rdkit.Chem.rdDepictor

Package rdkit :: Package Chem :: Module rdDepictor |
[hide private]
[frames] | no frames]

# Module rdDepictor

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

Functions | [hide private]
Compute2DCoords(...) Compute2DCoords( (Mol)mol [, (bool)canonOrient=True [, (bool)clearConfs=True [, (dict)coordMap={} [, (int)nFlipsPerSample=0 [, (int)nSample=0 [, (int)sampleSeed=0 [, (bool)permuteDeg4Nodes=False [, (float)bondLength=-1.0]]]]]]]]) -> int : Compute 2D coordinates for a molecule. |
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 [, (float)bondLength=-1.0]]]]]]]]) -> int : Compute 2D coordinates for a molecule such that the inter-atom distances mimic those in a user-provided distance matrix. |
GenerateDepictionMatching2DStructure(...) GenerateDepictionMatching2DStructure( (Mol)mol, (Mol)reference [, (int)confId=-1 [, (AtomPairsParameters)refPatt=None [, (bool)acceptFailure=False]]]) -> None : Generate a depiction for a molecule where a piece of the molecule is constrained to have the same coordinates as a reference. |
GenerateDepictionMatching3DStructure(...) GenerateDepictionMatching3DStructure( (Mol)mol, (Mol)reference [, (int)confId=-1 [, (AtomPairsParameters)refPatt=None [, (bool)acceptFailure=False]]]) -> None : Generate a depiction for a molecule where a piece of the molecule is constrained to have coordinates similar to those of a 3D reference structure. |

Variables | [hide private]
| __package__ = `None` hash(x)

Function Details | [hide private]

### Compute2DCoords(...) |
    Compute2DCoords( (Mol)mol [, (bool)canonOrient=True [, (bool)clearConfs=True [, (dict)coordMap={} [, (int)nFlipsPerSample=0 [, (int)nSample=0 [, (int)sampleSeed=0 [, (bool)permuteDeg4Nodes=False [, (float)bondLength=-1.0]]]]]]]]) -> 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
             bondLength - change the default bond length for depiction

          RETURNS:

             ID of the conformation added to the molecule

        C++ signature :
            unsigned int Compute2DCoords(RDKit::ROMol {lvalue} [,bool=True [,bool=True [,boost::python::dict {lvalue}={} [,unsigned int=0 [,unsigned int=0 [,int=0 [,bool=False [,double=-1.0]]]]]]]])

### 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 [, (float)bondLength=-1.0]]]]]]]]) -> 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
             bondLength - change the default bond length for depiction

          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 [,double=-1.0]]]]]]]])

### GenerateDepictionMatching2DStructure(...) |
    GenerateDepictionMatching2DStructure( (Mol)mol, (Mol)reference [, (int)confId=-1 [, (AtomPairsParameters)refPatt=None [, (bool)acceptFailure=False]]]) -> None :
        Generate a depiction for a molecule where a piece of the
          molecule is constrained to have the same coordinates as a reference.

          This is useful for, for example, generating depictions of SAR data
          sets so that the cores of the molecules are all oriented the same way.
          ARGUMENTS:

          mol -    the molecule to be aligned, this will come back
                   with a single conformer.
          reference -    a molecule with the reference atoms to align to;
                         this should have a depiction.
          confId -       (optional) the id of the reference conformation to use
          referencePattern -  (optional) a query molecule to be used to
                              generate the atom mapping between the molecule
                              and the reference.
          acceptFailure - (optional) if True, standard depictions will be generated
                          for molecules that don't have a substructure match to the
                          reference; if False, throws a DepictException.

        C++ signature :
            void GenerateDepictionMatching2DStructure(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,int=-1 [,boost::python::api::object=None [,bool=False]]])

### GenerateDepictionMatching3DStructure(...) |
    GenerateDepictionMatching3DStructure( (Mol)mol, (Mol)reference [, (int)confId=-1 [, (AtomPairsParameters)refPatt=None [, (bool)acceptFailure=False]]]) -> None :
        Generate a depiction for a molecule where a piece of the molecule
          is constrained to have coordinates similar to those of a 3D reference
          structure.
          ARGUMENTS:

          mol -    the molecule to be aligned, this will come back
                   with a single conformer containing the 2D coordinates.
          reference -    a molecule with the reference atoms to align to.
                         By default this should be the same as mol, but with
                         3D coordinates
          confId -       (optional) the id of the reference conformation to use
          referencePattern -  (optional) a query molecule to map a subset of
                              the reference onto the mol, so that only some of the
                              atoms are aligned.
          acceptFailure - (optional) if True, standard depictions will be generated
                          for molecules that don't match the reference or the
                          referencePattern; if False, throws a DepictException.

        C++ signature :
            void GenerateDepictionMatching3DStructure(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,int=-1 [,boost::python::api::object=None [,bool=False]]])