pymatgen.io.cif — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.cif

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

    """
    Wrapper classes for Cif input and output from Structures.
    """

    import math
    import re
    import os
    import textwrap
    import warnings
    from collections import OrderedDict, deque
    from io import StringIO
    import numpy as np
    from functools import partial
    from pathlib import Path
    from inspect import getfullargspec as getargspec
    from itertools import groupby
    from pymatgen.core.periodic_table import Element, Specie, get_el_sp, DummySpecie
    from monty.io import zopen
    from pymatgen.util.coord import in_coord_list_pbc, find_in_coord_list_pbc
    from monty.string import remove_non_ascii
    from pymatgen.core.lattice import Lattice
    from pymatgen.core.structure import Structure
    from pymatgen.core.composition import Composition
    from pymatgen.core.operations import SymmOp
    from pymatgen.symmetry.groups import SpaceGroup, SYMM_DATA
    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
    from pymatgen.electronic_structure.core import Magmom
    from pymatgen.core.operations import MagSymmOp
    from pymatgen.symmetry.maggroups import MagneticSpaceGroup

    __author__ = "Shyue Ping Ong, Will Richards, Matthew Horton"
    __copyright__ = "Copyright 2011, The Materials Project"
    __version__ = "4.0"
    __maintainer__ = "Shyue Ping Ong"
    __email__ = "shyuep@gmail.com"
    __status__ = "Production"
    __date__ = "Sep 23, 2011"

    sub_spgrp = partial(re.sub, r"[\s_]", "")

    space_groups = {sub_spgrp(k): k for k in SYMM_DATA['space_group_encoding'].keys()}  # type: ignore

    space_groups.update({sub_spgrp(k): k for k in SYMM_DATA['space_group_encoding'].keys()})  # type: ignore

    _COD_DATA = None

    def _get_cod_data():
        global _COD_DATA
        if _COD_DATA is None:
            import pymatgen
            with open(os.path.join(pymatgen.symmetry.__path__[0],
                                   "symm_ops.json")) \
                    as f:
                import json
                _COD_DATA = json.load(f)

        return _COD_DATA

    class CifBlock:
        """
        Object for storing cif data. All data is stored in a single dictionary.
        Data inside loops are stored in lists in the data dictionary, and
        information on which keys are grouped together are stored in the loops
        attribute.
        """
        maxlen = 70  # not quite 80 so we can deal with semicolons and things

        def __init__(self, data, loops, header):
            """
            Args:
                data: dict or OrderedDict of data to go into the cif. Values should
                        be convertible to string, or lists of these if the key is
                        in a loop
                loops: list of lists of keys, grouped by which loop they should
                        appear in
                header: name of the block (appears after the data_ on the first
                    line)
            """
            self.loops = loops
            self.data = data
            # AJ says: CIF Block names cannot be more than 75 characters or you
            # get an Exception
            self.header = header[:74]

        def __eq__(self, other):
            return self.loops == other.loops \
                   and self.data == other.data \
                   and self.header == other.header

        def __getitem__(self, key):
            return self.data[key]

        def __str__(self):
            """
            Returns the cif string for the data block
            """
            s = ["data_{}".format(self.header)]
            keys = self.data.keys()
            written = []
            for k in keys:
                if k in written:
                    continue
                for l in self.loops:
                    # search for a corresponding loop
                    if k in l:
                        s.append(self._loop_to_string(l))
                        written.extend(l)
                        break
                if k not in written:
                    # k didn't belong to a loop
                    v = self._format_field(self.data[k])
                    if len(k) + len(v) + 3 < self.maxlen:
                        s.append("{}   {}".format(k, v))
                    else:
                        s.extend([k, v])
            return "\n".join(s)

        def _loop_to_string(self, loop):
            s = "loop_"
            for l in loop:
                s += '\n ' + l
            for fields in zip(*[self.data[k] for k in loop]):
                line = "\n"
                for val in map(self._format_field, fields):
                    if val[0] == ";":
                        s += line + "\n" + val
                        line = "\n"
                    elif len(line) + len(val) + 2 < self.maxlen:
                        line += "  " + val
                    else:
                        s += line
                        line = '\n  ' + val
                s += line
            return s

        def _format_field(self, v):
            v = v.__str__().strip()
            if len(v) > self.maxlen:
                return ';\n' + textwrap.fill(v, self.maxlen) + '\n;'
            # add quotes if necessary
            if v == '':
                return '""'
            if (" " in v or v[0] == "_") \
                    and not (v[0] == "'" and v[-1] == "'") \
                    and not (v[0] == '"' and v[-1] == '"'):
                if "'" in v:
                    q = '"'
                else:
                    q = "'"
                v = q + v + q
            return v

        @classmethod
        def _process_string(cls, string):
            # remove comments
            string = re.sub(r"(\s|^)#.*$", "", string, flags=re.MULTILINE)
            # remove empty lines
            string = re.sub(r"^\s*\n", "", string, flags=re.MULTILINE)
            # remove non_ascii
            string = remove_non_ascii(string)
            # since line breaks in .cif files are mostly meaningless,
            # break up into a stream of tokens to parse, rejoining multiline
            # strings (between semicolons)
            q = deque()
            multiline = False
            ml = []
            # this regex splits on spaces, except when in quotes.
            # starting quotes must not be preceded by non-whitespace
            # (these get eaten by the first expression)
            # ending quotes must not be followed by non-whitespace
            p = re.compile(r'''([^'"\s][\S]*)|'(.*?)'(?!\S)|"(.*?)"(?!\S)''')
            for l in string.splitlines():
                if multiline:
                    if l.startswith(";"):
                        multiline = False
                        q.append(('', '', '', ' '.join(ml)))
                        ml = []
                        l = l[1:].strip()
                    else:
                        ml.append(l)
                        continue
                if l.startswith(";"):
                    multiline = True
                    ml.append(l[1:].strip())
                else:
                    for s in p.findall(l):
                        # s is tuple. location of the data in the tuple
                        # depends on whether it was quoted in the input
                        q.append(s)
            return q

        @classmethod
        def from_string(cls, string):
            """
            Reads CifBlock from string.

