pymatgen.analysis.molecule_matcher — pymatgen 2020.7.3 documentation

# Source code for pymatgen.analysis.molecule_matcher

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    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.
    """

    __author__ = "Xiaohui Qu"
    __copyright__ = "Copyright 2011, The Materials Project"
    __version__ = "1.0"
    __maintainer__ = "Xiaohui Qu"
    __email__ = "xhqu1981@gmail.com"
    __status__ = "Experimental"
    __date__ = "Jun 7, 2013"

    import re
    import math
    import abc
    import itertools
    import copy

    from monty.json import MSONable
    from monty.dev import requires

    try:
        from openbabel import openbabel as ob
        from pymatgen.io.babel import BabelMolAdaptor
    except ImportError:
        ob = None

    class AbstractMolAtomMapper(MSONable, metaclass=abc.ABCMeta):
        """
        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.
        """

        @abc.abstractmethod
        def uniform_labels(self, mol1, mol2):
            """
            Pair the geometrically equivalent atoms of the molecules.

            Args:
                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.
            """
            pass

        @abc.abstractmethod
        def get_molecule_hash(self, mol):
            """
            Defines a hash for molecules. This allows molecules to be grouped
            efficiently for comparison.

            Args:
                mol: The molecule. OpenBabel OBMol or pymatgen Molecule object

            Returns:
                A hashable object. Examples can be string formulas, etc.
            """
            pass

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (): Dict

            Returns:
                AbstractMolAtomMapper
            """
            for trans_modules in ['molecule_matcher']:
                import sys
                if sys.version_info > (3, 0):
                    level = 0  # Python 3.x
                else:
                    level = -1  # Python 2.x
                mod = __import__('pymatgen.analysis.' + trans_modules,
                                 globals(), locals(), [d['@class']], level)
                if hasattr(mod, d['@class']):
                    class_proxy = getattr(mod, d['@class'])
                    from_dict_proxy = getattr(class_proxy, "from_dict")
                    return from_dict_proxy(d)
            raise ValueError("Invalid Comparator dict")

    class IsomorphismMolAtomMapper(AbstractMolAtomMapper):
        """
        Pair atoms by isomorphism permutations in the OpenBabel::OBAlign class
        """

        def uniform_labels(self, mol1, mol2):
            """
            Pair the geometrically equivalent atoms of the molecules.
            Calculate RMSD on all possible isomorphism mappings and return mapping
            with the least RMSD

            Args:
                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.
            """
            obmol1 = BabelMolAdaptor(mol1).openbabel_mol
            obmol2 = BabelMolAdaptor(mol2).openbabel_mol

            h1 = self.get_molecule_hash(obmol1)
            h2 = self.get_molecule_hash(obmol2)
            if h1 != h2:
                return None, None

            query = ob.CompileMoleculeQuery(obmol1)
            isomapper = ob.OBIsomorphismMapper.GetInstance(query)
            isomorph = ob.vvpairUIntUInt()
            isomapper.MapAll(obmol2, isomorph)

            sorted_isomorph = [sorted(x, key=lambda morp: morp[0])
                               for x in isomorph]
            label2_list = tuple([tuple([p[1] + 1 for p in x])
                                 for x in sorted_isomorph])

            vmol1 = obmol1
            aligner = ob.OBAlign(True, False)
            aligner.SetRefMol(vmol1)
            least_rmsd = float("Inf")
            best_label2 = None
            label1 = list(range(1, obmol1.NumAtoms() + 1))
            # noinspection PyProtectedMember
            elements1 = InchiMolAtomMapper._get_elements(vmol1, label1)
            for label2 in label2_list:
                # noinspection PyProtectedMember
                elements2 = InchiMolAtomMapper._get_elements(obmol2, label2)
                if elements1 != elements2:
                    continue
                vmol2 = ob.OBMol()
                for i in label2:
                    vmol2.AddAtom(obmol2.GetAtom(i))
                aligner.SetTargetMol(vmol2)
                aligner.Align()
                rmsd = aligner.GetRMSD()
                if rmsd < least_rmsd:
                    least_rmsd = rmsd
                    best_label2 = copy.copy(label2)
            return label1, best_label2

