Chem.rdDepictor

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(...) Compute 2D coordinates for a molecule. | source code
Compute2DCoordsMimicDistmat(...) 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
    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:
        Compute2DCoords(RDKit::ROMol {lvalue} mol, bool canonOrient=False, bool clearConfs=True, boost::python::dict {lvalue} coordMap={}, unsigned int nFlipsPerSample=0, unsigned int nSample=0, int sampleSeed=0, bool permuteDeg4Nodes=False) -> unsigned int

### Compute2DCoordsMimicDistmat(...) | source code
    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:
        Compute2DCoordsMimicDistmat(RDKit::ROMol {lvalue} mol, boost::python::api::object distMat, bool canonOrient=False, bool clearConfs=True, double weightDistMat=0.5, unsigned int nFlipsPerSample=3, unsigned int nSample=100, int sampleSeed=100, bool permuteDeg4Nodes=True) -> unsigned int