amd.io._parse_sitesym_pymatgen() - Code Metrics - Inspection of "more cleanup" - dwiddo/average-minimum-distance - Measure and Improve Code Quality continuously with Scrutinizer

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amd.io._parse_sitesym_pymatgen() F

↳ Parent: amd.io
Complexity

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Size

Total Lines	78
Code Lines	56
Duplication

Lines	0
Ratio	0 %
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Changes
Metric	Value
eloc	56
dl	0
loc	78
rs	0.5999
c	0
b	0
f	0
cc	19
nop	1
How to fix Long Method Complexity

"""Tools for reading crystals from files, or from the CSD with
``csd-python-api``. The readers return
:class:`amd.PeriodicSet <.periodicset.PeriodicSet>` objects representing
the crystal which can be passed to :func:`amd.AMD() <.calculate.AMD>`
and :func:`amd.PDD() <.calculate.PDD>`.
"""

import os
import re
import functools
import warnings
import errno
from typing import Tuple

import numpy as np
import numba

from .utils import cellpar_to_cell
from .periodicset import PeriodicSet


def _custom_warning(message, category, filename, lineno, *args, **kwargs):
    return f'{category.__name__}: {message}\n'
warnings.formatwarning = _custom_warning

_EQUIV_SITE_TOL = 1e-3

CIF_TAGS = {
    'cellpar': [
        '_cell_length_a',
        '_cell_length_b',
        '_cell_length_c',
        '_cell_angle_alpha',
        '_cell_angle_beta',
        '_cell_angle_gamma',],

    'atom_site_fract': [
        '_atom_site_fract_x',
        '_atom_site_fract_y',
        '_atom_site_fract_z',],

    'atom_site_cartn': [
        '_atom_site_cartn_x',
        '_atom_site_cartn_y',
        '_atom_site_cartn_z',],

    'atom_symbol': [
        '_atom_site_type_symbol',
        '_atom_site_label',],

    'symop': [
        '_symmetry_equiv_pos_as_xyz',
        '_space_group_symop_operation_xyz',
        '_space_group_symop.operation_xyz',
        '_symmetry_equiv_pos_as_xyz_',
        '_space_group_symop_operation_xyz_',],

    'spacegroup_name': [
        '_space_group_name_Hall',
        '_symmetry_space_group_name_hall',
        '_space_group_name_H-M_alt',
        '_symmetry_space_group_name_H-M',
        '_symmetry_space_group_name_H_M',
        '_symmetry_space_group_name_h-m',],

    'spacegroup_number': [
        '_space_group_IT_number',
        '_symmetry_Int_Tables_number',
        '_space_group_IT_number_',
        '_symmetry_Int_Tables_number_',],
}


class _Reader:

    _DISORDER_OPTIONS = {'skip', 'ordered_sites', 'all_sites'}
    _CCDC_IMPORT_ERR_MSG = 'Failed to import csd-python-api, please check ' \
                           'it is installed and licensed.'

    def __init__(self, iterable, converter, show_warnings=True):
        self._iterator = iter(iterable)
        self._converter = converter
        self.show_warnings = show_warnings

    def __iter__(self):
        if self._iterator is None or self._converter is None:
            raise RuntimeError(f'{self.__class__.__name__} not initialized.')
        return self

    def __next__(self):
        """Iterates over self._iterator, passing items through
        self._converter. Catches :class:`ParseError <.io.ParseError>`
        and warnings raised in self._converter, optionally printing
        them.
        """

        if not self.show_warnings:
            warnings.simplefilter('ignore')

        while True:

            item = next(self._iterator)

            with warnings.catch_warnings(record=True) as warning_msgs:
                msg = None
                try:
                    periodic_set = self._converter(item)
                except ParseError as err:
                    msg = str(err)

            if msg:
                warnings.warn(msg)
                continue

            for warning in warning_msgs:
                msg = f'(name={periodic_set.name}) {warning.message}'
                warnings.warn(msg, category=warning.category)

            return periodic_set

    def read(self):
        """Reads the crystal(s), returns one
        :class:`amd.PeriodicSet <.periodicset.PeriodicSet>` if there is
        only one, otherwise returns a list.
        """

        l = list(self)
        if len(l) == 1:
            return l[0]
        return l


class CifReader(_Reader):
    """Read all structures in a .cif file or all files in a folder
    with ase or csd-python-api (if installed), yielding
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>` s.

    Parameters
    ----------
    path : str
        Path to a .CIF file or directory. (Other files are accepted when
        using ``reader='ccdc'``, if csd-python-api is installed.)
    reader : str, optional
        The backend package used to parse the CIF. The default is 
        :code:`ase`, :code:`pymatgen` and :code:`gemmi` are also
        accepted, as well as :code:`ccdc` if csd-python-api is 
        installed. The ccdc reader should be able to read any format
        accepted by :class:`ccdc.io.EntryReader`, though only CIFs have
        been tested.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystals.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.
    heaviest_component : bool, optional
        csd-python-api only. Removes all but the heaviest molecule in
        the asymmeric unit, intended for removing solvents.
    molecular_centres : bool, default False
        csd-python-api only. Extract the centres of molecules in the
        unit cell and store in the attribute molecular_centres.
    show_warnings : bool, optional
        Controls whether warnings that arise during reading are printed.

    Yields
    ------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        data, e.g. the crystal's name and information about the
        asymmetric unit.