        def get_molecule_hash(self, mol):
            """
            Return inchi as molecular hash
            """
            obconv = ob.OBConversion()
            obconv.SetOutFormat(str("inchi"))
            obconv.AddOption(str("X"), ob.OBConversion.OUTOPTIONS, str("DoNotAddH"))
            inchi_text = obconv.WriteString(mol)
            match = re.search(r"InChI=(?P<inchi>.+)\n", inchi_text)
            return match.group("inchi")

        def as_dict(self):
            """
            Returns:
                Jsonable dict.
            """
            return {"version": __version__, "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__}

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict representation

            Returns:
                IsomorphismMolAtomMapper
            """
            return IsomorphismMolAtomMapper()

    class InchiMolAtomMapper(AbstractMolAtomMapper):
        """
        Pair atoms by inchi labels.
        """

        def __init__(self, angle_tolerance=10.0):
            """
            Args:
                angle_tolerance (float): Angle threshold to assume linear molecule. In degrees.
            """
            self._angle_tolerance = angle_tolerance
            self._assistant_mapper = IsomorphismMolAtomMapper()

        def as_dict(self):
            """
            Returns:
                MSONAble dict.
            """
            return {"version": __version__, "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__,
                    "angle_tolerance": self._angle_tolerance}

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict Representation

            Returns:
                InchiMolAtomMapper
            """
            return InchiMolAtomMapper(angle_tolerance=d["angle_tolerance"])

        @staticmethod
        def _inchi_labels(mol):
            """
            Get the inchi canonical labels of the heavy atoms in the molecule

            Args:
                mol: The molecule. OpenBabel OBMol object

            Returns:
                The label mappings. List of tuple of canonical label,
                original label
                List of equivalent atoms.
            """
            obconv = ob.OBConversion()
            obconv.SetOutFormat(str("inchi"))
            obconv.AddOption(str("a"), ob.OBConversion.OUTOPTIONS)
            obconv.AddOption(str("X"), ob.OBConversion.OUTOPTIONS, str("DoNotAddH"))
            inchi_text = obconv.WriteString(mol)
            match = re.search(r"InChI=(?P<inchi>.+)\nAuxInfo=.+"
                              r"/N:(?P<labels>[0-9,;]+)/(E:(?P<eq_atoms>[0-9,"
                              r";\(\)]*)/)?", inchi_text)
            inchi = match.group("inchi")
            label_text = match.group("labels")
            eq_atom_text = match.group("eq_atoms")
            heavy_atom_labels = tuple([int(i) for i in label_text.replace(
                ';', ',').split(',')])
            eq_atoms = []
            if eq_atom_text is not None:
                eq_tokens = re.findall(r'\(((?:[0-9]+,)+[0-9]+)\)', eq_atom_text
                                       .replace(';', ','))
                eq_atoms = tuple([tuple([int(i) for i in t.split(',')])
                                  for t in eq_tokens])
            return heavy_atom_labels, eq_atoms, inchi

        @staticmethod
        def _group_centroid(mol, ilabels, group_atoms):
            """
            Calculate the centroids of a group atoms indexed by the labels of inchi

            Args:
                mol: The molecule. OpenBabel OBMol object
                ilabel: inchi label map

            Returns:
                Centroid. Tuple (x, y, z)
            """
            c1x, c1y, c1z = 0.0, 0.0, 0.0
            for i in group_atoms:
                orig_idx = ilabels[i - 1]
                oa1 = mol.GetAtom(orig_idx)
                c1x += float(oa1.x())
                c1y += float(oa1.y())
                c1z += float(oa1.z())
            num_atoms = len(group_atoms)
            c1x /= num_atoms
            c1y /= num_atoms
            c1z /= num_atoms
            return c1x, c1y, c1z

        def _virtual_molecule(self, mol, ilabels, eq_atoms):
            """
            Create a virtual molecule by unique atoms, the centriods of the
            equivalent atoms

