pymatgen.analysis.molecule_matcher module

This module provides classes to perform fitting of molecule with arbitrary atom orders. This module is supposed to perform exact comparisons without the atom order correspondence prerequisite, while molecule_structure_comparator is supposed to do rough comparisons with the atom order correspondence prerequisite.

class AbstractMolAtomMapper[source]

Bases: monty.json.MSONable

Abstract molecular atom order mapping class. A mapping will be able to find the uniform atom order of two molecules that can pair the geometrically equivalent atoms.

classmethod from_dict(d)[source]
Parameters

() (d) – Dict

Returns

AbstractMolAtomMapper

abstract get_molecule_hash(mol)[source]

Defines a hash for molecules. This allows molecules to be grouped efficiently for comparison.

Parameters

mol – The molecule. OpenBabel OBMol or pymatgen Molecule object

Returns

A hashable object. Examples can be string formulas, etc.

abstract uniform_labels(mol1, mol2)[source]

Pair the geometrically equivalent atoms of the molecules.

Parameters

  • mol1 – First molecule. OpenBabel OBMol or pymatgen Molecule object.

  • mol2 – Second molecule. OpenBabel OBMol or pymatgen Molecule object.

Returns

(list1, list2) if uniform atom order is found. list1 and list2 are for mol1 and mol2, respectively. Their length equal to the number of atoms. They represents the uniform atom order of the two molecules. The value of each element is the original atom index in mol1 or mol2 of the current atom in uniform atom order. (None, None) if unform atom is not available.

class InchiMolAtomMapper(angle_tolerance=10.0)[source]

Bases: pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper

Pair atoms by inchi labels.

Parameters

angle_tolerance (float) – Angle threshold to assume linear molecule. In degrees.

as_dict()[source]
Returns

MSONAble dict.

classmethod from_dict(d)[source]
Parameters

d (dict) – Dict Representation

Returns

InchiMolAtomMapper

get_molecule_hash(mol)[source]

Return inchi as molecular hash

uniform_labels(mol1, mol2)[source]
Parameters
Returns

Labels

class IsomorphismMolAtomMapper[source]

Bases: pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper

Pair atoms by isomorphism permutations in the OpenBabel::OBAlign class

as_dict()[source]
Returns

Jsonable dict.

classmethod from_dict(d)[source]
Parameters

d (dict) – Dict representation

Returns

IsomorphismMolAtomMapper

get_molecule_hash(mol)[source]

Return inchi as molecular hash

uniform_labels(mol1, mol2)[source]

Pair the geometrically equivalent atoms of the molecules. Calculate RMSD on all possible isomorphism mappings and return mapping with the least RMSD

Parameters

  • mol1 – First molecule. OpenBabel OBMol or pymatgen Molecule object.

  • mol2 – Second molecule. OpenBabel OBMol or pymatgen Molecule object.

Returns

(list1, list2) if uniform atom order is found. list1 and list2 are for mol1 and mol2, respectively. Their length equal to the number of atoms. They represents the uniform atom order of the two molecules. The value of each element is the original atom index in mol1 or mol2 of the current atom in uniform atom order. (None, None) if unform atom is not available.

class MoleculeMatcher(tolerance=0.01, mapper=<pymatgen.analysis.molecule_matcher.InchiMolAtomMapper object>)[source]

Bases: monty.json.MSONable

Class to match molecules and identify whether molecules are the same.

Parameters

  • tolerance (float) – RMSD difference threshold whether two molecules are different

  • mapper (AbstractMolAtomMapper) – MolAtomMapper object that is able to map the atoms of two molecule to uniform order

as_dict()[source]
Returns

MSONAble dict.

fit(mol1, mol2)[source]

Fit two molecules.

Parameters

  • mol1 – First molecule. OpenBabel OBMol or pymatgen Molecule object

  • mol2 – Second molecule. OpenBabel OBMol or pymatgen Molecule object

Returns

A boolean value indicates whether two molecules are the same.

classmethod from_dict(d)[source]
Parameters

d (dict) – Dict representation

Returns

MoleculeMatcher

get_rmsd(mol1, mol2)[source]

Get RMSD between two molecule with arbitrary atom order.

Returns

RMSD if topology of the two molecules are the same Infinite if the topology is different

group_molecules(mol_list)[source]

Group molecules by structural equality.

Parameters

mol_list – List of OpenBabel OBMol or pymatgen objects

Returns

A list of lists of matched molecules Assumption: if s1=s2 and s2=s3, then s1=s3 This may not be true for small tolerances.