Module rdMolAlign

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:
    AlignMol(RDKit::ROMol {lvalue} prbMol, RDKit::ROMol refMol, int prbCid=-1, int refCid=-1, boost::python::api::object atomMap=[], boost::python::api::object weights=[], bool reflect=False, unsigned int maxIters=50) -> double

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:
    AlignMolConformers(RDKit::ROMol {lvalue} mol, boost::python::api::object atomIds=[], boost::python::api::object confIds=[], boost::python::api::object weights=[], bool reflect=False, unsigned int maxIters=50) -> void*

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:
    GetAlignmentTransform(RDKit::ROMol prbMol, RDKit::ROMol refMol, int prbCid=-1, int refCid=-1, boost::python::api::object atomMap=[], boost::python::api::object weights=[], bool reflect=False, unsigned int maxIters=50) -> _object*