rdkit.Chem.rdMolAlign module

Module containing functions to align a molecule to a second molecule

rdkit.Chem.rdMolAlign.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 one 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 minimizing 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]]]]]])

rdkit.Chem.rdMolAlign.AlignMolConformers((Mol)mol[, (AtomPairsParameters)atomIds=[][, (AtomPairsParameters)confIds=[][, (AtomPairsParameters)weights=[][, (bool)reflect=False[, (int)maxIters=50[, (AtomPairsParameters)RMSlist=None]]]]]]) → None :

Align 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 alignment - 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 minimizing 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]]]]]])

rdkit.Chem.rdMolAlign.CalcRMS((Mol)prbMol, (Mol)refMol[, (int)prbId=-1[, (int)refId=-1[, (AtomPairsParameters)map=None[, (int)maxMatches=1000000[, (bool)symmetrizeConjugatedTerminalGroups=True[, (AtomPairsParameters)weights=[]]]]]]]) → float :

Returns the RMS between two molecules, taking symmetry into account.

In contrast to getBestRMS, the RMS is computed ‘in place’, i.e. probe molecules are not aligned to the reference ahead of the RMS calculation. This is useful, for example, to compute the RMSD between docking poses and the co-crystallized ligand.

Note: This function will attempt to match all permutations of matching atom orders in both molecules, for some molecules it will lead to ‘combinatorial explosion’ especially if hydrogens are present.

ARGUMENTS

• prbMol: the molecule to be aligned to the reference

• refMol: the reference molecule

• prbCId: (optional) probe conformation to use

• refCId: (optional) reference conformation to use

• map: (optional) a list of lists of (probeAtomId, refAtomId)

  tuples with the atom-atom mappings of the two molecules. If not provided, these will be generated using a substructure search.

• maxMatches: (optional) if map isn’t specified, this will be

  the max number of matches found in a SubstructMatch()

• symmetrizeConjugatedTerminalGroups: (optional) if set, conjugated

  terminal functional groups (like nitro or carboxylate) will be considered symmetrically

• weights: (optional) weights for mapping

RETURNS The best RMSD found

C++ signature :

double CalcRMS(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,int=-1 [,int=-1 [,boost::python::api::object=None [,int=1000000 [,bool=True [,boost::python::api::object=[]]]]]]])

rdkit.Chem.rdMolAlign.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 one 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 minimizing 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]]]]]])

rdkit.Chem.rdMolAlign.GetAllConformerBestRMS((Mol)mol[, (int)numThreads=1[, (AtomPairsParameters)map=None[, (int)maxMatches=1000000[, (bool)symmetrizeConjugatedTerminalGroups=True[, (AtomPairsParameters)weights=[]]]]]]) → tuple :

Returns the symmetric distance matrix between the conformers of a molecule.

getBestRMS() is used to calculate the inter-conformer distances

ARGUMENTS

• mol: the molecule to be considered

• numThreads: (optional) number of threads to use

• map: (optional) a list of lists of (probeAtomId,refAtomId)

  tuples with the atom-atom mappings of the two molecules. If not provided, these will be generated using a substructure search.

• maxMatches: (optional) if map isn’t specified, this will be

  the max number of matches found in a SubstructMatch()

• symmetrizeConjugatedTerminalGroups: (optional) if set, conjugated

  terminal functional groups (like nitro or carboxylate) will be considered symmetrically

• weights: (optional) weights for mapping

RETURNS A tuple with the best RMSDS. The ordering is [(1,0),(2,0),(2,1),(3,0),… etc]

C++ signature :

boost::python::tuple GetAllConformerBestRMS(RDKit::ROMol {lvalue} [,int=1 [,boost::python::api::object=None [,int=1000000 [,bool=True [,boost::python::api::object=[]]]]]])

rdkit.Chem.rdMolAlign.GetBestAlignmentTransform((Mol)prbMol, (Mol)refMol[, (int)prbCid=-1[, (int)refCid=-1[, (AtomPairsParameters)map=[][, (int)maxMatches=1000000[, (bool)symmetrizeConjugatedTerminalGroups=True[, (AtomPairsParameters)weights=[][, (bool)reflect=False[, (int)maxIters=50[, (int)numThreads=1]]]]]]]]]) → object :

Compute the optimal RMS, transformation and atom map for aligning

two molecules, taking symmetry into account. Molecule coordinates are left unaltered.