            :param string: String representation.
            :return: CifBlock
            """
            q = cls._process_string(string)
            header = q.popleft()[0][5:]
            data = OrderedDict()
            loops = []
            while q:
                s = q.popleft()
                # cif keys aren't in quotes, so show up in s[0]
                if s[0] == "_eof":
                    break
                if s[0].startswith("_"):
                    try:
                        data[s[0]] = "".join(q.popleft())
                    except IndexError:
                        data[s[0]] = ""
                elif s[0].startswith("loop_"):
                    columns = []
                    items = []
                    while q:
                        s = q[0]
                        if s[0].startswith("loop_") or not s[0].startswith("_"):
                            break
                        columns.append("".join(q.popleft()))
                        data[columns[-1]] = []
                    while q:
                        s = q[0]
                        if s[0].startswith("loop_") or s[0].startswith("_"):
                            break
                        items.append("".join(q.popleft()))
                    n = len(items) // len(columns)
                    assert len(items) % n == 0
                    loops.append(columns)
                    for k, v in zip(columns * n, items):
                        data[k].append(v.strip())
                elif "".join(s).strip() != "":
                    warnings.warn("Possible issue in cif file"
                                  " at line: {}".format("".join(s).strip()))
            return cls(data, loops, header)

    class CifFile:
        """
        Reads and parses CifBlocks from a .cif file or string
        """

        def __init__(self, data, orig_string=None, comment=None):
            """
            Args:
                data (OrderedDict): Of CifBlock objects.å
                orig_string (str): The original cif string.
                comment (str): Comment string.
            """
            self.data = data
            self.orig_string = orig_string
            self.comment = comment or "# generated using pymatgen"

        def __str__(self):
            s = ["%s" % v for v in self.data.values()]
            return self.comment + "\n" + "\n".join(s) + "\n"

        @classmethod
        def from_string(cls, string):
            """
            Reads CifFile from a string.

            :param string: String representation.
            :return: CifFile
            """
            d = OrderedDict()
            for x in re.split(r"^\s*data_", "x\n" + string,
                              flags=re.MULTILINE | re.DOTALL)[1:]:

                # Skip over Cif block that contains powder diffraction data.
                # Some elements in this block were missing from CIF files in
                # Springer materials/Pauling file DBs.
                # This block anyway does not contain any structure information, and
                # CifParser was also not parsing it.
                if 'powder_pattern' in re.split(r"\n", x, 1)[0]:
                    continue
                c = CifBlock.from_string("data_" + x)
                d[c.header] = c
            return cls(d, string)

        @classmethod
        def from_file(cls, filename):
            """
            Reads CifFile from a filename.

            :param filename: Filename
            :return: CifFile
            """
            with zopen(str(filename), "rt", errors="replace") as f:
                return cls.from_string(f.read())

    class CifParser:
        """
        Parses a CIF file. Attempts to fix CIFs that are out-of-spec, but will
        issue warnings if corrections applied. These are also stored in the
        CifParser's errors attribute.
        """

        def __init__(self, filename, occupancy_tolerance=1., site_tolerance=1e-4):
            """
            Args:
                filename (str): CIF filename, bzipped or gzipped CIF files are fine too.
                occupancy_tolerance (float): If total occupancy of a site is between 1
                    and occupancy_tolerance, the occupancies will be scaled down to 1.
                site_tolerance (float): This tolerance is used to determine if two
                    sites are sitting in the same position, in which case they will be
                    combined to a single disordered site. Defaults to 1e-4.
            """
            self._occupancy_tolerance = occupancy_tolerance
            self._site_tolerance = site_tolerance
            if isinstance(filename, (str, Path)):
                self._cif = CifFile.from_file(filename)
            else:
                self._cif = CifFile.from_string(filename.read())

            # store if CIF contains features from non-core CIF dictionaries
            # e.g. magCIF
            self.feature_flags = {}
            self.warnings = []

            def is_magcif():
                """
                Checks to see if file appears to be a magCIF file (heuristic).
                """
                # Doesn't seem to be a canonical way to test if file is magCIF or
                # not, so instead check for magnetic symmetry datanames
                prefixes = ['_space_group_magn', '_atom_site_moment',
                            '_space_group_symop_magn']
                for d in self._cif.data.values():
                    for k in d.data.keys():
                        for prefix in prefixes:
                            if prefix in k:
                                return True
                return False

            self.feature_flags['magcif'] = is_magcif()

            def is_magcif_incommensurate():
                """
                Checks to see if file contains an incommensurate magnetic
                structure (heuristic).
                """
                # Doesn't seem to be a canonical way to test if magCIF file
                # describes incommensurate strucure or not, so instead check
                # for common datanames
                if not self.feature_flags["magcif"]:
                    return False
                prefixes = ['_cell_modulation_dimension', '_cell_wave_vector']
                for d in self._cif.data.values():
                    for k in d.data.keys():
                        for prefix in prefixes:
                            if prefix in k:
                                return True
                return False

            self.feature_flags['magcif_incommensurate'] = is_magcif_incommensurate()

            for k in self._cif.data.keys():
                # pass individual CifBlocks to _sanitize_data
                self._cif.data[k] = self._sanitize_data(self._cif.data[k])

        @staticmethod
        def from_string(cif_string, occupancy_tolerance=1.):
            """
            Creates a CifParser from a string.

            Args:
                cif_string (str): String representation of a CIF.
                occupancy_tolerance (float): If total occupancy of a site is
                    between 1 and occupancy_tolerance, the occupancies will be
                    scaled down to 1.

            Returns:
                CifParser
            """
            stream = StringIO(cif_string)
            return CifParser(stream, occupancy_tolerance)

        def _sanitize_data(self, data):
            """
            Some CIF files do not conform to spec. This function corrects
            known issues, particular in regards to Springer materials/
            Pauling files.

            This function is here so that CifParser can assume its
            input conforms to spec, simplifying its implementation.
            :param data: CifBlock
            :return: data CifBlock
            """

            """
            This part of the code deals with handling formats of data as found in
            CIF files extracted from the Springer Materials/Pauling File
            databases, and that are different from standard ICSD formats.
            """

            # check for implicit hydrogens, warn if any present
            if "_atom_site_attached_hydrogens" in data.data.keys():
                attached_hydrogens = [str2float(x) for x in data.data['_atom_site_attached_hydrogens']
                                      if str2float(x) != 0]
                if len(attached_hydrogens) > 0:
                    self.warnings.append("Structure has implicit hydrogens defined, "
                                         "parsed structure unlikely to be suitable for use "
                                         "in calculations unless hydrogens added.")