    Examples
    --------

        ::

            # Put all crystals in a .CIF in a list
            structures = list(amd.CifReader('mycif.cif'))

            # Can also accept path to a directory, reading all files inside
            structures = list(amd.CifReader('path/to/folder'))

            # Reads just one if the .CIF has just one crystal
            periodic_set = amd.CifReader('mycif.cif').read()

            # List of AMDs (k=100) of crystals in a .CIF
            amds = [amd.AMD(periodic_set, 100) for periodic_set in amd.CifReader('mycif.cif')]
    """

    def __init__(
            self,
            path,
            reader='ase',
            remove_hydrogens=False,
            disorder='skip',
            heaviest_component=False,
            molecular_centres=False,
            show_warnings=True,
    ):

        if disorder not in CifReader._DISORDER_OPTIONS:
            msg = 'disorder parameter must be one of ' \
                  f'{CifReader._DISORDER_OPTIONS} (passed "{disorder}")'
            raise ValueError(msg)

        if reader != 'ccdc':
            if heaviest_component:
                msg = 'Parameter heaviest_component only implemented for ' \
                      'reader="ccdc".'
                raise NotImplementedError(msg)

            if molecular_centres:
                msg = 'Parameter molecular_centres only implemented for ' \
                      'reader="ccdc".'
                raise NotImplementedError(msg)

        if reader in ('ase', 'pycodcif'):
            from ase.io.cif import parse_cif
            extensions = {'cif'}
            file_parser = functools.partial(parse_cif, reader=reader)
            converter = functools.partial(
                periodicset_from_ase_cifblock,
                remove_hydrogens=remove_hydrogens,
                disorder=disorder
            )

        elif reader == 'pymatgen':
            extensions = {'cif'}
            file_parser = CifReader._pymatgen_cifblock_generator
            converter = functools.partial(
                periodicset_from_pymatgen_cifblock,
                remove_hydrogens=remove_hydrogens,
                disorder=disorder
            )

        elif reader == 'gemmi':
            import gemmi
            extensions = {'cif'}
            file_parser = gemmi.cif.read_file
            converter = functools.partial(
                periodicset_from_gemmi_block,
                remove_hydrogens=remove_hydrogens,
                disorder=disorder
            )

        elif reader == 'ccdc':
            try:
                import ccdc.io
            except (ImportError, RuntimeError) as e:
                raise ImportError(_Reader._CCDC_IMPORT_ERR_MSG) from e

            extensions = ccdc.io.EntryReader.known_suffixes
            file_parser = ccdc.io.EntryReader
            converter = functools.partial(
                periodicset_from_ccdc_entry,
                remove_hydrogens=remove_hydrogens,
                disorder=disorder,
                molecular_centres=molecular_centres,
                heaviest_component=heaviest_component
            )

        else:
            raise ValueError(f'Unknown reader "{reader}".')

        if os.path.isfile(path):
            iterable = file_parser(path)
        elif os.path.isdir(path):
            iterable = CifReader._dir_generator(path, file_parser, extensions)
        else:
            raise FileNotFoundError(
                errno.ENOENT, os.strerror(errno.ENOENT), path)

        super().__init__(iterable, converter, show_warnings=show_warnings)

    @staticmethod
    def _dir_generator(path, callable, extensions):
        for file in os.listdir(path):
            suff = os.path.splitext(file)[1][1:]
            if suff.lower() in extensions:
                yield from callable(os.path.join(path, file))

    @staticmethod
    def _pymatgen_cifblock_generator(path):
        """Path to .cif --> generator of pymatgen CifBlock objects."""
        from pymatgen.io.cif import CifFile
        yield from CifFile.from_file(path).data.values()


class CSDReader(_Reader):
    """Read structures from the CSD with csd-python-api, yielding
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>` s.

    Parameters
    ----------
    refcodes : str or List[str], optional
        Single or list of CSD refcodes to read. If None or 'CSD',
        iterates over the whole CSD.
    families : bool, optional
        Read all entries whose refcode starts with the given strings, or
        'families' (e.g. giving 'DEBXIT' reads all entries starting with
        DEBXIT).
    remove_hydrogens : bool, optional
        Remove hydrogens from the crystals.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.
    heaviest_component : bool, optional
        Removes all but the heaviest molecule in the asymmeric unit,
        intended for removing solvents.
    molecular_centres : bool, default False
        Extract the centres of molecules in the unit cell and store in
        attribute molecular_centres.
    show_warnings : bool, optional
        Controls whether warnings that arise during reading are printed.

    Yields
    ------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.

    Examples
    --------

        ::

            # Put these entries in a list
            refcodes = ['DEBXIT01', 'DEBXIT05', 'HXACAN01']
            structures = list(amd.CSDReader(refcodes))

            # Read refcode families (any whose refcode starts with strings in the list)
            refcode_families = ['ACSALA', 'HXACAN']
            structures = list(amd.CSDReader(refcode_families, families=True))

            # Get AMDs (k=100) for crystals in these families
            refcodes = ['ACSALA', 'HXACAN']
            amds = []
            for periodic_set in amd.CSDReader(refcodes, families=True):
                amds.append(amd.AMD(periodic_set, 100))

            # Giving the reader nothing reads from the whole CSD.
            for periodic_set in amd.CSDReader():
                ...
    """

    def __init__(
            self,
            refcodes=None,
            families=False,
            remove_hydrogens=False,
            disorder='skip',
            heaviest_component=False,
            molecular_centres=False,
            show_warnings=True,
    ):

        try:
            import ccdc.io
        except (ImportError, RuntimeError) as _:
            raise ImportError(_Reader._CCDC_IMPORT_ERR_MSG)

        if disorder not in _Reader._DISORDER_OPTIONS:
            msg = 'disorder parameter must be one of ' \
                  f'{_Reader._DISORDER_OPTIONS} (passed {disorder})'
            raise ValueError(msg)

        if isinstance(refcodes, str) and refcodes.lower() == 'csd':
            refcodes = None

        if refcodes is None:
            families = False
        else:
            if isinstance(refcodes, str):
                refcodes = [refcodes]
            else:
                refcodes = list(refcodes)

        if families:
            refcodes = self._refcodes_from_families_ccdc(refcodes)

        entry_reader = ccdc.io.EntryReader('CSD')
        converter = functools.partial(
            periodicset_from_ccdc_entry,
            remove_hydrogens=remove_hydrogens,
            disorder=disorder,
            molecular_centres=molecular_centres,
            heaviest_component=heaviest_component
        )
        iterable = self._ccdc_generator(refcodes, entry_reader)
        super().__init__(iterable, converter, show_warnings=show_warnings)

    @staticmethod
    def _ccdc_generator(refcodes, entry_reader):
        """Generates ccdc Entries from CSD refcodes.
        """

        if refcodes is None:
            for entry in entry_reader:
                yield entry
        else:
            for refcode in refcodes:
                try:
                    entry = entry_reader.entry(refcode)
                    yield entry
                except RuntimeError:
                    warnings.warn(f'{refcode} not found in database')

