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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
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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]]]]]])
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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]]]]]])
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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]]]]]])
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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=[]]]]]]]]]])
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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=[]]]]]]]]]])
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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=[]]]]]]]]]])
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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=[]]]]]]]]]])
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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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