            # Check to see if "_atom_site_type_symbol" exists, as some test CIFs do
            # not contain this key.
            if "_atom_site_type_symbol" in data.data.keys():

                # Keep a track of which data row needs to be removed.
                # Example of a row: Nb,Zr '0.8Nb + 0.2Zr' .2a .m-3m 0 0 0 1 14
                # 'rhombic dodecahedron, Nb<sub>14</sub>'
                # Without this code, the above row in a structure would be parsed
                # as an ordered site with only Nb (since
                # CifParser would try to parse the first two characters of the
                # label "Nb,Zr") and occupancy=1.
                # However, this site is meant to be a disordered site with 0.8 of
                # Nb and 0.2 of Zr.
                idxs_to_remove = []

                new_atom_site_label = []
                new_atom_site_type_symbol = []
                new_atom_site_occupancy = []
                new_fract_x = []
                new_fract_y = []
                new_fract_z = []

                for idx, el_row in enumerate(data["_atom_site_label"]):

                    # CIF files from the Springer Materials/Pauling File have
                    # switched the label and symbol. Thus, in the
                    # above shown example row, '0.8Nb + 0.2Zr' is the symbol.
                    # Below, we split the strings on ' + ' to
                    # check if the length (or number of elements) in the label and
                    # symbol are equal.
                    if len(data["_atom_site_type_symbol"][idx].split(' + ')) > \
                            len(data["_atom_site_label"][idx].split(' + ')):

                        # Dictionary to hold extracted elements and occupancies
                        els_occu = {}

                        # parse symbol to get element names and occupancy and store
                        # in "els_occu"
                        symbol_str = data["_atom_site_type_symbol"][idx]
                        symbol_str_lst = symbol_str.split(' + ')
                        for elocc_idx in range(len(symbol_str_lst)):
                            # Remove any bracketed items in the string
                            symbol_str_lst[elocc_idx] = re.sub(
                                r'\([0-9]*\)', '',
                                symbol_str_lst[elocc_idx].strip())

                            # Extract element name and its occupancy from the
                            # string, and store it as a
                            # key-value pair in "els_occ".
                            els_occu[str(re.findall(r'\D+', symbol_str_lst[
                                elocc_idx].strip())[1]).replace('<sup>', '')] = \
                                float('0' + re.findall(r'\.?\d+', symbol_str_lst[
                                    elocc_idx].strip())[1])

                        x = str2float(data["_atom_site_fract_x"][idx])
                        y = str2float(data["_atom_site_fract_y"][idx])
                        z = str2float(data["_atom_site_fract_z"][idx])

                        for et, occu in els_occu.items():
                            # new atom site labels have 'fix' appended
                            new_atom_site_label.append(
                                et + '_fix' + str(len(new_atom_site_label)))
                            new_atom_site_type_symbol.append(et)
                            new_atom_site_occupancy.append(str(occu))
                            new_fract_x.append(str(x))
                            new_fract_y.append(str(y))
                            new_fract_z.append(str(z))

                        idxs_to_remove.append(idx)

                # Remove the original row by iterating over all keys in the CIF
                # data looking for lists, which indicates
                # multiple data items, one for each row, and remove items from the
                # list that corresponds to the removed row,
                # so that it's not processed by the rest of this function (which
                # would result in an error).
                for original_key in data.data:
                    if isinstance(data.data[original_key], list):
                        for id in sorted(idxs_to_remove, reverse=True):
                            del data.data[original_key][id]

                if len(idxs_to_remove) > 0:
                    self.warnings.append("Pauling file corrections applied.")

                    data.data["_atom_site_label"] += new_atom_site_label
                    data.data["_atom_site_type_symbol"] += new_atom_site_type_symbol
                    data.data["_atom_site_occupancy"] += new_atom_site_occupancy
                    data.data["_atom_site_fract_x"] += new_fract_x
                    data.data["_atom_site_fract_y"] += new_fract_y
                    data.data["_atom_site_fract_z"] += new_fract_z

            """
            This fixes inconsistencies in naming of several magCIF tags
            as a result of magCIF being in widespread use prior to
            specification being finalized (on advice of Branton Campbell).
            """

            if self.feature_flags["magcif"]:

                # CIF-1 style has all underscores, interim standard
                # had period before magn instead of before the final
                # component (e.g. xyz)
                # we want to standardize on a specific key, to simplify
                # parsing code
                correct_keys = ["_space_group_symop_magn_operation.xyz",
                                "_space_group_symop_magn_centering.xyz",
                                "_space_group_magn.name_BNS",
                                "_space_group_magn.number_BNS",
                                "_atom_site_moment_crystalaxis_x",
                                "_atom_site_moment_crystalaxis_y",
                                "_atom_site_moment_crystalaxis_z",
                                "_atom_site_moment_label"]

                # cannot mutate OrderedDict during enumeration,
                # so store changes we want to make
                changes_to_make = {}

                for original_key in data.data:
                    for correct_key in correct_keys:
                        # convert to all underscore
                        trial_key = "_".join(correct_key.split("."))
                        test_key = "_".join(original_key.split("."))
                        if trial_key == test_key:
                            changes_to_make[correct_key] = original_key

                # make changes
                for correct_key, original_key in changes_to_make.items():
                    data.data[correct_key] = data.data[original_key]

                # renamed_keys maps interim_keys to final_keys
                renamed_keys = {
                    "_magnetic_space_group.transform_to_standard_Pp_abc":
                        "_space_group_magn.transform_BNS_Pp_abc"}
                changes_to_make = {}

                for interim_key, final_key in renamed_keys.items():
                    if data.data.get(interim_key):
                        changes_to_make[final_key] = interim_key

                if len(changes_to_make) > 0:
                    self.warnings.append("Keys changed to match new magCIF specification.")

                for final_key, interim_key in changes_to_make.items():
                    data.data[final_key] = data.data[interim_key]