    @staticmethod
    def _refcodes_from_families_ccdc(refcode_families):
        """List of strings --> all CSD refcodes starting with any of the
        strings. Intended to be passed a list of families and return all
        refcodes in them.
        """

        try:
            import ccdc.search
        except (ImportError, RuntimeError) as _:
            raise ImportError(_Reader._CCDC_IMPORT_ERR_MSG)

        all_refcodes = []
        for refcode in refcode_families:
            query = ccdc.search.TextNumericSearch()
            query.add_identifier(refcode)
            hits = [hit.identifier for hit in query.search()]
            all_refcodes.extend(hits)

        # filter to unique refcodes
        seen = set()
        seen_add = seen.add
        refcodes = [
            refcode for refcode in all_refcodes
            if not (refcode in seen or seen_add(refcode))]

        return refcodes


class ParseError(ValueError):
    """Raised when an item cannot be parsed into a periodic set.
    """
    pass


def periodicset_from_ase_cifblock(
        block,
        remove_hydrogens=False,
        disorder='skip'
) -> PeriodicSet:
    """:class:`ase.io.cif.CIFBlock` --> 
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`.
    :class:`ase.io.cif.CIFBlock` is the type returned by
    :class:`ase.io.cif.parse_cif`.

    Parameters
    ----------
    block : :class:`ase.io.cif.CIFBlock`
        An ase :class:`ase.io.cif.CIFBlock` object representing a
        crystal.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystal.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.

    Returns
    -------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.

    Raises
    ------
    ParseError
        Raised if the structure fails to be parsed for any of the
        following: 1. Required data is missing (e.g. cell parameters),
        2. The motif is empty after removing H or disordered sites,
        3. :code:``disorder == 'skip'`` and disorder is found on any
        atom.
    """

    import ase
    import ase.spacegroup

    # Unit cell
    cellpar = [block.get(tag) for tag in CIF_TAGS['cellpar']]
    if None in cellpar:
        raise ParseError(f'{block.name} has missing cell data')
    cell = cellpar_to_cell(*cellpar)

    # Asymmetric unit coordinates. ase removes uncertainty brackets
    cartesian = False # flag needed for later
    asym_unit = [block.get(name) for name in CIF_TAGS['atom_site_fract']]
    if None in asym_unit: # missing scaled coords, try Cartesian
        asym_unit = [block.get(name) for name in CIF_TAGS['atom_site_cartn']]
        if None in asym_unit:
            raise ParseError(f'{block.name} has missing coordinates')
        cartesian = True
    asym_unit = list(zip(*asym_unit)) # transpose [xs,ys,zs] -> [p1,p2,...]

    # Atomic types
    asym_symbols = block._get_any(CIF_TAGS['atom_symbol'])
    if asym_symbols is None:
        warnings.warn('missing atomic types will be labelled 0')
        asym_types = [0] * len(asym_unit)
    else:
        asym_types = []
        for label in asym_symbols:
            if label in ('.', '?'):
                warnings.warn('missing atomic types will be labelled 0')
                num = 0
            else:
                sym = re.search(r'([A-Z][a-z]?)', label).group(0)
                if sym == 'D':
                    sym = 'H'
                num = ase.data.atomic_numbers[sym]
            asym_types.append(num)

    # Find where sites have disorder if necassary
    has_disorder = []
    if disorder != 'all_sites':
        occupancies = block.get('_atom_site_occupancy')
        if occupancies is None:
            occupancies = np.ones((len(asym_unit), ))
        labels = block.get('_atom_site_label')
        if labels is None:
            labels = [''] * len(asym_unit)
        for lab, occ in zip(labels, occupancies):
            has_disorder.append(_has_disorder(lab, occ))

    # Remove sites with ?, . or other invalid string for coordinates
    invalid = []
    for i, xyz in enumerate(asym_unit):
        if not all(isinstance(coord, (int, float)) for coord in xyz):
            invalid.append(i)
    if invalid:
        warnings.warn('atoms without sites or missing data will be removed')
        asym_unit = [c for i, c in enumerate(asym_unit) if i not in invalid]
        asym_types = [t for i, t in enumerate(asym_types) if i not in invalid]
        if disorder != 'all_sites':
            has_disorder = [d for i, d in enumerate(has_disorder)
                            if i not in invalid]

    remove_sites = []

    if remove_hydrogens:
        remove_sites.extend(i for i, num in enumerate(asym_types) if num == 1)

    # Remove atoms with fractional occupancy or raise ParseError
    if disorder != 'all_sites':

        for i, dis in enumerate(has_disorder):
            if i in remove_sites:
                continue
            if dis:
                if disorder == 'skip':
                    msg = f"{block.name} has disorder, pass " \
                           "disorder='ordered_sites'or 'all_sites' to " \
                           "remove/ignore disorder"
                    raise ParseError(msg)
                elif disorder == 'ordered_sites':
                    remove_sites.append(i)

    # Asymmetric unit
    asym_unit = [c for i, c in enumerate(asym_unit) if i not in remove_sites]
    asym_types = [t for i, t in enumerate(asym_types) if i not in remove_sites]
    if len(asym_unit) == 0:
        raise ParseError(f'{block.name} has no valid sites')
    asym_unit = np.array(asym_unit)

    # If Cartesian coords were given, convert to scaled
    if cartesian:
        asym_unit = asym_unit @ np.linalg.inv(cell)
    asym_unit = np.mod(asym_unit, 1)
    # asym_unit = _snap_small_prec_coords(asym_unit, 1e-4) # recommended by pymatgen

    # Remove overlapping sites unless disorder == 'all_sites'
    if disorder != 'all_sites':
        keep_sites = _unique_sites(asym_unit, _EQUIV_SITE_TOL)
        if not np.all(keep_sites):
            msg = 'may have overlapping sites, duplicates will be removed'
            warnings.warn(msg)
            asym_unit = asym_unit[keep_sites]
            asym_types = [t for t, keep in zip(asym_types, keep_sites) if keep]