This function will attempt to align all permutations of matching atom orders in both molecules, for some molecules it will lead to ‘combinatorial explosion’ especially if hydrogens are present. Use ‘GetAlignmentTransform’ to align molecules without changing the atom order.

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)

• map: (optional) a list of lists of (probeAtomId, refAtomId)

  tuples with the atom-atom mappings of the two molecules. If not provided, these will be generated using a substructure search.

• maxMatches (optional) if atomMap is empty, this will be the max number of

  matches found in a SubstructMatch().

• symmetrizeConjugatedTerminalGroups (optional) if set, conjugated

  terminal functional groups (like nitro or carboxylate) will be considered symmetrically.

• 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 minimizing the RMSD

• numThreads (optional) number of threads to use

RETURNS a tuple of (RMSD value, best transform matrix, best atom map)

C++ signature :

_object* GetBestAlignmentTransform(RDKit::ROMol,RDKit::ROMol [,int=-1 [,int=-1 [,boost::python::api::object=[] [,int=1000000 [,bool=True [,boost::python::api::object=[] [,bool=False [,unsigned int=50 [,int=1]]]]]]]]])

rdkit.Chem.rdMolAlign.GetBestRMS((Mol)prbMol, (Mol)refMol[, (int)prbId=-1[, (int)refId=-1[, (AtomPairsParameters)map=None[, (int)maxMatches=1000000[, (bool)symmetrizeConjugatedTerminalGroups=True[, (AtomPairsParameters)weights=[][, (int)numThreads=1]]]]]]]) → float :

Returns the optimal RMS for aligning two molecules, taking

symmetry into account. As a side-effect, the probe molecule is left in the aligned state.

Note: This function will attempt to align all permutations of matching atom orders in both molecules, for some molecules it will lead to ‘combinatorial explosion’ especially if hydrogens are present. Use ‘rdkit.Chem.AllChem.AlignMol’ to align molecules without changing the atom order.

ARGUMENTS

• prbMol: the molecule to be aligned to the reference

• refMol: the reference molecule

• prbId: (optional) probe conformation to use

• refId: (optional) reference conformation to use

• map: (optional) a list of lists of (probeAtomId,refAtomId)

  tuples with the atom-atom mappings of the two molecules. If not provided, these will be generated using a substructure search.

• maxMatches: (optional) if map isn’t specified, this will be

  the max number of matches found in a SubstructMatch()

• symmetrizeConjugatedTerminalGroups: (optional) if set, conjugated

  terminal functional groups (like nitro or carboxylate) will be considered symmetrically

• weights: (optional) weights for mapping

• numThreads: (optional) number of threads to use

RETURNS The best RMSD found

C++ signature :

double GetBestRMS(RDKit::ROMol {lvalue},RDKit::ROMol {lvalue} [,int=-1 [,int=-1 [,boost::python::api::object=None [,int=1000000 [,bool=True [,boost::python::api::object=[] [,int=1]]]]]]])

rdkit.Chem.rdMolAlign.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 minimizing 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=[]]]]]]]]]])

rdkit.Chem.rdMolAlign.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

• numThreadsthe 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 minimizing 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=[]]]]]]]]]])

rdkit.Chem.rdMolAlign.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 minimizing 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=[]]]]]]]]]])

rdkit.Chem.rdMolAlign.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

• numThreadsthe 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 minimizing 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=[]]]]]]]]]])

class rdkit.Chem.rdMolAlign.O3A

Bases: instance

Open3DALIGN object

Raises an exception This class cannot be instantiated from Python

Align((O3A)self) → float :

aligns probe molecule onto reference molecule

C++ signature :

double Align(RDKit::MolAlign::PyO3A {lvalue})

Matches((O3A)self) → list :

returns the AtomMap as found by Open3DALIGN

C++ signature :

boost::python::list Matches(RDKit::MolAlign::PyO3A {lvalue})

Score((O3A)self) → float :

returns the O3AScore of the alignment

C++ signature :

double Score(RDKit::MolAlign::PyO3A {lvalue})

Trans((O3A)self) → object :

returns the transformation which aligns probe molecule onto reference molecule

C++ signature :

_object* Trans(RDKit::MolAlign::PyO3A {lvalue})

Weights((O3A)self) → list :

returns the weight vector as found by Open3DALIGN

C++ signature :

boost::python::list Weights(RDKit::MolAlign::PyO3A {lvalue})

rdkit.Chem.rdMolAlign.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]])