            # check for finite precision frac co-ordinates (e.g. 0.6667 instead of 0.6666666...7)
            # this can sometimes cause serious issues when applying symmetry operations
            important_fracs = (1 / 3., 2 / 3.)
            fracs_to_change = {}
            for label in ('_atom_site_fract_x', '_atom_site_fract_y', '_atom_site_fract_z'):
                if label in data.data.keys():
                    for idx, frac in enumerate(data.data[label]):
                        try:
                            frac = str2float(frac)
                        except Exception:
                            # co-ordinate might not be defined e.g. '?'
                            continue
                        for comparison_frac in important_fracs:
                            if abs(1 - frac / comparison_frac) < 1e-4:
                                fracs_to_change[(label, idx)] = str(comparison_frac)
            if fracs_to_change:
                self.warnings.append("Some fractional co-ordinates rounded to ideal values to "
                                     "avoid issues with finite precision.")
                for (label, idx), val in fracs_to_change.items():
                    data.data[label][idx] = val

            return data

        def _unique_coords(self, coords_in, magmoms_in=None, lattice=None):
            """
            Generate unique coordinates using coord and symmetry positions
            and also their corresponding magnetic moments, if supplied.
            """
            coords = []
            if magmoms_in:
                magmoms = []
                if len(magmoms_in) != len(coords_in):
                    raise ValueError
                for tmp_coord, tmp_magmom in zip(coords_in, magmoms_in):
                    for op in self.symmetry_operations:
                        coord = op.operate(tmp_coord)
                        coord = np.array([i - math.floor(i) for i in coord])
                        if isinstance(op, MagSymmOp):
                            # Up to this point, magmoms have been defined relative
                            # to crystal axis. Now convert to Cartesian and into
                            # a Magmom object.
                            magmom = Magmom.from_moment_relative_to_crystal_axes(
                                op.operate_magmom(tmp_magmom),
                                lattice=lattice
                            )
                        else:
                            magmom = Magmom(tmp_magmom)
                        if not in_coord_list_pbc(coords, coord,
                                                 atol=self._site_tolerance):
                            coords.append(coord)
                            magmoms.append(magmom)
                return coords, magmoms
            else:
                for tmp_coord in coords_in:
                    for op in self.symmetry_operations:
                        coord = op.operate(tmp_coord)
                        coord = np.array([i - math.floor(i) for i in coord])
                        if not in_coord_list_pbc(coords, coord,
                                                 atol=self._site_tolerance):
                            coords.append(coord)
                return coords, [Magmom(0)] * len(coords)  # return dummy magmoms

        def get_lattice(self, data, length_strings=("a", "b", "c"),
                        angle_strings=("alpha", "beta", "gamma"),
                        lattice_type=None):
            """
            Generate the lattice from the provided lattice parameters. In
            the absence of all six lattice parameters, the crystal system
            and necessary parameters are parsed
            """
            try:

                lengths = [str2float(data["_cell_length_" + i])
                           for i in length_strings]
                angles = [str2float(data["_cell_angle_" + i])
                          for i in angle_strings]
                if not lattice_type:
                    return Lattice.from_parameters(*lengths, *angles)

                else:
                    return getattr(Lattice, lattice_type)(*(lengths + angles))

            except KeyError:
                # Missing Key search for cell setting
                for lattice_lable in ["_symmetry_cell_setting",
                                      "_space_group_crystal_system"]:
                    if data.data.get(lattice_lable):
                        lattice_type = data.data.get(lattice_lable).lower()
                        try:

                            required_args = getargspec(
                                getattr(Lattice, lattice_type)).args

                            lengths = (l for l in length_strings
                                       if l in required_args)
                            angles = (a for a in angle_strings
                                      if a in required_args)
                            return self.get_lattice(data, lengths, angles,
                                                    lattice_type=lattice_type)
                        except AttributeError as exc:
                            self.warnings.append(str(exc))
                            warnings.warn(exc)

                    else:
                        return None

        def get_symops(self, data):
            """
            In order to generate symmetry equivalent positions, the symmetry
            operations are parsed. If the symops are not present, the space
            group symbol is parsed, and symops are generated.
            """
            symops = []
            for symmetry_label in ["_symmetry_equiv_pos_as_xyz",
                                   "_symmetry_equiv_pos_as_xyz_",
                                   "_space_group_symop_operation_xyz",
                                   "_space_group_symop_operation_xyz_"]:
                if data.data.get(symmetry_label):
                    xyz = data.data.get(symmetry_label)
                    if isinstance(xyz, str):
                        msg = "A 1-line symmetry op P1 CIF is detected!"
                        warnings.warn(msg)
                        self.warnings.append(msg)
                        xyz = [xyz]
                    try:
                        symops = [SymmOp.from_xyz_string(s)
                                  for s in xyz]
                        break
                    except ValueError:
                        continue
            if not symops:
                # Try to parse symbol
                for symmetry_label in ["_symmetry_space_group_name_H-M",
                                       "_symmetry_space_group_name_H_M",
                                       "_symmetry_space_group_name_H-M_",
                                       "_symmetry_space_group_name_H_M_",
                                       "_space_group_name_Hall",
                                       "_space_group_name_Hall_",
                                       "_space_group_name_H-M_alt",
                                       "_space_group_name_H-M_alt_",
                                       "_symmetry_space_group_name_hall",
                                       "_symmetry_space_group_name_hall_",
                                       "_symmetry_space_group_name_h-m",
                                       "_symmetry_space_group_name_h-m_"]:
                    sg = data.data.get(symmetry_label)

                    if sg:
                        sg = sub_spgrp(sg)
                        try:
                            spg = space_groups.get(sg)
                            if spg:
                                symops = SpaceGroup(spg).symmetry_ops
                                msg = "No _symmetry_equiv_pos_as_xyz type key found. " \
                                      "Spacegroup from %s used." % symmetry_label
                                warnings.warn(msg)
                                self.warnings.append(msg)
                                break
                        except ValueError:
                            # Ignore any errors
                            pass

                        try:
                            for d in _get_cod_data():
                                if sg == re.sub(r"\s+", "",
                                                d["hermann_mauguin"]):
                                    xyz = d["symops"]
                                    symops = [SymmOp.from_xyz_string(s)
                                              for s in xyz]
                                    msg = "No _symmetry_equiv_pos_as_xyz type key found. " \
                                          "Spacegroup from %s used." % symmetry_label
                                    warnings.warn(msg)
                                    self.warnings.append(msg)
                                    break
                        except Exception:
                            continue