            Args:
                mol: The molecule. OpenBabel OBMol object
                ilables: inchi label map
                eq_atoms: equivalent atom labels
                farthest_group_idx: The equivalent atom group index in which
                    there is the farthest atom to the centroid

            Return:
                The virtual molecule
            """
            vmol = ob.OBMol()

            non_unique_atoms = set([a for g in eq_atoms for a in g])
            all_atoms = set(range(1, len(ilabels) + 1))
            unique_atom_labels = sorted(all_atoms - non_unique_atoms)

            # try to align molecules using unique atoms
            for i in unique_atom_labels:
                orig_idx = ilabels[i - 1]
                oa1 = mol.GetAtom(orig_idx)
                a1 = vmol.NewAtom()
                a1.SetAtomicNum(oa1.GetAtomicNum())
                a1.SetVector(oa1.GetVector())

            # try to align using centroids of the equivalent atoms
            if vmol.NumAtoms() < 3:
                for symm in eq_atoms:
                    c1x, c1y, c1z = self._group_centroid(mol, ilabels, symm)
                    min_distance = float("inf")
                    for i in range(1, vmol.NumAtoms() + 1):
                        va = vmol.GetAtom(i)
                        distance = math.sqrt((c1x - va.x()) ** 2 + (c1y - va.y()) ** 2
                                             + (c1z - va.z()) ** 2)
                        if distance < min_distance:
                            min_distance = distance
                    if min_distance > 0.2:
                        a1 = vmol.NewAtom()
                        a1.SetAtomicNum(9)
                        a1.SetVector(c1x, c1y, c1z)

            return vmol

        @staticmethod
        def _align_heavy_atoms(mol1, mol2, vmol1, vmol2, ilabel1, ilabel2,
                               eq_atoms):
            """
            Align the label of topologically identical atoms of second molecule
            towards first molecule

            Args:
                mol1: First molecule. OpenBabel OBMol object
                mol2: Second molecule. OpenBabel OBMol object
                vmol1: First virtual molecule constructed by centroids. OpenBabel
                    OBMol object
                vmol2: First virtual molecule constructed by centroids. OpenBabel
                    OBMol object
                ilabel1: inchi label map of the first molecule
                ilabel2: inchi label map of the second molecule
                eq_atoms: equivalent atom lables

            Return:
                corrected inchi labels of heavy atoms of the second molecule
            """

            nvirtual = vmol1.NumAtoms()
            nheavy = len(ilabel1)

            for i in ilabel2:  # add all heavy atoms
                a1 = vmol1.NewAtom()
                a1.SetAtomicNum(1)
                a1.SetVector(0.0, 0.0, 0.0)  # useless, just to pair with vmol2
                oa2 = mol2.GetAtom(i)
                a2 = vmol2.NewAtom()
                a2.SetAtomicNum(1)
                # align using the virtual atoms, these atoms are not
                # used to align, but match by positions
                a2.SetVector(oa2.GetVector())

            aligner = ob.OBAlign(False, False)
            aligner.SetRefMol(vmol1)
            aligner.SetTargetMol(vmol2)
            aligner.Align()
            aligner.UpdateCoords(vmol2)

            canon_mol1 = ob.OBMol()
            for i in ilabel1:
                oa1 = mol1.GetAtom(i)
                a1 = canon_mol1.NewAtom()
                a1.SetAtomicNum(oa1.GetAtomicNum())
                a1.SetVector(oa1.GetVector())

            aligned_mol2 = ob.OBMol()
            for i in range(nvirtual + 1, nvirtual + nheavy + 1):
                oa2 = vmol2.GetAtom(i)
                a2 = aligned_mol2.NewAtom()
                a2.SetAtomicNum(oa2.GetAtomicNum())
                a2.SetVector(oa2.GetVector())