    # Get symmetry operations
    sitesym = block._get_any(CIF_TAGS['symop'])
    if sitesym is None:
        label_or_num = block._get_any(CIF_TAGS['spacegroup_name'])
        if label_or_num is None:
            label_or_num = block._get_any(CIF_TAGS['spacegroup_number'])
        if label_or_num is None:
            warnings.warn('no symmetry data found, defaulting to P1')
            label_or_num = 1
        spg = ase.spacegroup.Spacegroup(label_or_num)
        rot, trans = spg.get_op()
    else:
        if isinstance(sitesym, str):
            sitesym = [sitesym]
        rot, trans =  _parse_sitesyms(sitesym)

    fr_motif, asym_inds, muls, invs = _expand_asym_unit(asym_unit, rot, trans)
    types = np.array([asym_types[i] for i in invs])
    motif = fr_motif @ cell

    return PeriodicSet(
        motif=motif,
        cell=cell,
        name=block.name,
        asymmetric_unit=asym_inds,
        wyckoff_multiplicities=muls,
        types=types
    )


def periodicset_from_ase_atoms(
        atoms,
        remove_hydrogens=False
) -> PeriodicSet:
    """:class:`ase.atoms.Atoms` -->
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`. Does not have
    the option to remove disorder.

    Parameters
    ----------
    atoms : :class:`ase.atoms.Atoms`
        An ase :class:`ase.atoms.Atoms` object representing a crystal.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystal.

    Returns
    -------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.

    Raises
    ------
    ParseError
        Raised if there are no valid sites in atoms.
    """

    from ase.spacegroup import get_basis

    cell = atoms.get_cell().array

    remove_inds = []
    if remove_hydrogens:
        for i in np.where(atoms.get_atomic_numbers() == 1)[0]:
            remove_inds.append(i)
    for i in sorted(remove_inds, reverse=True):
        atoms.pop(i)

    if len(atoms) == 0:
        raise ParseError(f'ase Atoms object has no valid sites')

    # Symmetry operations from spacegroup 
    spg = None
    if 'spacegroup' in atoms.info:
        spg = atoms.info['spacegroup']
        rot, trans = spg.rotations, spg.translations
    else:
        warnings.warn('no symmetry data found, defaulting to P1')
        rot = np.identity(3)[None, :]
        trans = np.zeros((1, 3))

    # Asymmetric unit. ase default tol is 1e-5
    # do differently! get_basis determines a reduced asym unit from the atoms;
    # surely this is not needed!
    asym_unit = get_basis(atoms, spacegroup=spg, tol=_EQUIV_SITE_TOL)
    fr_motif, asym_inds, muls, _ = _expand_asym_unit(asym_unit, rot, trans)
    motif = fr_motif @ cell

    return PeriodicSet(
        motif=motif,
        cell=cell,
        asymmetric_unit=asym_inds,
        wyckoff_multiplicities=muls,
        types=atoms.get_atomic_numbers()
    )


def periodicset_from_pymatgen_cifblock(
        block,
        remove_hydrogens=False,
        disorder='skip'
) -> PeriodicSet:
    """:class:`pymatgen.io.cif.CifBlock` -->
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`.

    Parameters
    ----------
    block : :class:`pymatgen.io.cif.CifBlock`
        A pymatgen CifBlock object representing a crystal.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystal.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.

    Returns
    -------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.

    Raises
    ------
    ParseError
        Raised if the structure can/should not be parsed for the
        following reasons: 1. No sites found or motif is empty after
        removing Hydrogens & disorder, 2. A site has missing
        coordinates, 3. :code:``disorder == 'skip'`` and disorder is
        found on any atom.
    """

    from pymatgen.io.cif import str2float
    import pymatgen.core.periodic_table as periodic_table

    odict = block.data

    # Unit cell
    cellpar = [odict.get(tag) for tag in CIF_TAGS['cellpar']]
    if None in cellpar:
        raise ParseError(f'{block.header} has missing cell data')
    cellpar = [str2float(v) for v in cellpar]
    cell = cellpar_to_cell(*cellpar)

    # Asymmetric unit coordinates
    cartesian = False
    asym_unit = [odict.get(tag) for tag in CIF_TAGS['atom_site_fract']]

    if None in asym_unit: # missing scaled coordinates, try Cartesian
        asym_unit = [odict.get(tag) for tag in CIF_TAGS['atom_site_cartn']]
        if None in asym_unit:
            raise ParseError(f'{block.header} has no coordinates')
        cartesian = True

    asym_unit = list(zip(*asym_unit)) # transpose [xs,ys,zs] -> [p1,p2,...]
    asym_unit = [[str2float(coord) for coord in xyz] for xyz in asym_unit]

    # Atomic types
    for tag in CIF_TAGS['atom_symbol']:
        asym_symbols = odict.get(tag)
        if asym_symbols is not None:
            asym_types = []
            for label in asym_symbols:
                if label in ('.', '?'):
                    warnings.warn('missing atomic types will be labelled 0')
                    num = 0
                else:
                    sym = re.search(r'([A-Z][a-z]?)', label).group(0)
                    if sym == 'D':
                        sym = 'H'
                    num = periodic_table.Element[sym].number
                asym_types.append(num)
            break
    else:
        warnings.warn('missing atomic types will be labelled 0')
        asym_types = [0] * len(asym_unit)

    # Find where sites have disorder if necassary
    has_disorder = []
    if disorder != 'all_sites':
        occupancies = odict.get('_atom_site_occupancy')
        if occupancies is None:
            occupancies = np.ones((len(asym_unit), ))
        labels = odict.get('_atom_site_label')
        if labels is None:
            labels = [''] * len(asym_unit)
        for lab, occ in zip(labels, occupancies):
            has_disorder.append(_has_disorder(lab, occ))

    # Remove sites with ?, . or other invalid string for coordinates
    invalid = []
    for i, xyz in enumerate(asym_unit):
        if not all(isinstance(coord, (int, float)) for coord in xyz):
            invalid.append(i)

    if invalid:
        warnings.warn('atoms without sites or missing data will be removed')
        asym_unit = [c for i, c in enumerate(asym_unit) if i not in invalid]
        asym_types = [c for i, c in enumerate(asym_types) if i not in invalid]
        if disorder != 'all_sites':
            has_disorder = [d for i, d in enumerate(has_disorder) 
                            if i not in invalid]

    remove_sites = []

    if remove_hydrogens:
        remove_sites.extend((i for i, n in enumerate(asym_types) if n == 1))


