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Module containing functions to align a molecule to a second molecule
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O3A Open3DALIGN object |
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__package__ = None hash(x) |
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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( (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( (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( (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( (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( (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( (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( (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]]) |
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