            canon_label2 = list(range(1, nheavy + 1))
            for symm in eq_atoms:
                for i in symm:
                    canon_label2[i - 1] = -1
            for symm in eq_atoms:
                candidates1 = list(symm)
                candidates2 = list(symm)
                for c2 in candidates2:
                    distance = 99999.0
                    canon_idx = candidates1[0]
                    a2 = aligned_mol2.GetAtom(c2)
                    for c1 in candidates1:
                        a1 = canon_mol1.GetAtom(c1)
                        d = a1.GetDistance(a2)
                        if d < distance:
                            distance = d
                            canon_idx = c1
                    canon_label2[c2 - 1] = canon_idx
                    candidates1.remove(canon_idx)

            canon_inchi_orig_map2 = [(canon, inchi, orig)
                                     for canon, inchi, orig in
                                     zip(canon_label2, list(range(1, nheavy + 1)),
                                         ilabel2)]
            canon_inchi_orig_map2.sort(key=lambda m: m[0])
            heavy_atom_indices2 = tuple([x[2] for x in canon_inchi_orig_map2])
            return heavy_atom_indices2

        @staticmethod
        def _align_hydrogen_atoms(mol1, mol2, heavy_indices1,
                                  heavy_indices2):
            """
            Align the label of topologically identical atoms of second molecule
            towards first molecule

            Args:
                mol1: First molecule. OpenBabel OBMol object
                mol2: Second molecule. OpenBabel OBMol object
                heavy_indices1: inchi label map of the first molecule
                heavy_indices2: label map of the second molecule

            Return:
                corrected label map of all atoms of the second molecule
            """
            num_atoms = mol2.NumAtoms()
            all_atom = set(range(1, num_atoms + 1))
            hydrogen_atoms1 = all_atom - set(heavy_indices1)
            hydrogen_atoms2 = all_atom - set(heavy_indices2)
            label1 = heavy_indices1 + tuple(hydrogen_atoms1)
            label2 = heavy_indices2 + tuple(hydrogen_atoms2)

            cmol1 = ob.OBMol()
            for i in label1:
                oa1 = mol1.GetAtom(i)
                a1 = cmol1.NewAtom()
                a1.SetAtomicNum(oa1.GetAtomicNum())
                a1.SetVector(oa1.GetVector())
            cmol2 = ob.OBMol()
            for i in label2:
                oa2 = mol2.GetAtom(i)
                a2 = cmol2.NewAtom()
                a2.SetAtomicNum(oa2.GetAtomicNum())
                a2.SetVector(oa2.GetVector())

            aligner = ob.OBAlign(False, False)
            aligner.SetRefMol(cmol1)
            aligner.SetTargetMol(cmol2)
            aligner.Align()
            aligner.UpdateCoords(cmol2)

            hydrogen_label2 = []
            hydrogen_label1 = list(range(len(heavy_indices1) + 1, num_atoms + 1))
            for h2 in range(len(heavy_indices2) + 1, num_atoms + 1):
                distance = 99999.0
                idx = hydrogen_label1[0]
                a2 = cmol2.GetAtom(h2)
                for h1 in hydrogen_label1:
                    a1 = cmol1.GetAtom(h1)
                    d = a1.GetDistance(a2)
                    if d < distance:
                        distance = d
                        idx = h1
                hydrogen_label2.append(idx)
                hydrogen_label1.remove(idx)

            hydrogen_orig_idx2 = label2[len(heavy_indices2):]
            hydrogen_canon_orig_map2 = [(canon, orig) for canon, orig
                                        in zip(hydrogen_label2,
                                               hydrogen_orig_idx2)]
            hydrogen_canon_orig_map2.sort(key=lambda m: m[0])
            hydrogen_canon_indices2 = [x[1] for x in hydrogen_canon_orig_map2]

            canon_label1 = label1
            canon_label2 = heavy_indices2 + tuple(hydrogen_canon_indices2)

            return canon_label1, canon_label2

        @staticmethod
        def _get_elements(mol, label):
            """
            The the elements of the atoms in the specified order

            Args:
                mol: The molecule. OpenBabel OBMol object.
                label: The atom indices. List of integers.