    # Remove atoms with fractional occupancy or raise ParseError
    if disorder != 'all_sites':

        for i, dis in enumerate(has_disorder):
            if i in remove_sites:
                continue
            if dis:
                if disorder == 'skip':
                    msg = f"{block.header} has disorder, pass " \
                            "disorder='ordered_sites' or 'all_sites' to " \
                            "remove/ignore disorder"
                    raise ParseError(msg)
                elif disorder == 'ordered_sites':
                    remove_sites.append(i)

    # Asymmetric unit
    asym_unit = [c for i, c in enumerate(asym_unit) if i not in remove_sites]
    asym_types = [t for i, t in enumerate(asym_types) if i not in remove_sites]
    if len(asym_unit) == 0:
        raise ParseError(f'{block.header} has no valid sites')
    asym_unit = np.array(asym_unit)

    # If Cartesian coords were given, convert to scaled
    if cartesian:
        asym_unit = asym_unit @ np.linalg.inv(cell)
    asym_unit = np.mod(asym_unit, 1)
    # asym_unit = _snap_small_prec_coords(asym_unit) # recommended by pymatgen

    # Remove overlapping sites unless disorder == 'all_sites'
    if disorder != 'all_sites':      
        keep_sites = _unique_sites(asym_unit, _EQUIV_SITE_TOL)
        if not np.all(keep_sites):
            msg = 'may have overlapping sites; duplicates will be removed'
            warnings.warn(msg)
        asym_unit = asym_unit[keep_sites]
        asym_types = [sym for sym, keep in zip(asym_types, keep_sites) if keep]

    # Apply symmetries to asymmetric unit
    rot, trans = _get_syms_pymatgen(odict)
    fr_motif, asym_inds, muls, invs = _expand_asym_unit(asym_unit, rot, trans)
    types = np.array([asym_types[i] for i in invs])
    motif = fr_motif @ cell

    return PeriodicSet(
        motif=motif,
        cell=cell,
        name=block.header,
        asymmetric_unit=asym_inds,
        wyckoff_multiplicities=muls,
        types=types
    )


def periodicset_from_pymatgen_structure(
        structure,
        remove_hydrogens=False,
        disorder='skip'
) -> PeriodicSet:
    """:class:`pymatgen.core.structure.Structure` -->
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`.
    Does not set the name of the periodic set, as there seems to be no
    name attribute in the pymatgen Structure object.

    Parameters
    ----------
    structure : :class:`pymatgen.core.structure.Structure`
        A pymatgen Structure object representing a crystal.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystal.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.

    Returns
    -------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.
    
    Raises
    ------
    ParseError
        Raised if the :code:`disorder == 'skip'` and 
        :code:`not structure.is_ordered`
    """

    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

    if remove_hydrogens:
        structure.remove_species(['H', 'D'])

    # Disorder
    if disorder == 'skip':
        if not structure.is_ordered:
            msg = f"pymatgen Structure has disorder, pass " \
                   "disorder='ordered_sites' or 'all_sites' to " \
                   "remove/ignore disorder"
            raise ParseError(msg)
    elif disorder == 'ordered_sites':
        remove_inds = []
        for i, comp in enumerate(structure.species_and_occu):
            if comp.num_atoms < 1:
                remove_inds.append(i)
        structure.remove_sites(remove_inds)

    motif = structure.cart_coords
    cell = structure.lattice.matrix
    sym_structure = SpacegroupAnalyzer(structure).get_symmetrized_structure()
    asym_unit = np.array([l[0] for l in sym_structure.equivalent_indices])
    muls = np.array([len(l) for l in sym_structure.equivalent_indices])
    types = np.array(sym_structure.atomic_numbers)

    return PeriodicSet(
        motif=motif,
        cell=cell,
        asymmetric_unit=asym_unit,
        wyckoff_multiplicities=muls,
        types=types
    )


def periodicset_from_ccdc_entry(
        entry,
        remove_hydrogens=False,
        disorder='skip',
        heaviest_component=False,
        molecular_centres=False
) -> PeriodicSet:
    """:class:`ccdc.entry.Entry` -->
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`.
    Entry is the type returned by :class:`ccdc.io.EntryReader`.

    Parameters
    ----------
    entry : :class:`ccdc.entry.Entry`
        A ccdc Entry object representing a database entry.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystal.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.
    heaviest_component : bool, optional
        Removes all but the heaviest molecule in the asymmeric unit,
        intended for removing solvents.
    molecular_centres : bool, default False
        Extract the centres of molecules in the unit cell and store in
        the attribute molecular_centres of the returned PeriodicSet.

    Returns
    -------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.

    Raises
    ------
    ParseError
        Raised if the structure fails parsing for any of the following:
        1. entry.has_3d_structure is False, 2.
        :code:``disorder == 'skip'`` and disorder is found on any atom,
        3. entry.crystal.molecule.all_atoms_have_sites is False,
        4. a.fractional_coordinates is None for any a in
        entry.crystal.disordered_molecule, 5. The motif is empty after
        removing Hydrogens and disordered sites.
    """

    # Entry specific flag
    if not entry.has_3d_structure:
        raise ParseError(f'{entry.identifier} has no 3D structure')

    # Disorder
    if disorder == 'skip' and entry.has_disorder:
        msg = f"{entry.identifier} has disorder, pass " \
                "disorder='ordered_sites' or 'all_sites' to remove/ignore" \
                "disorder"
        raise ParseError(msg)

    return periodicset_from_ccdc_crystal(
        entry.crystal,
        remove_hydrogens=remove_hydrogens,
        disorder=disorder,
        heaviest_component=heaviest_component,
        molecular_centres=molecular_centres
    )


def periodicset_from_ccdc_crystal(
        crystal,
        remove_hydrogens=False,
        disorder='skip',
        heaviest_component=False,
        molecular_centres=False
) -> PeriodicSet:
    """:class:`ccdc.crystal.Crystal` -->
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`.
    Crystal is the type returned by :class:`ccdc.io.CrystalReader`.

