]]])