rdkit.Chem.rdDepictor

Package rdkit :: Package Chem :: Module rdDepictor |
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# Module rdDepictor

    Module containing the functionality to compute 2D coordinates for a molecule

Functions | [hide private]
Compute2DCoords(...) Compute2DCoords( (Mol)mol [, (bool)canonOrient=False [, (bool)clearConfs=True [, (dict)coordMap={} [, (int)nFlipsPerSample=0 [, (int)nSample=0 [, (int)sampleSeed=0 [, (bool)permuteDeg4Nodes=False]]]]]]]) -> int : Compute 2D coordinates for a molecule. | source code
Compute2DCoordsMimicDistmat(...) Compute2DCoordsMimicDistmat( (Mol)mol, (AtomPairsParameters)distMat [, (bool)canonOrient=False [, (bool)clearConfs=True [, (float)weightDistMat=0.5 [, (int)nFlipsPerSample=3 [, (int)nSample=100 [, (int)sampleSeed=100 [, (bool)permuteDeg4Nodes=True]]]]]]]) -> int : Compute 2D coordinates for a molecule such that the inter-atom distances mimic those in a user-provided distance matrix. | source code

Function Details | [hide private]

### Compute2DCoords(...) | source code
    Compute2DCoords( (Mol)mol [, (bool)canonOrient=False [, (bool)clearConfs=True [, (dict)coordMap={} [, (int)nFlipsPerSample=0 [, (int)nSample=0 [, (int)sampleSeed=0 [, (bool)permuteDeg4Nodes=False]]]]]]]) -> int :
        Compute 2D coordinates for a molecule.
          The resulting coordinates are stored on each atom of the molecule

          ARGUMENTS:

             mol - the molecule of interest
             canonOrient - orient the molecule in a canonical way
             clearConfs - if true, all existing conformations on the molecule
                     will be cleared
             coordMap - a dictionary mapping atom Ids -> Point2D objects
                        with starting coordinates for atoms that should
                        have their positions locked.
             nFlipsPerSample - number of rotatable bonds that are
                        flipped at random at a time.
             nSample - Number of random samplings of rotatable bonds.
             sampleSeed - seed for the random sampling process.
             permuteDeg4Nodes - allow permutation of bonds at a degree 4
                         node during the sampling process

          RETURNS:

             ID of the conformation added to the molecule

        C++ signature :
            unsigned int Compute2DCoords(RDKit::ROMol {lvalue} [,bool=False [,bool=True [,boost::python::dict {lvalue}={} [,unsigned int=0 [,unsigned int=0 [,int=0 [,bool=False]]]]]]])

### Compute2DCoordsMimicDistmat(...) | source code
    Compute2DCoordsMimicDistmat( (Mol)mol, (AtomPairsParameters)distMat [, (bool)canonOrient=False [, (bool)clearConfs=True [, (float)weightDistMat=0.5 [, (int)nFlipsPerSample=3 [, (int)nSample=100 [, (int)sampleSeed=100 [, (bool)permuteDeg4Nodes=True]]]]]]]) -> int :
        Compute 2D coordinates for a molecule such
          that the inter-atom distances mimic those in a user-provided
          distance matrix.
          The resulting coordinates are stored on each atom of the molecule

          ARGUMENTS:

             mol - the molecule of interest
             distMat - distance matrix that we want the 2D structure to mimic
             canonOrient - orient the molecule in a canonical way
             clearConfs - if true, all existing conformations on the molecule
                     will be cleared
             weightDistMat - weight assigned in the cost function to mimicing
                             the distance matrix.
                             This must be between (0.0,1.0). (1.0-weightDistMat)
                             is then the weight assigned to improving
                             the density of the 2D structure i.e. try to
                             make it spread out
             nFlipsPerSample - number of rotatable bonds that are
                        flipped at random at a time.
             nSample - Number of random samplings of rotatable bonds.
             sampleSeed - seed for the random sampling process.
             permuteDeg4Nodes - allow permutation of bonds at a degree 4
                         node during the sampling process

          RETURNS:

             ID of the conformation added to the molecule

        C++ signature :
            unsigned int Compute2DCoordsMimicDistmat(RDKit::ROMol {lvalue},boost::python::api::object [,bool=False [,bool=True [,double=0.5 [,unsigned int=3 [,unsigned int=100 [,int=100 [,bool=True]]]]]]])