rdkit.Chem.rdMolAlign

Package rdkit :: Package Chem :: Module rdMolAlign |
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# Module rdMolAlign

    Module containing functions to align a molecule to a second molecule

Classes | [hide private]
| O3A Open3DALIGN object

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 |
AlignMolConformers(...) AlignMolConformers( (Mol)mol [, (AtomPairsParameters)atomIds=[] [, (AtomPairsParameters)confIds=[] [, (AtomPairsParameters)weights=[] [, (bool)reflect=False [, (int)maxIters=50 [, (AtomPairsParameters)RMSlist=None]]]]]]) -> None : Alignment conformations in a molecule to each other |
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 |
GetCrippenO3A(...) GetCrippenO3A( (Mol)prbMol, (Mol)refMol [, (list)prbCrippenContribs=[] [, (list)refCrippenContribs=[] [, (int)prbCid=-1 [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> O3A : Get an O3A object with atomMap and weights vectors to overlay the probe molecule onto the reference molecule based on Crippen logP atom contributions |
GetCrippenO3AForProbeConfs(...) GetCrippenO3AForProbeConfs( (Mol)prbMol, (Mol)refMol [, (int)numThreads=1 [, (list)prbCrippenContribs=[] [, (list)refCrippenContribs=[] [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> tuple : Get a vector of O3A objects for the overlay of all the probe molecule's conformations onto the reference molecule based on MMFF atom types and charges |
GetO3A(...) GetO3A( (Mol)prbMol, (Mol)refMol [, (AtomPairsParameters)prbPyMMFFMolProperties=None [, (AtomPairsParameters)refPyMMFFMolProperties=None [, (int)prbCid=-1 [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> O3A : Get an O3A object with atomMap and weights vectors to overlay the probe molecule onto the reference molecule based on MMFF atom types and charges |
GetO3AForProbeConfs(...) GetO3AForProbeConfs( (Mol)prbMol, (Mol)refMol [, (int)numThreads=1 [, (AtomPairsParameters)prbPyMMFFMolProperties=None [, (AtomPairsParameters)refPyMMFFMolProperties=None [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> tuple : Get a vector of O3A objects for the overlay of all the probe molecule's conformations onto the reference molecule based on MMFF atom types and charges |
RandomTransform(...) RandomTransform( (Mol)mol [, (int)cid=-1 [, (int)seed=-1]]) -> None : Perform a random transformation on a molecule |

Variables | [hide private]
| __package__ = `None` hash(x)

Function Details | [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.
              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 iterations 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(...) |
    AlignMolConformers( (Mol)mol [, (AtomPairsParameters)atomIds=[] [, (AtomPairsParameters)confIds=[] [, (AtomPairsParameters)weights=[] [, (bool)reflect=False [, (int)maxIters=50 [, (AtomPairsParameters)RMSlist=None]]]]]]) -> 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 iterations used in mimizing the RMSD
              - RMSlist   if provided, fills in the RMS values between the reference
                      conformation and the other aligned conformations

        C++ signature :
            void AlignMolConformers(RDKit::ROMol {lvalue} [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=[] [,bool=False [,unsigned int=50 [,boost::python::api::object=None]]]]]])

### 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. 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 iterations 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]]]]]])

### GetCrippenO3A(...) |
    GetCrippenO3A( (Mol)prbMol, (Mol)refMol [, (list)prbCrippenContribs=[] [, (list)refCrippenContribs=[] [, (int)prbCid=-1 [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> O3A :
        Get an O3A object with atomMap and weights vectors to overlay
              the probe molecule onto the reference molecule based on
              Crippen logP atom contributions