    Parameters
    ----------
    crystal : :class:`ccdc.crystal.Crystal`
        A ccdc Crystal object representing a crystal structure.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystal.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.
    heaviest_component : bool, optional
        Removes all but the heaviest molecule in the asymmeric unit,
        intended for removing solvents.
    molecular_centres : bool, default False
        Extract the centres of molecules in the unit cell and store in
        the attribute molecular_centres of the returned PeriodicSet.

    Returns
    -------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.

    Raises
    ------
    ParseError
        Raised if the structure fails parsing for any of the following:
        1. :code:``disorder == 'skip'`` and disorder is found on any
        atom, 2. crystal.molecule.all_atoms_have_sites is False,
        3. a.fractional_coordinates is None for any a in
        crystal.disordered_molecule, 4. The motif is empty after
        removing H, disordered sites or solvents.
    """

    molecule = crystal.disordered_molecule

    # Disorder
    if disorder == 'skip':
        if crystal.has_disorder or \
         any(_has_disorder(a.label, a.occupancy) for a in molecule.atoms):
            msg = f"{crystal.identifier} has disorder, pass " \
                   "disorder='ordered_sites' or 'all_sites' to remove/ignore" \
                   "disorder"
            raise ParseError(msg)

    elif disorder == 'ordered_sites':
        molecule.remove_atoms(
            a for a in molecule.atoms if _has_disorder(a.label, a.occupancy)
        )

    if remove_hydrogens:
        molecule.remove_atoms(
            a for a in molecule.atoms if a.atomic_symbol in 'HD'
        )

    if heaviest_component and len(molecule.components) > 1:
        molecule = _heaviest_component_ccdc(molecule)

    # Remove atoms with missing coordinates and warn
    if any(a.fractional_coordinates is None for a in molecule.atoms):
        warnings.warn('atoms without sites or missing data will be removed')
        molecule.remove_atoms(
            a for a in molecule.atoms if a.fractional_coordinates is None
        )

    crystal.molecule = molecule
    cell = cellpar_to_cell(*crystal.cell_lengths, *crystal.cell_angles)

    if molecular_centres:
        frac_centres = _frac_molecular_centres_ccdc(crystal)
        mol_centres = frac_centres @ cell
        return PeriodicSet(mol_centres, cell, name=crystal.identifier)

    asym_atoms = crystal.asymmetric_unit_molecule.atoms
    # check for None?
    asym_unit = np.array([tuple(a.fractional_coordinates) for a in asym_atoms])

    if asym_unit.shape[0] == 0:
        raise ParseError(f'{crystal.identifier} has no valid sites')

    asym_unit = np.mod(asym_unit, 1)
    # asym_unit = _snap_small_prec_coords(asym_unit) # recommended by pymatgen
    asym_types = [a.atomic_number for a in asym_atoms]

    # Disorder
    if disorder != 'all_sites':
        keep_sites = _unique_sites(asym_unit, _EQUIV_SITE_TOL)
        if not np.all(keep_sites):
            msg = 'may have overlapping sites; duplicates will be removed'
            warnings.warn(msg)
        asym_unit = asym_unit[keep_sites]
        asym_types = [sym for sym, keep in zip(asym_types, keep_sites) if keep]

    # Symmetry operations
    sitesym = crystal.symmetry_operators
    # try spacegroup numbers?
    if not sitesym:
        warnings.warn('no symmetry data found, defaulting to P1')
        sitesym = ['x,y,z']

    # Apply symmetries to asymmetric unit
    rot, trans = _parse_sitesyms(sitesym)
    fr_motif, asym_inds, muls, invs = _expand_asym_unit(asym_unit, rot, trans)
    motif = fr_motif @ cell
    types = np.array([asym_types[i] for i in invs])

    return PeriodicSet(
        motif=motif,
        cell=cell,
        name=crystal.identifier,
        asymmetric_unit=asym_inds,
        wyckoff_multiplicities=muls,
        types=types
    )


def periodicset_from_gemmi_block(
        block,
        remove_hydrogens=False,
        disorder='skip'
) -> PeriodicSet:
    """:class:`gemmi.cif.Block` -->
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`.
    Block is the type returned by :class:`gemmi.cif.read_file`.

    Parameters
    ----------
    block : :class:`ase.io.cif.CIFBlock`
        An ase CIFBlock object representing a crystal.
    remove_hydrogens : bool, optional
        Remove Hydrogens from the crystal.
    disorder : str, optional
        Controls how disordered structures are handled. Default is
        ``skip`` which skips any crystal with disorder, since disorder
        conflicts with the periodic set model. To read disordered
        structures anyway, choose either :code:`ordered_sites` to remove
        atoms with disorder or :code:`all_sites` include all atoms
        regardless of disorder.

    Returns
    -------
    :class:`amd.PeriodicSet <.periodicset.PeriodicSet>`
        Represents the crystal as a periodic set, consisting of a finite
        set of points (motif) and lattice (unit cell). Contains other
        useful data, e.g. the crystal's name and information about the
        asymmetric unit for calculation.

    Raises
    ------
    ParseError
        Raised if the structure fails to be parsed for any of the
        following: 1. Required data is missing (e.g. cell parameters),
        2. :code:``disorder == 'skip'`` and disorder is found on any
        atom, 3. The motif is empty after removing H or disordered
        sites.
    """

    import gemmi
    from gemmi.cif import as_number, as_string, as_int

    # Unit cell
    cellpar = [as_number(block.find_value(tag))
               for tag in CIF_TAGS['cellpar']]
    if None in cellpar:
        raise ParseError(f'{block.name} has missing cell data')
    cell = cellpar_to_cell(*cellpar)

    xyz_loop = block.find(CIF_TAGS['atom_site_fract']).loop
    if xyz_loop is None:
        # check for Cartesian coordinates
        raise ParseError(f'{block.name} has missing coordinate data')

    # Asymmetric unit coordinates
    loop_dict = _loop_to_dict_gemmi(xyz_loop)
    xyz_str = [loop_dict[t] for t in CIF_TAGS['atom_site_fract']]
    asym_unit = [[as_number(c) for c in coords] for coords in xyz_str]
    asym_unit = np.mod(np.array(asym_unit).T, 1)
    # asym_unit = _snap_small_prec_coords(asym_unit) # recommended by pymatgen

