Chem.rdShapeHelpers

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(...) Compute the lower and upper corners of a cuboid that will fit the conformer... | source code
ComputeConfDimsAndOffset(...) Compute the size of the box that can fit the conformations, and offset ... | source code
ComputeUnionBox(...) Compute the union of two boxes, so that all the points in both boxes are ... | source code
EncodeShape(...) 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. | source code
ShapeProtrudeDist(...) 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. | source code
ShapeTanimotoDist(...) 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. | source code

Function Details | [hide private]

### ComputeConfBox(...) | source code
    Compute the lower and upper corners of a cuboid that will fit the conformer
    C++ signature:
        ComputeConfBox(RDKit::Conformer conf, boost::python::api::object trans=None, double padding=2.0) -> boost::python::tuple

### ComputeConfDimsAndOffset(...) | source code
    Compute the size of the box that can fit the conformations, and offset
       of the box from the origin

    C++ signature:
        ComputeConfDimsAndOffset(RDKit::Conformer conf, boost::python::api::object trans=None, double padding=2.0) -> boost::python::tuple

### ComputeUnionBox(...) | source code
    Compute the union of two boxes, so that all the points in both boxes are
        contain in the new box
    C++ signature:
        ComputeUnionBox(boost::python::tuple, boost::python::tuple) -> boost::python::tuple

### EncodeShape(...) | source code
    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:
        EncodeShape(RDKit::ROMol mol, RDGeom::UniformGrid3D {lvalue} grid, int confId=-1, boost::python::api::object trans=None, double vdwScale=0.80000000000000004, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=True) -> void*

### ShapeProtrudeDist(...) | source code
    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:
        ShapeProtrudeDist(RDKit::ROMol mol1, RDKit::ROMol mol2, int confId1=-1, int confId2=-1, double gridSpacing=0.5, RDKit::DiscreteValueVect::DiscreteValueType bitsPerPoint=DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE, double vdwScale=0.80000000000000004, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=True, bool allowReordering=True) -> double

### ShapeTanimotoDist(...) | source code
    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:
        ShapeTanimotoDist(RDKit::ROMol mol1, RDKit::ROMol mol2, int confId1=-1, int confId2=-1, double gridSpacing=0.5, RDKit::DiscreteValueVect::DiscreteValueType bitsPerPoint=DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE, double vdwScale=0.80000000000000004, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=True) -> double