             ARGUMENTS
              - prbMol                   molecule that is to be aligned
              - refMol                   molecule used as the reference for the alignment
              - prbCrippenContribs       Crippen atom contributions for the probe molecule
                                         as a list of (logp, mr) tuples, as returned
                                         by _CalcCrippenContribs()
              - refCrippenContribs       Crippen atom contributions for the reference molecule
                                         as a list of (logp, mr) tuples, as returned
                                         by _CalcCrippenContribs()
              - 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)
              - reflect                  if true reflect the conformation of the probe molecule
                                         (defaults to false)
              - maxIters                 maximum number of iterations used in mimizing the RMSD
                                         (defaults to 50)
              - options                  least 2 significant bits encode accuracy
                                         (0: maximum, 3: minimum; defaults to 0)
                                         bit 3 triggers local optimization of the alignment
                                         (no computation of the cost matrix; defaults: off)
              - constraintMap            a vector of pairs of atom IDs (probe AtomId, ref AtomId)
                                         which shall be used for the alignment (defaults to [])
              - constraintWeights        optionally specify weights for each of the constraints
                                         (weights default to 100.0)

              RETURNS
              The O3A object

        C++ signature :
            RDKit::MolAlign::PyO3A* GetCrippenO3A(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,boost::python::list=[] [,boost::python::list=[] [,int=-1 [,int=-1 [,bool=False [,unsigned int=50 [,unsigned int=0 [,boost::python::list=[] [,boost::python::list=[]]]]]]]]]])

### GetCrippenO3AForProbeConfs(...) |
    GetCrippenO3AForProbeConfs( (Mol)prbMol, (Mol)refMol [, (int)numThreads=1 [, (list)prbCrippenContribs=[] [, (list)refCrippenContribs=[] [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> tuple :
        Get a vector of O3A objects for the overlay of all
              the probe molecule's conformations onto the reference molecule based on
              MMFF atom types and charges

             ARGUMENTS
              - prbMol                   molecule that is to be aligned
              - refMol                   molecule used as the reference for the alignment
              - numThreads :             the number of threads to use, only has an effect if
                                         the RDKit was built with thread support (defaults to 1)
              - prbCrippenContribs       Crippen atom contributions for the probe molecule
                                         as a list of (logp, mr) tuples, as returned
                                         by _CalcCrippenContribs()
              - refCrippenContribs       Crippen atom contributions for the reference molecule
                                         as a list of (logp, mr) tuples, as returned
                                         by _CalcCrippenContribs()
              - refCid                   ID of the conformation in the ref molecule to which
                                         the alignment is computed (defaults to first conformation)
              - reflect                  if true reflect the conformation of the probe molecule
                                         (defaults to false)
              - maxIters                 maximum number of iterations used in mimizing the RMSD
                                         (defaults to 50)
              - options                  least 2 significant bits encode accuracy
                                         (0: maximum, 3: minimum; defaults to 0)
                                         bit 3 triggers local optimization of the alignment
                                         (no computation of the cost matrix; defaults: off)
              - constraintMap            a vector of pairs of atom IDs (probe AtomId, ref AtomId)
                                         which shall be used for the alignment (defaults to [])
              - constraintWeights        optionally specify weights for each of the constraints
                                         (weights default to 100.0)

              RETURNS
              A vector of O3A objects

        C++ signature :
            boost::python::tuple GetCrippenO3AForProbeConfs(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,int=1 [,boost::python::list=[] [,boost::python::list=[] [,int=-1 [,bool=False [,unsigned int=50 [,unsigned int=0 [,boost::python::list=[] [,boost::python::list=[]]]]]]]]]])

### GetO3A(...) |
    GetO3A( (Mol)prbMol, (Mol)refMol [, (AtomPairsParameters)prbPyMMFFMolProperties=None [, (AtomPairsParameters)refPyMMFFMolProperties=None [, (int)prbCid=-1 [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> O3A :
        Get an O3A object with atomMap and weights vectors to overlay
              the probe molecule onto the reference molecule based on
              MMFF atom types and charges