    # Asymmetric unit types
    if '_atom_site_type_symbol' in loop_dict:
        asym_syms = loop_dict['_atom_site_type_symbol']
        asym_types = [gemmi.Element(s).atomic_number for s in asym_syms]
    else:
        warnings.warn('missing atomic types will be labelled 0')
        asym_types = [0 for _ in range(len(asym_unit))]

    remove_sites = []

    # Disorder
    if '_atom_site_label' in loop_dict:
        labels = loop_dict['_atom_site_label']
    else:
        labels = [''] * xyz_loop.length()

    if '_atom_site_occupancy' in loop_dict:
        occupancies = [as_number(occ)
                       for occ in loop_dict['_atom_site_occupancy']]
    else:
        occupancies = [None for _ in range(xyz_loop.length())]

    if disorder == 'skip':
        if any(_has_disorder(l, o) for l, o in zip(labels, occupancies)):
            msg = f"{block.name} has disorder, pass " \
                   "disorder='ordered_sites' or 'all_sites' to " \
                   "remove/ignore disorder"
            raise ParseError(msg)
    elif disorder == 'ordered_sites':
        for i, (lab, occ) in enumerate(zip(labels, occupancies)):
            if _has_disorder(lab, occ):
                remove_sites.append(i)

    if remove_hydrogens:
        remove_sites.extend(
            i for i, num in enumerate(asym_types) if num == 1
        )

    # Asymmetric unit
    asym_unit = np.delete(asym_unit, remove_sites, axis=0)
    asym_types = [s for i, s in enumerate(asym_types) if i not in remove_sites]
    if asym_unit.shape[0] == 0:
        raise ParseError(f'{block.name} has no valid sites')

    # Remove overlapping sites unless disorder == 'all_sites'
    if disorder != 'all_sites':
        keep_sites = _unique_sites(asym_unit, _EQUIV_SITE_TOL)
        if not np.all(keep_sites):
            msg = 'may have overlapping sites; duplicates will be removed'
            warnings.warn(msg)
        asym_unit = asym_unit[keep_sites]
        asym_types = [sym for sym, keep in zip(asym_types, keep_sites) if keep]

    # Get symmetry operations
    sitesym = []
    for tag in CIF_TAGS['symop']:
        symop_loop = block.find([tag]).loop
        if symop_loop is not None:
            sitesym = _loop_to_dict_gemmi(symop_loop)[tag]
            break

    if not sitesym:
        for tag in CIF_TAGS['spacegroup_name']:
            label_or_num = block.find_value(tag)
            if label_or_num is not None:
                label_or_num = as_string(label_or_num)
                break
        if label_or_num is None:

            for tag in CIF_TAGS['spacegroup_number']:
                label_or_num = block.find_value(tag)
                if label_or_num is not None:
                    label_or_num = as_int(label_or_num)
                    break
        if label_or_num is None:
            warnings.warn('no symmetry data found, defaulting to P1')
            label_or_num = 1
        ops = list(gemmi.SpaceGroup(label_or_num).operations())
        rot = np.array([np.array(o.rot) / o.DEN for o in ops])
        trans = np.array([np.array(o.tran) / o.DEN for o in ops])
    else:
        rot, trans =  _parse_sitesyms(sitesym)

    fr_motif, asym_inds, muls, invs = _expand_asym_unit(asym_unit, rot, trans)
    types = np.array([asym_types[i] for i in invs])
    motif = fr_motif @ cell

    return PeriodicSet(
        motif=motif,
        cell=cell,
        name=block.name,
        asymmetric_unit=asym_inds,
        wyckoff_multiplicities=muls,
        types=types
    )


def _parse_sitesyms(symmetries):
    """Parses a sequence of symmetries in xyz form and returns rotation
    and translation arrays. Similar to function found in ase.spacegroup.
    """

    nsyms = len(symmetries)
    rotations = np.zeros((nsyms, 3, 3), dtype=np.float64)
    translations = np.zeros((nsyms, 3), dtype=np.float64)

    for i, sym in enumerate(symmetries):
        for ind, element in enumerate(sym.split(',')):

            is_positive = True
            is_fraction = False
            sng_trans = None
            fst_trans = []
            snd_trans = []

            for char in element.lower():
                if char == '+':
                    is_positive = True
                elif char == '-':
                    is_positive = False
                elif char == '/':
                    is_fraction = True
                elif char in 'xyz':
                    rot_sgn = 1.0 if is_positive else -1.0
                    rotations[i][ind][ord(char) - ord('x')] = rot_sgn

                elif char.isdigit() or char == '.':
                    if sng_trans is None:
                        sng_trans = 1.0 if is_positive else -1.0
                    if is_fraction:
                        snd_trans.append(char)
                    else:
                        fst_trans.append(char)

            if not fst_trans:
                e_trans = 0.0
            else:
                e_trans = sng_trans * float(''.join(fst_trans))

            if is_fraction:
                e_trans /= float(''.join(snd_trans))

            translations[i][ind] = e_trans

    return rotations, translations


def _expand_asym_unit(
        asym_unit: np.ndarray,
        rotations: np.ndarray,
        translations: np.ndarray
) -> Tuple[np.ndarray, ...]:
    """Asymmetric unit frac coords, list of rotations & translations -->
    full fractional motif, asymmetric unit indices, multiplicities and
    inverses (which motif points come from where in the asym unit).
    """

    frac_motif = []     # Full motif
    asym_inds = [0]     # Indices of asymmetric unit 
    multiplicities = [] # Wyckoff multiplicities
    inverses = []       # Motif -> Asymmetric unit
    m, dims = asym_unit.shape

    # Apply all symmetries first
    expanded_sites = np.zeros((m, len(rotations), dims), dtype=np.float64)
    for i in range(m):
        expanded_sites[i] = np.dot(rotations, asym_unit[i]) + translations
    expanded_sites = np.mod(expanded_sites, 1)

    for inv, sites in enumerate(expanded_sites):

        multiplicity = 0

        for site_ in sites:

            if not frac_motif:
                frac_motif.append(site_)
                inverses.append(inv)
                multiplicity += 1
                continue

