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=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.
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]]]]]]]])