             ARGUMENTS
              - prbMol                   molecule that is to be aligned
              - refMol                   molecule used as the reference for the alignment
              - prbPyMMFFMolProperties   PyMMFFMolProperties object for the probe molecule as returned
                                         by SetupMMFFForceField()
              - refPyMMFFMolProperties   PyMMFFMolProperties object for the reference molecule as returned
                                         by SetupMMFFForceField()
              - 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)
              - reflect                  if true reflect the conformation of the probe molecule
                                         (defaults to false)
              - maxIters                 maximum number of iterations used in mimizing the RMSD
                                         (defaults to 50)
              - options                  least 2 significant bits encode accuracy
                                         (0: maximum, 3: minimum; defaults to 0)
                                         bit 3 triggers local optimization of the alignment
                                         (no computation of the cost matrix; defaults: off)
              - constraintMap            a vector of pairs of atom IDs (probe AtomId, ref AtomId)
                                         which shall be used for the alignment (defaults to [])
              - constraintWeights        optionally specify weights for each of the constraints
                                         (weights default to 100.0)

              RETURNS
              The O3A object

        C++ signature :
            RDKit::MolAlign::PyO3A* GetO3A(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1 [,int=-1 [,bool=False [,unsigned int=50 [,unsigned int=0 [,boost::python::list=[] [,boost::python::list=[]]]]]]]]]])

### GetO3AForProbeConfs(...) |
    GetO3AForProbeConfs( (Mol)prbMol, (Mol)refMol [, (int)numThreads=1 [, (AtomPairsParameters)prbPyMMFFMolProperties=None [, (AtomPairsParameters)refPyMMFFMolProperties=None [, (int)refCid=-1 [, (bool)reflect=False [, (int)maxIters=50 [, (int)options=0 [, (list)constraintMap=[] [, (list)constraintWeights=[]]]]]]]]]]) -> tuple :
        Get a vector of O3A objects for the overlay of all
              the probe molecule's conformations onto the reference molecule based on
              MMFF atom types and charges

             ARGUMENTS
              - prbMol                   molecule that is to be aligned
              - refMol                   molecule used as the reference for the alignment
              - numThreads :             the number of threads to use, only has an effect if
                                         the RDKit was built with thread support (defaults to 1)
                                         If set to zero, the max supported by the system will be used.
              - prbPyMMFFMolProperties   PyMMFFMolProperties object for the probe molecule as returned
                                         by SetupMMFFForceField()
              - refPyMMFFMolProperties   PyMMFFMolProperties object for the reference molecule as returned
                                         by SetupMMFFForceField()
              - refCid                   ID of the conformation in the ref molecule to which
                                         the alignment is computed (defaults to first conformation)
              - reflect                  if true reflect the conformation of the probe molecule
                                         (defaults to false)
              - maxIters                 maximum number of iterations used in mimizing the RMSD
                                         (defaults to 50)
              - options                  least 2 significant bits encode accuracy
                                         (0: maximum, 3: minimum; defaults to 0)
                                         bit 3 triggers local optimization of the alignment
                                         (no computation of the cost matrix; defaults: off)
              - constraintMap            a vector of pairs of atom IDs (probe AtomId, ref AtomId)
                                         which shall be used for the alignment (defaults to [])
              - constraintWeights        optionally specify weights for each of the constraints
                                         (weights default to 100.0)

              RETURNS
              A vector of O3A objects

        C++ signature :
            boost::python::tuple GetO3AForProbeConfs(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,int=1 [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1 [,bool=False [,unsigned int=50 [,unsigned int=0 [,boost::python::list=[] [,boost::python::list=[]]]]]]]]]])

### RandomTransform(...) |
    RandomTransform( (Mol)mol [, (int)cid=-1 [, (int)seed=-1]]) -> None :
        Perform a random transformation on a molecule

             ARGUMENTS
              - mol    molecule that is to be transformed
              - cid    ID of the conformation in the mol to be transformed
                       (defaults to first conformation)
              - seed   seed used to initialize the random generator
                       (defaults to -1, that is no seeding)

        C++ signature :
            void RandomTransform(RDKit::ROMol {lvalue} [,int=-1 [,int=-1]])