            # check if site_ overlaps with existing sites
            diffs1 = np.abs(site_ - frac_motif)
            diffs2 = np.abs(diffs1 - 1)
            mask = np.all((diffs1 <= _EQUIV_SITE_TOL) | 
                          (diffs2 <= _EQUIV_SITE_TOL), axis=-1)

            if np.any(mask): # site is not new
                where_equal = np.argwhere(mask).flatten()
                for ind in where_equal:
                    if inverses[ind] == inv: # site is invariant
                        pass
                    else: # equivalent to a different site
                        msg = f'has equivalent sites at positions ' \
                              f'{inverses[ind]}, {inv}'
                        warnings.warn(msg)
            else: # new site
                frac_motif.append(site_)
                inverses.append(inv)
                multiplicity += 1

        if multiplicity > 0:
            multiplicities.append(multiplicity)
            asym_inds.append(len(frac_motif))

    frac_motif = np.array(frac_motif, dtype=np.float64)
    asym_inds = np.array(asym_inds[:-1], dtype=np.int32)
    multiplicities = np.array(multiplicities, dtype=np.int32)

    return frac_motif, asym_inds, multiplicities, inverses


@numba.njit()
def _unique_sites(asym_unit, tol):
    """Uniquify (within tol) a list of fractional coordinates,
    considering all points modulo 1. Returns an array of bools such that
    asym_unit[_unique_sites(asym_unit, tol)] is the uniquified list.
    """
    
    site_diffs1 = np.abs(np.expand_dims(asym_unit, 1) - asym_unit)
    site_diffs2 = np.abs(site_diffs1 - 1)
    sites_neq_mask = (site_diffs1 > tol) & (site_diffs2 > tol)
    overlapping = np.triu(sites_neq_mask.sum(axis=-1) == 0, 1)
    return overlapping.sum(axis=0) == 0


def _has_disorder(label, occupancy):
    """Return True if label ends with ? or occupancy is a number < 1.
    """
    return (np.isscalar(occupancy) and occupancy < 1) or label.endswith('?')


def _get_syms_pymatgen(data):
    """Parse symmetry operations given by data = block.data where block
    is a pymatgen CifBlock object. If the symops are not present the
    space group symbol/international number is parsed and symops are
    generated.
    """

    from pymatgen.symmetry.groups import SpaceGroup
    from pymatgen.core.operations import SymmOp
    import pymatgen.io.cif

    symops = []

    # Try xyz symmetry operations
    for symmetry_label in CIF_TAGS['symop']:
        xyz = data.get(symmetry_label)
        if not xyz:
            continue
        if isinstance(xyz, str):
            xyz = [xyz]
        try:
            symops = [SymmOp.from_xyz_string(s) for s in xyz]
            break
        except ValueError:
            continue

    # Try spacegroup symbol
    if not symops:
        for symmetry_label in CIF_TAGS['spacegroup_name']:
            sg = data.get(symmetry_label)
            if not sg:
                continue
            sg = re.sub(r'[\s_]', '', sg)

            try:
                spg = pymatgen.io.cif.space_groups.get(sg)
                if not spg:
                    continue
                symops = SpaceGroup(spg).symmetry_ops
                break
            except ValueError:
                pass

            try:
                for d in pymatgen.io.cif._get_cod_data():
                    if sg == re.sub(r'\s+', '', d['hermann_mauguin']):
                        symops = [SymmOp.from_xyz_string(s)
                                  for s in d['symops']]
                        break
            except Exception as e:
                continue

            if symops:
                break

    # Try international number
    if not symops:
        for symmetry_label in CIF_TAGS['spacegroup_number']:
            num = data.get(symmetry_label)
            if not num:
                continue

            try:
                i = int(pymatgen.io.cif.str2float(num))
                symops = SpaceGroup.from_int_number(i).symmetry_ops
                break
            except ValueError:
                continue

    if not symops:
        warnings.warn('no symmetry data found, defaulting to P1')
        symops = [SymmOp.from_xyz_string('x,y,z')]

    rotations = [op.rotation_matrix for op in symops]
    translations = [op.translation_vector for op in symops]

    return rotations, translations


def _frac_molecular_centres_ccdc(crystal):
    """Returns the geometric centres of molecules in the unit cell.
    Expects a ccdc Crystal object and returns fractional coordiantes.
    """

    frac_centres = []
    for comp in crystal.packing(inclusion='CentroidIncluded').components:
        coords = [a.fractional_coordinates for a in comp.atoms]
        frac_centres.append((sum(ax) / len(coords) for ax in zip(*coords)))

    frac_centres = np.mod(np.array(frac_centres), 1)
    return frac_centres[_unique_sites(frac_centres, _EQUIV_SITE_TOL)]


def _heaviest_component_ccdc(molecule):
    """Removes all but the heaviest component of the asymmetric unit.
    Intended for removing solvents. Expects and returns a ccdc Molecule
    object.
    """

    component_weights = []
    for component in molecule.components:
        weight = 0
        for a in component.atoms:
            if isinstance(a.atomic_weight, (float, int)):
                if isinstance(a.occupancy, (float, int)):
                    weight += a.occupancy * a.atomic_weight
                else:
                    weight += a.atomic_weight
        component_weights.append(weight)
    largest_component_ind = np.argmax(np.array(component_weights))
    molecule = molecule.components[largest_component_ind]
    return molecule


def _loop_to_dict_gemmi(gemmi_loop):
    """gemmi Loop object --> dict, tags: values
    """

    tablified_loop = [[] for _ in range(len(gemmi_loop.tags))]
    n_cols = gemmi_loop.width()
    for i, item in enumerate(gemmi_loop.values):
        tablified_loop[i % n_cols].append(item)
    return {tag: l for tag, l in zip(gemmi_loop.tags, tablified_loop)}


def _snap_small_prec_coords(frac_coords, tol):
    """Find where frac_coords is within 1e-4 of 1/3 or 2/3, change to
    1/3 and 2/3. Recommended by pymatgen's CIF parser.
    """
    frac_coords[np.abs(1 - 3 * frac_coords) < tol] = 1 / 3.
    frac_coords[np.abs(1 - 3 * frac_coords / 2) < tol] = 2 / 3.
    return frac_coords

dwiddo / average-minimum-distance

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