            Returns:
                Elements. List of integers.
            """
            elements = [int(mol.GetAtom(i).GetAtomicNum()) for i in label]
            return elements

        def _is_molecule_linear(self, mol):
            """
            Is the molecule a linear one

            Args:
                mol: The molecule. OpenBabel OBMol object.

            Returns:
                Boolean value.
            """
            if mol.NumAtoms() < 3:
                return True
            a1 = mol.GetAtom(1)
            a2 = mol.GetAtom(2)
            for i in range(3, mol.NumAtoms() + 1):
                angle = float(mol.GetAtom(i).GetAngle(a2, a1))
                if angle < 0.0:
                    angle = -angle
                if angle > 90.0:
                    angle = 180.0 - angle
                if angle > self._angle_tolerance:
                    return False
            return True

        def uniform_labels(self, mol1, mol2):
            """
            Args:
                mol1 (Molecule): Molecule 1
                mol2 (Molecule): Molecule 2

            Returns:
                Labels
            """
            obmol1 = BabelMolAdaptor(mol1).openbabel_mol
            obmol2 = BabelMolAdaptor(mol2).openbabel_mol

            ilabel1, iequal_atom1, inchi1 = self._inchi_labels(obmol1)
            ilabel2, iequal_atom2, inchi2 = self._inchi_labels(obmol2)

            if inchi1 != inchi2:
                return None, None  # Topoligically different

            if iequal_atom1 != iequal_atom2:
                raise Exception("Design Error! Equavilent atoms are inconsistent")

            vmol1 = self._virtual_molecule(obmol1, ilabel1, iequal_atom1)
            vmol2 = self._virtual_molecule(obmol2, ilabel2, iequal_atom2)

            if vmol1.NumAtoms() != vmol2.NumAtoms():
                return None, None

            if vmol1.NumAtoms() < 3 or self._is_molecule_linear(vmol1) \
                    or self._is_molecule_linear(vmol2):
                # using isomorphism for difficult (actually simple) molecules
                clabel1, clabel2 = self._assistant_mapper.uniform_labels(mol1, mol2)
            else:
                heavy_atom_indices2 = self._align_heavy_atoms(obmol1, obmol2,
                                                              vmol1, vmol2, ilabel1,
                                                              ilabel2, iequal_atom1)
                clabel1, clabel2 = self._align_hydrogen_atoms(obmol1, obmol2,
                                                              ilabel1,
                                                              heavy_atom_indices2)
            if clabel1 and clabel2:
                elements1 = self._get_elements(obmol1, clabel1)
                elements2 = self._get_elements(obmol2, clabel2)

                if elements1 != elements2:
                    return None, None

            return clabel1, clabel2

        def get_molecule_hash(self, mol):
            """
            Return inchi as molecular hash
            """
            obmol = BabelMolAdaptor(mol).openbabel_mol
            inchi = self._inchi_labels(obmol)[2]
            return inchi

    class MoleculeMatcher(MSONable):
        """
        Class to match molecules and identify whether molecules are the same.
        """

        @requires(ob,
                  "BabelMolAdaptor requires openbabel to be installed with "
                  "Python bindings. Please get it at http://openbabel.org "
                  "(version >=3.0.0).")
        def __init__(self, tolerance=0.01, mapper=InchiMolAtomMapper()):
            """
            Args:
                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
            """
            self._tolerance = tolerance
            self._mapper = mapper

        def fit(self, mol1, mol2):
            """
            Fit two molecules.