                        if symops:
                            break
            if not symops:
                # Try to parse International number
                for symmetry_label in ["_space_group_IT_number",
                                       "_space_group_IT_number_",
                                       "_symmetry_Int_Tables_number",
                                       "_symmetry_Int_Tables_number_"]:
                    if data.data.get(symmetry_label):
                        try:
                            i = int(str2float(data.data.get(symmetry_label)))
                            symops = SpaceGroup.from_int_number(i).symmetry_ops
                            break
                        except ValueError:
                            continue

            if not symops:
                msg = "No _symmetry_equiv_pos_as_xyz type key found. " \
                      "Defaulting to P1."
                warnings.warn(msg)
                self.warnings.append(msg)
                symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]

            return symops

        def get_magsymops(self, data):
            """
            Equivalent to get_symops except for magnetic symmetry groups.
            Separate function since additional operation for time reversal symmetry
            (which changes magnetic moments on sites) needs to be returned.
            """
            magsymmops = []

            # check to see if magCIF file explicitly contains magnetic symmetry operations
            if data.data.get("_space_group_symop_magn_operation.xyz"):

                xyzt = data.data.get("_space_group_symop_magn_operation.xyz")
                if isinstance(xyzt, str):
                    xyzt = [xyzt]
                magsymmops = [MagSymmOp.from_xyzt_string(s) for s in xyzt]

                if data.data.get("_space_group_symop_magn_centering.xyz"):

                    xyzt = data.data.get("_space_group_symop_magn_centering.xyz")
                    if isinstance(xyzt, str):
                        xyzt = [xyzt]
                    centering_symops = [MagSymmOp.from_xyzt_string(s) for s in xyzt]

                    all_ops = []
                    for op in magsymmops:
                        for centering_op in centering_symops:
                            new_translation = [i - np.floor(i) for i
                                               in
                                               op.translation_vector + centering_op.translation_vector]
                            new_time_reversal = op.time_reversal * centering_op.time_reversal
                            all_ops.append(
                                MagSymmOp.from_rotation_and_translation_and_time_reversal(
                                    rotation_matrix=op.rotation_matrix,
                                    translation_vec=new_translation,
                                    time_reversal=new_time_reversal))
                    magsymmops = all_ops

            # else check to see if it specifies a magnetic space group
            elif data.data.get("_space_group_magn.name_BNS") or data.data.get(
                    "_space_group_magn.number_BNS"):

                if data.data.get("_space_group_magn.name_BNS"):
                    # get BNS label for MagneticSpaceGroup()
                    id = data.data.get("_space_group_magn.name_BNS")
                else:
                    # get BNS number for MagneticSpaceGroup()
                    # by converting string to list of ints
                    id = list(map(int, (
                        data.data.get("_space_group_magn.number_BNS").split("."))))

                if data.data.get("_space_group_magn.transform_BNS_Pp_abc"):
                    if data.data.get(
                            "_space_group_magn.transform_BNS_Pp_abc") != "a,b,c;0,0,0":

                        jf = data.data.get("_space_group_magn.transform_BNS_Pp_abc")
                        msg = MagneticSpaceGroup(id, jf)

                elif data.data.get("_space_group_magn.transform_BNS_Pp"):
                    return NotImplementedError(
                        "Incomplete specification to implement.")
                else:
                    msg = MagneticSpaceGroup(id)

                magsymmops = msg.symmetry_ops

            if not magsymmops:
                msg = "No magnetic symmetry detected, using primitive symmetry."
                warnings.warn(msg)
                self.warnings.append(msg)
                magsymmops = [MagSymmOp.from_xyzt_string("x, y, z, 1")]

            return magsymmops

        def parse_oxi_states(self, data):
            """
            Parse oxidation states from data dictionary
            """
            try:
                oxi_states = {
                    data["_atom_type_symbol"][i]:
                        str2float(data["_atom_type_oxidation_number"][i])
                    for i in range(len(data["_atom_type_symbol"]))}
                # attempt to strip oxidation state from _atom_type_symbol
                # in case the label does not contain an oxidation state
                for i, symbol in enumerate(data["_atom_type_symbol"]):
                    oxi_states[re.sub(r"\d?[\+,\-]?$", "", symbol)] = \
                        str2float(data["_atom_type_oxidation_number"][i])

            except (ValueError, KeyError):
                oxi_states = None
            return oxi_states

        def parse_magmoms(self, data, lattice=None):
            """
            Parse atomic magnetic moments from data dictionary
            """
            if lattice is None:
                raise Exception(
                    'Magmoms given in terms of crystal axes in magCIF spec.')
            try:
                magmoms = {
                    data["_atom_site_moment_label"][i]:
                        np.array(
                            [str2float(data["_atom_site_moment_crystalaxis_x"][i]),
                             str2float(data["_atom_site_moment_crystalaxis_y"][i]),
                             str2float(data["_atom_site_moment_crystalaxis_z"][i])]
                        )
                    for i in range(len(data["_atom_site_moment_label"]))
                }
            except (ValueError, KeyError):
                return None
            return magmoms

        def _parse_symbol(self, sym):
            """
            Parse a string with a symbol to extract a string representing an element.

            Args:
                sym (str): A symbol to be parsed.

            Returns:
                A string with the parsed symbol. None if no parsing was possible.
            """
            # Common representations for elements/water in cif files
            # TODO: fix inconsistent handling of water
            special = {"Hw": "H", "Ow": "O", "Wat": "O",
                       "wat": "O", "OH": "", "OH2": "", "NO3": "N"}

            parsed_sym = None
            # try with special symbols, otherwise check the first two letters,
            # then the first letter alone. If everything fails try extracting the
            # first letters.
            m_sp = re.match("|".join(special.keys()), sym)
            if m_sp:
                parsed_sym = special[m_sp.group()]
            elif Element.is_valid_symbol(sym[:2].title()):
                parsed_sym = sym[:2].title()
            elif Element.is_valid_symbol(sym[0].upper()):
                parsed_sym = sym[0].upper()
            else:
                m = re.match(r"w?[A-Z][a-z]*", sym)
                if m:
                    parsed_sym = m.group()

            if parsed_sym is not None and (m_sp or not re.match(r"{}\d*".format(parsed_sym), sym)):
                msg = "{} parsed as {}".format(sym, parsed_sym)
                warnings.warn(msg)
                self.warnings.append(msg)

            return parsed_sym

        def _get_structure(self, data, primitive):
            """
            Generate structure from part of the cif.
            """

            def get_num_implicit_hydrogens(sym):
                num_h = {"Wat": 2, "wat": 2, "O-H": 1}
                return num_h.get(sym[:3], 0)

            lattice = self.get_lattice(data)

