rdkit.Chem.rdShapeHelpers

Package rdkit :: Package Chem :: Module rdShapeHelpers |
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# Module rdShapeHelpers

    Module containing functions to encode ans compre 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 | source code
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 | source code
ComputeUnionBox(...) ComputeUnionBox( (tuple)arg1, (tuple)arg2) -> tuple : Compute the union of two boxes, so that all the points in both boxes are contain in the new box | source code
EncodeShape(...) EncodeShape( (Mol)mol, (UniformGrid3D_)grid [, (int)confId=-1 [, (AtomPairsParameters)trans=None [, (float)vdwScale=0.80000000000000004 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True]]]]]]) -> None : Encode the shape of a molecule (one of it conformer) onto a grid | source code
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=0.80000000000000004 [, (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 | source code
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=0.80000000000000004 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True]]]]]]]]) -> float : Compute the shape tanimoto distance between two molecule based on a predefined alignment | source code

Function Details | [hide private]

### ComputeConfBox(...) | source code
    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(...) | source code
    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(...) | source code
    ComputeUnionBox( (tuple)arg1, (tuple)arg2) -> tuple :
        Compute the union of two boxes, so that all the points in both boxes are
            contain in the new box

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

### EncodeShape(...) | source code
    EncodeShape( (Mol)mol, (UniformGrid3D_)grid [, (int)confId=-1 [, (AtomPairsParameters)trans=None [, (float)vdwScale=0.80000000000000004 [, (float)stepSize=0.25 [, (int)maxLayers=-1 [, (bool)ignoreHs=True]]]]]]) -> None :
        Encode the shape of a molecule (one of it 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 remain 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 occupany
            - 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 allowed the number of bits
                          use 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=0.80000000000000004 [,double=0.25 [,int=-1 [,bool=True]]]]]])

### ShapeProtrudeDist(...) | source code
    ShapeProtrudeDist( (Mol)mol1, (Mol)mol2 [, (int)confId1=-1 [, (int)confId2=-1 [, (float)gridSpacing=0.5 [, (DiscreteValueType)bitsPerPoint=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (float)vdwScale=0.80000000000000004 [, (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 occupan
            - 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 : 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=0.80000000000000004 [,double=0.25 [,int=-1 [,bool=True [,bool=True]]]]]]]]])

### ShapeTanimotoDist(...) | source code
    ShapeTanimotoDist( (Mol)mol1, (Mol)mol2 [, (int)confId1=-1 [, (int)confId2=-1 [, (float)gridSpacing=0.5 [, (DiscreteValueType)bitsPerPoint=rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE [, (float)vdwScale=0.80000000000000004 [, (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 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 occupan
            - 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 : 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=0.80000000000000004 [,double=0.25 [,int=-1 [,bool=True]]]]]]]])