Module rdDepictor

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( (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( (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( (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]]])