            # if magCIF, get magnetic symmetry moments and magmoms
            # else standard CIF, and use empty magmom dict
            if self.feature_flags["magcif_incommensurate"]:
                raise NotImplementedError(
                    "Incommensurate structures not currently supported.")
            elif self.feature_flags["magcif"]:
                self.symmetry_operations = self.get_magsymops(data)
                magmoms = self.parse_magmoms(data, lattice=lattice)
            else:
                self.symmetry_operations = self.get_symops(data)
                magmoms = {}

            oxi_states = self.parse_oxi_states(data)

            coord_to_species = OrderedDict()
            coord_to_magmoms = OrderedDict()

            def get_matching_coord(coord):
                keys = list(coord_to_species.keys())
                coords = np.array(keys)
                for op in self.symmetry_operations:
                    c = op.operate(coord)
                    inds = find_in_coord_list_pbc(coords, c,
                                                  atol=self._site_tolerance)
                    # cant use if inds, because python is dumb and np.array([0]) evaluates
                    # to False
                    if len(inds):
                        return keys[inds[0]]
                return False

            for i in range(len(data["_atom_site_label"])):
                try:
                    # If site type symbol exists, use it. Otherwise, we use the
                    # label.
                    symbol = self._parse_symbol(data["_atom_site_type_symbol"][i])
                    num_h = get_num_implicit_hydrogens(
                        data["_atom_site_type_symbol"][i])
                except KeyError:
                    symbol = self._parse_symbol(data["_atom_site_label"][i])
                    num_h = get_num_implicit_hydrogens(data["_atom_site_label"][i])
                if not symbol:
                    continue

                if oxi_states is not None:
                    o_s = oxi_states.get(symbol, 0)
                    # use _atom_site_type_symbol if possible for oxidation state
                    if "_atom_site_type_symbol" in data.data.keys():
                        oxi_symbol = data["_atom_site_type_symbol"][i]
                        o_s = oxi_states.get(oxi_symbol, o_s)
                    try:
                        el = Specie(symbol, o_s)
                    except Exception:
                        el = DummySpecie(symbol, o_s)
                else:
                    el = get_el_sp(symbol)

                x = str2float(data["_atom_site_fract_x"][i])
                y = str2float(data["_atom_site_fract_y"][i])
                z = str2float(data["_atom_site_fract_z"][i])
                magmom = magmoms.get(data["_atom_site_label"][i],
                                     np.array([0, 0, 0]))

                try:
                    occu = str2float(data["_atom_site_occupancy"][i])
                except (KeyError, ValueError):
                    occu = 1

                if occu > 0:
                    coord = (x, y, z)
                    match = get_matching_coord(coord)
                    comp_d = {el: occu}
                    if num_h > 0:
                        comp_d["H"] = num_h
                        self.warnings.append("Structure has implicit hydrogens defined, "
                                             "parsed structure unlikely to be suitable for use "
                                             "in calculations unless hydrogens added.")
                    comp = Composition(comp_d)
                    if not match:
                        coord_to_species[coord] = comp
                        coord_to_magmoms[coord] = magmom
                    else:
                        coord_to_species[match] += comp
                        # disordered magnetic not currently supported
                        coord_to_magmoms[match] = None

            sum_occu = [sum(c.values()) for c in coord_to_species.values()
                        if not set(c.elements) == {Element("O"), Element("H")}]
            if any([o > 1 for o in sum_occu]):
                msg = "Some occupancies ({}) sum to > 1! If they are within " \
                      "the occupancy_tolerance, they will be rescaled. " \
                      "The current occupancy_tolerance is set to: {}".format(sum_occu, self._occupancy_tolerance)
                warnings.warn(msg)
                self.warnings.append(msg)

            allspecies = []
            allcoords = []
            allmagmoms = []
            allhydrogens = []

            # check to see if magCIF file is disordered
            if self.feature_flags["magcif"]:
                for k, v in coord_to_magmoms.items():
                    if v is None:
                        # Proposed solution to this is to instead store magnetic
                        # moments as Specie 'spin' property, instead of site
                        # property, but this introduces ambiguities for end user
                        # (such as unintended use of `spin` and Specie will have
                        # fictious oxidation state).
                        raise NotImplementedError(
                            'Disordered magnetic structures not currently supported.')

            if coord_to_species.items():
                for comp, group in groupby(
                        sorted(list(coord_to_species.items()), key=lambda x: x[1]),
                        key=lambda x: x[1]):
                    tmp_coords = [site[0] for site in group]
                    tmp_magmom = [coord_to_magmoms[tmp_coord] for tmp_coord in
                                  tmp_coords]

                    if self.feature_flags["magcif"]:
                        coords, magmoms = self._unique_coords(tmp_coords,
                                                              magmoms_in=tmp_magmom,
                                                              lattice=lattice)
                    else:
                        coords, magmoms = self._unique_coords(tmp_coords)

                    if set(comp.elements) == {Element("O"), Element("H")}:
                        # O with implicit hydrogens
                        im_h = comp["H"]
                        species = Composition({"O": comp["O"]})
                    else:
                        im_h = 0
                        species = comp

                    allhydrogens.extend(len(coords) * [im_h])
                    allcoords.extend(coords)
                    allspecies.extend(len(coords) * [species])
                    allmagmoms.extend(magmoms)

                # rescale occupancies if necessary
                for i, species in enumerate(allspecies):
                    totaloccu = sum(species.values())
                    if 1 < totaloccu <= self._occupancy_tolerance:
                        allspecies[i] = species / totaloccu

            if allspecies and len(allspecies) == len(allcoords) \
                    and len(allspecies) == len(allmagmoms):
                site_properties = dict()
                if any(allhydrogens):
                    assert len(allhydrogens) == len(allcoords)
                    site_properties["implicit_hydrogens"] = allhydrogens

                if self.feature_flags["magcif"]:
                    site_properties["magmom"] = allmagmoms

                if len(site_properties) == 0:
                    site_properties = None

                struct = Structure(lattice, allspecies, allcoords,
                                   site_properties=site_properties)

                struct = struct.get_sorted_structure()

                if primitive and self.feature_flags['magcif']:
                    struct = struct.get_primitive_structure(use_site_props=True)
                elif primitive:
                    struct = struct.get_primitive_structure()
                    struct = struct.get_reduced_structure()

                return struct

        def get_structures(self, primitive=True):
            """
            Return list of structures in CIF file. primitive boolean sets whether a
            conventional cell structure or primitive cell structure is returned.