            Args:
                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.
            """
            return self.get_rmsd(mol1, mol2) < self._tolerance

        def get_rmsd(self, mol1, mol2):
            """
            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
            """
            label1, label2 = self._mapper.uniform_labels(mol1, mol2)
            if label1 is None or label2 is None:
                return float("Inf")
            return self._calc_rms(mol1, mol2, label1, label2)

        @staticmethod
        def _calc_rms(mol1, mol2, clabel1, clabel2):
            """
            Calculate the RMSD.

            Args:
                mol1: The first molecule. OpenBabel OBMol or pymatgen Molecule
                    object
                mol2: The second molecule. OpenBabel OBMol or pymatgen Molecule
                    object
                clabel1: The atom indices that can reorder the first molecule to
                    uniform atom order
                clabel1: The atom indices that can reorder the second molecule to
                    uniform atom order

            Returns:
                The RMSD.
            """
            obmol1 = BabelMolAdaptor(mol1).openbabel_mol
            obmol2 = BabelMolAdaptor(mol2).openbabel_mol

            cmol1 = ob.OBMol()
            for i in clabel1:
                oa1 = obmol1.GetAtom(i)
                a1 = cmol1.NewAtom()
                a1.SetAtomicNum(oa1.GetAtomicNum())
                a1.SetVector(oa1.GetVector())
            cmol2 = ob.OBMol()
            for i in clabel2:
                oa2 = obmol2.GetAtom(i)
                a2 = cmol2.NewAtom()
                a2.SetAtomicNum(oa2.GetAtomicNum())
                a2.SetVector(oa2.GetVector())

            aligner = ob.OBAlign(True, False)
            aligner.SetRefMol(cmol1)
            aligner.SetTargetMol(cmol2)
            aligner.Align()
            return aligner.GetRMSD()

        def group_molecules(self, mol_list):
            """
            Group molecules by structural equality.

            Args:
                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.
            """
            mol_hash = [(i, self._mapper.get_molecule_hash(m))
                        for i, m in enumerate(mol_list)]
            mol_hash.sort(key=lambda x: x[1])

            # Use molecular hash to pre-group molecules.
            raw_groups = tuple([tuple([m[0] for m in g]) for k, g
                                in itertools.groupby(mol_hash,
                                                     key=lambda x: x[1])])

            group_indices = []
            for rg in raw_groups:
                mol_eq_test = [(p[0], p[1], self.fit(mol_list[p[0]],
                                                     mol_list[p[1]]))
                               for p in itertools.combinations(sorted(rg), 2)]
                mol_eq = set([(p[0], p[1]) for p in mol_eq_test if p[2]])
                not_alone_mols = set(itertools.chain.from_iterable(mol_eq))
                alone_mols = set(rg) - not_alone_mols
                group_indices.extend([[m] for m in alone_mols])
                while len(not_alone_mols) > 0:
                    current_group = {not_alone_mols.pop()}
                    while len(not_alone_mols) > 0:
                        candidate_pairs = set(
                            [tuple(sorted(p)) for p
                             in itertools.product(current_group, not_alone_mols)])
                        mutual_pairs = candidate_pairs & mol_eq
                        if len(mutual_pairs) == 0:
                            break
                        mutual_mols = set(itertools.chain
                                          .from_iterable(mutual_pairs))
                        current_group |= mutual_mols
                        not_alone_mols -= mutual_mols
                    group_indices.append(sorted(current_group))

            group_indices.sort(key=lambda x: (len(x), -x[0]), reverse=True)
            all_groups = [[mol_list[i] for i in g] for g in group_indices]
            return all_groups

        def as_dict(self):
            """
            Returns:
                MSONAble dict.
            """
            return {"version": __version__, "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__,
                    "tolerance": self._tolerance, "mapper": self._mapper.as_dict()}

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict representation

            Returns:
                MoleculeMatcher
            """
            return MoleculeMatcher(
                tolerance=d["tolerance"],
                mapper=AbstractMolAtomMapper.from_dict(d["mapper"]))