Chem.rdMolAlign

Package Chem :: Module rdMolAlign |
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# Module rdMolAlign

    Module containing functions to align a molecule to a second molecule

Functions | [hide private]
AlignMol(...) 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. | source code
AlignMolConformers(...) AlignMolConformers( (Mol)mol [, (AtomPairsParameters)atomIds=[] [, (AtomPairsParameters)confIds=[] [, (AtomPairsParameters)weights=[] [, (bool)reflect=False [, (int)maxIters=50]]]]]) -> None :... | source code
GetAlignmentTransform(...) 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. | source code

Function Details | [hide private]

### AlignMol(...) | source code
    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(...) | source code
    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(...) | source code
    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]]]]]])