            Args:
                primitive (bool): Set to False to return conventional unit cells.
                    Defaults to True. With magnetic CIF files, will return primitive
                    magnetic cell which may be larger than nuclear primitive cell.

            Returns:
                List of Structures.
            """
            structures = []
            for i, d in enumerate(self._cif.data.values()):
                try:
                    s = self._get_structure(d, primitive)
                    if s:
                        structures.append(s)
                except (KeyError, ValueError) as exc:
                    # Warn the user (Errors should never pass silently)
                    # A user reported a problem with cif files produced by Avogadro
                    # in which the atomic coordinates are in Cartesian coords.
                    self.warnings.append(str(exc))
                    warnings.warn("No structure parsed for %d structure in CIF. Section of CIF file below." % (i + 1))
                    warnings.warn(str(d))
                    warnings.warn("Error is %s." % str(exc))

            if self.warnings:
                warnings.warn("Issues encountered while parsing CIF: %s" % "\n".join(self.warnings))
            if len(structures) == 0:
                raise ValueError("Invalid cif file with no structures!")
            return structures

        def get_bibtex_string(self):
            """
            Get BibTeX reference from CIF file.
            :param data:
            :return: BibTeX string
            """

            try:
                from pybtex.database import BibliographyData, Entry
            except ImportError:
                raise RuntimeError("Bibliographic data extraction requires pybtex.")

            bibtex_keys = {'author': ('_publ_author_name', '_citation_author_name'),
                           'title': ('_publ_section_title', '_citation_title'),
                           'journal': ('_journal_name_full', '_journal_name_abbrev',
                                       '_citation_journal_full', '_citation_journal_abbrev'),
                           'volume': ('_journal_volume', '_citation_journal_volume'),
                           'year': ('_journal_year', '_citation_year'),
                           'number': ('_journal_number', '_citation_number'),
                           'page_first': ('_journal_page_first', '_citation_page_first'),
                           'page_last': ('_journal_page_last', '_citation_page_last'),
                           'doi': ('_journal_DOI', '_citation_DOI')}

            entries = {}

            # TODO: parse '_publ_section_references' when it exists?
            # TODO: CIF specification supports multiple citations.

            for idx, data in enumerate(self._cif.data.values()):

                # convert to lower-case keys, some cif files inconsistent
                data = {k.lower(): v for k, v in data.data.items()}

                bibtex_entry = {}

                for field, tags in bibtex_keys.items():
                    for tag in tags:
                        if tag in data:
                            if isinstance(data[tag], list):
                                bibtex_entry[field] = data[tag][0]
                            else:
                                bibtex_entry[field] = data[tag]

                # convert to bibtex author format ('and' delimited)
                if 'author' in bibtex_entry:
                    # separate out semicolon authors
                    if isinstance(bibtex_entry["author"], str):
                        if ";" in bibtex_entry["author"]:
                            bibtex_entry["author"] = bibtex_entry["author"].split(";")

                    if isinstance(bibtex_entry['author'], list):
                        bibtex_entry['author'] = ' and '.join(bibtex_entry['author'])

                # convert to bibtex page range format, use empty string if not specified
                if ('page_first' in bibtex_entry) or ('page_last' in bibtex_entry):
                    bibtex_entry['pages'] = '{0}--{1}'.format(bibtex_entry.get('page_first', ''),
                                                              bibtex_entry.get('page_last', ''))
                    bibtex_entry.pop('page_first', None)  # and remove page_first, page_list if present
                    bibtex_entry.pop('page_last', None)

                # cite keys are given as cif-reference-idx in order they are found
                entries['cifref{}'.format(idx)] = Entry('article', list(bibtex_entry.items()))

            return BibliographyData(entries).to_string(bib_format='bibtex')

        def as_dict(self):
            """
            :return: MSONable dict
            """
            d = OrderedDict()
            for k, v in self._cif.data.items():
                d[k] = {}
                for k2, v2 in v.data.items():
                    d[k][k2] = v2
            return d

        @property
        def has_errors(self):
            """
            :return: Whether there are errors/warnings detected in CIF parsing.
            """
            return len(self.warnings) > 0

    class CifWriter:
        """
        A wrapper around CifFile to write CIF files from pymatgen structures.
        """
        def __init__(self, struct, symprec=None, write_magmoms=False,
                     significant_figures=8, angle_tolerance=5.0):
            """
            Args:
                struct (Structure): structure to write
                symprec (float): If not none, finds the symmetry of the structure
                    and writes the cif with symmetry information. Passes symprec
                    to the SpacegroupAnalyzer.
                write_magmoms (bool): If True, will write magCIF file. Incompatible
                    with symprec
                significant_figures (int): Specifies precision for formatting of floats.
                    Defaults to 8.
                angle_tolerance (float): Angle tolerance for symmetry finding. Passes
                    angle_tolerance to the SpacegroupAnalyzer. Used only if symprec
                    is not None.
            """

            if write_magmoms and symprec:
                warnings.warn(
                    "Magnetic symmetry cannot currently be detected by pymatgen,"
                    "disabling symmetry detection.")
                symprec = None

            format_str = "{:.%df}" % significant_figures

            block = OrderedDict()
            loops = []
            spacegroup = ("P 1", 1)
            if symprec is not None:
                sf = SpacegroupAnalyzer(struct, symprec, angle_tolerance=angle_tolerance)
                spacegroup = (sf.get_space_group_symbol(),
                              sf.get_space_group_number())
                # Needs the refined struture when using symprec. This converts
                # primitive to conventional structures, the standard for CIF.
                struct = sf.get_refined_structure()

            latt = struct.lattice
            comp = struct.composition
            no_oxi_comp = comp.element_composition
            block["_symmetry_space_group_name_H-M"] = spacegroup[0]
            for cell_attr in ['a', 'b', 'c']:
                block["_cell_length_" + cell_attr] = format_str.format(
                    getattr(latt, cell_attr))
            for cell_attr in ['alpha', 'beta', 'gamma']:
                block["_cell_angle_" + cell_attr] = format_str.format(
                    getattr(latt, cell_attr))
            block["_symmetry_Int_Tables_number"] = spacegroup[1]
            block["_chemical_formula_structural"] = no_oxi_comp.reduced_formula
            block["_chemical_formula_sum"] = no_oxi_comp.formula
            block["_cell_volume"] = format_str.format(latt.volume)

            reduced_comp, fu = no_oxi_comp.get_reduced_composition_and_factor()
            block["_cell_formula_units_Z"] = str(int(fu))

