Module rdMolAlign

AlignMol( (Mol)prbMol, (Mol)refMol [, (int)prbCid=-1 [, (int)refCid=-1 [, (AtomPairsParameters)atomMap=[] [, (AtomPairsParameters)weights=[] [, (bool)reflect=False [, (int)maxIters=50]]]]]]) -> float :
    Optimally (minimum RMSD) align a molecule to another molecule
         
          The 3D transformation required to align the specied conformation in the probe molecule
          to a specified conformation in the reference molecule is computed so that the root mean
          squared distance between a specified set of atoms is minimized. 
          This transform is then applied to the specified conformation in the probe molecule
         
         ARGUMENTS
          - prbMol    molecule that is to be aligned
          - refMol    molecule used as the reference for the alignment
          - prbCid    ID of the conformation in the probe to be used 
                           for the alignment (defaults to first conformation)
          - refCid    ID of the conformation in the ref molecule to which 
                           the alignment is computed (defaults to first conformation)
          - atomMap   a vector of pairs of atom IDs (probe AtomId, ref AtomId)
                           used to compute the alignments. If this mapping is 
                           not specified an attempt is made to generate on by
                           substructure matching
          - weights   Optionally specify weights for each of the atom pairs
          - reflect   if true reflect the conformation of the probe molecule
          - maxIters  maximum number of iteration used in mimizing the RMSD
           
          RETURNS
          RMSD value
        
    

    C++ signature :
        double AlignMol(RDKit::ROMol {lvalue},RDKit::ROMol [,int=-1 [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,bool=False [,unsigned int=50]]]]]])

AlignMolConformers( (Mol)mol [, (AtomPairsParameters)atomIds=[] [, (AtomPairsParameters)confIds=[] [, (AtomPairsParameters)weights=[] [, (bool)reflect=False [, (int)maxIters=50]]]]]) -> None :
    Alignment conformations in a molecule to each other
         
          The first conformation in the molecule is used as the reference
         
         ARGUMENTS
          - mol       molecule of interest
          - atomIds   List of atom ids to use a points for alingment - defaults to all atoms
          - confIds   Ids of conformations to align - defaults to all conformers 
          - weights   Optionally specify weights for each of the atom pairs
          - reflect   if true reflect the conformation of the probe molecule
          - maxIters  maximum number of iteration used in mimizing the RMSD
           
          RETURNS
          RMSD value
        
    

    C++ signature :
        void AlignMolConformers(RDKit::ROMol {lvalue} [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=[] [,bool=False [,unsigned int=50]]]]])

GetAlignmentTransform( (Mol)prbMol, (Mol)refMol [, (int)prbCid=-1 [, (int)refCid=-1 [, (AtomPairsParameters)atomMap=[] [, (AtomPairsParameters)weights=[] [, (bool)reflect=False [, (int)maxIters=50]]]]]]) -> object :
    Compute the transformation required to align a molecule
         
          The 3D transformation required to align the specied conformation in the probe molecule
          to a specified conformation in the reference molecule is computed so that the root mean
          squared distance between a specified set of atoms is minimized
         
         ARGUMENTS
          - prbMol    molecule that is to be aligned
          - refMol    molecule used as the reference for the alignment
          - prbCid    ID of the conformation in the probe to be used 
                           for the alignment (defaults to first conformation)
          - refCid    ID of the conformation in the ref molecule to which 
                           the alignment is computed (defaults to first conformation)
          - atomMap   a vector of pairs of atom IDs (probe AtomId, ref AtomId)
                           used to compute the alignments. If this mapping is 
                           not specified an attempt is made to generate on by
                           substructure matching
          - weights   Optionally specify weights for each of the atom pairs
          - reflect   if true reflect the conformation of the probe molecule
          - maxIters  maximum number of iteration used in mimizing the RMSD
           
          RETURNS
          a tuple of (RMSD value, transform matrix) 
        
    

    C++ signature :
        _object* GetAlignmentTransform(RDKit::ROMol,RDKit::ROMol [,int=-1 [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,bool=False [,unsigned int=50]]]]]])