            if symprec is None:
                block["_symmetry_equiv_pos_site_id"] = ["1"]
                block["_symmetry_equiv_pos_as_xyz"] = ["x, y, z"]
            else:
                sf = SpacegroupAnalyzer(struct, symprec)

                symmops = []
                for op in sf.get_symmetry_operations():
                    v = op.translation_vector
                    symmops.append(SymmOp.from_rotation_and_translation(
                        op.rotation_matrix, v))

                ops = [op.as_xyz_string() for op in symmops]
                block["_symmetry_equiv_pos_site_id"] = \
                    ["%d" % i for i in range(1, len(ops) + 1)]
                block["_symmetry_equiv_pos_as_xyz"] = ops

            loops.append(["_symmetry_equiv_pos_site_id",
                          "_symmetry_equiv_pos_as_xyz"])

            try:
                symbol_to_oxinum = OrderedDict([
                    (el.__str__(),
                     float(el.oxi_state))
                    for el in sorted(comp.elements)])
                block["_atom_type_symbol"] = symbol_to_oxinum.keys()
                block["_atom_type_oxidation_number"] = symbol_to_oxinum.values()
                loops.append(["_atom_type_symbol", "_atom_type_oxidation_number"])
            except (TypeError, AttributeError):
                symbol_to_oxinum = OrderedDict([(el.symbol, 0) for el in
                                                sorted(comp.elements)])

            atom_site_type_symbol = []
            atom_site_symmetry_multiplicity = []
            atom_site_fract_x = []
            atom_site_fract_y = []
            atom_site_fract_z = []
            atom_site_label = []
            atom_site_occupancy = []
            atom_site_moment_label = []
            atom_site_moment_crystalaxis_x = []
            atom_site_moment_crystalaxis_y = []
            atom_site_moment_crystalaxis_z = []
            count = 0
            if symprec is None:
                for site in struct:
                    for sp, occu in sorted(site.species.items()):
                        atom_site_type_symbol.append(sp.__str__())
                        atom_site_symmetry_multiplicity.append("1")
                        atom_site_fract_x.append(format_str.format(site.a))
                        atom_site_fract_y.append(format_str.format(site.b))
                        atom_site_fract_z.append(format_str.format(site.c))
                        atom_site_label.append("{}{}".format(sp.symbol, count))
                        atom_site_occupancy.append(occu.__str__())

                        magmom = Magmom(
                            site.properties.get('magmom', getattr(sp, 'spin', 0)))
                        if write_magmoms and abs(magmom) > 0:
                            moment = Magmom.get_moment_relative_to_crystal_axes(
                                magmom, latt)
                            atom_site_moment_label.append(
                                "{}{}".format(sp.symbol, count))
                            atom_site_moment_crystalaxis_x.append(format_str.format(moment[0]))
                            atom_site_moment_crystalaxis_y.append(format_str.format(moment[1]))
                            atom_site_moment_crystalaxis_z.append(format_str.format(moment[2]))

                        count += 1
            else:
                # The following just presents a deterministic ordering.
                unique_sites = [
                    (sorted(sites, key=lambda s: tuple([abs(x) for x in
                                                        s.frac_coords]))[0],
                     len(sites))
                    for sites in sf.get_symmetrized_structure().equivalent_sites
                ]
                for site, mult in sorted(
                        unique_sites,
                        key=lambda t: (t[0].species.average_electroneg,
                                       -t[1], t[0].a, t[0].b, t[0].c)):
                    for sp, occu in site.species.items():
                        atom_site_type_symbol.append(sp.__str__())
                        atom_site_symmetry_multiplicity.append("%d" % mult)
                        atom_site_fract_x.append(format_str.format(site.a))
                        atom_site_fract_y.append(format_str.format(site.b))
                        atom_site_fract_z.append(format_str.format(site.c))
                        atom_site_label.append("{}{}".format(sp.symbol, count))
                        atom_site_occupancy.append(occu.__str__())
                        count += 1

            block["_atom_site_type_symbol"] = atom_site_type_symbol
            block["_atom_site_label"] = atom_site_label
            block["_atom_site_symmetry_multiplicity"] = \
                atom_site_symmetry_multiplicity
            block["_atom_site_fract_x"] = atom_site_fract_x
            block["_atom_site_fract_y"] = atom_site_fract_y
            block["_atom_site_fract_z"] = atom_site_fract_z
            block["_atom_site_occupancy"] = atom_site_occupancy
            loops.append(["_atom_site_type_symbol",
                          "_atom_site_label",
                          "_atom_site_symmetry_multiplicity",
                          "_atom_site_fract_x",
                          "_atom_site_fract_y",
                          "_atom_site_fract_z",
                          "_atom_site_occupancy"])
            if write_magmoms:
                block["_atom_site_moment_label"] = atom_site_moment_label
                block[
                    "_atom_site_moment_crystalaxis_x"] = atom_site_moment_crystalaxis_x
                block[
                    "_atom_site_moment_crystalaxis_y"] = atom_site_moment_crystalaxis_y
                block[
                    "_atom_site_moment_crystalaxis_z"] = atom_site_moment_crystalaxis_z
                loops.append(["_atom_site_moment_label",
                              "_atom_site_moment_crystalaxis_x",
                              "_atom_site_moment_crystalaxis_y",
                              "_atom_site_moment_crystalaxis_z"])
            d = OrderedDict()
            d[comp.reduced_formula] = CifBlock(block, loops, comp.reduced_formula)
            self._cf = CifFile(d)

        @property
        def ciffile(self):
            """
            Returns: CifFile associated with the CifWriter.
            """
            return self._cf

        def __str__(self):
            """
            Returns the cif as a string.
            """
            return self._cf.__str__()

        def write_file(self, filename):
            """
            Write the cif file.
            """
            with zopen(filename, "wt") as f:
                f.write(self.__str__())

    def str2float(text):
        """
        Remove uncertainty brackets from strings and return the float.
        """

        try:
            # Note that the ending ) is sometimes missing. That is why the code has
            # been modified to treat it as optional. Same logic applies to lists.
            return float(re.sub(r"\(.+\)*", "", text))
        except TypeError:
            if isinstance(text, list) and len(text) == 1:
                return float(re.sub(r"\(.+\)*", "", text[0]))
        except ValueError as ex:
            if text.strip() == ".":
                return 0
            raise ex