cif.py

# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved.                     #
# This file is part of the AiiDA code.                                    #
#                                                                         #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida_core #
# For further information on the license, see the LICENSE.txt file        #
# For further information please visit http://www.aiida.net               #
###########################################################################
# pylint: disable=invalid-name,too-many-locals,too-many-statements
"""Tools for handling Crystallographic Information Files (CIF)"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division

from six.moves import range

from aiida.orm.data.singlefile import SinglefileData
from aiida.orm.calculation.inline import optional_inline
from aiida.common.utils import HiddenPrints


class InvalidOccupationsError(Exception):
    """
    An exception that will be raised if pymatgen fails to parse the structure from a
    cif because some site occupancies exceed the occupancy tolerance. This often happens
    for structures that have attached species, such as hydrogen, and specify a placeholder
    position for it, leading to occupancies greater than one. Pymatgen only issues a
    warning in this case and simply does not return a structure
    """


ase_loops = {
    '_atom_site': [
        '_atom_site_label',
        '_atom_site_occupancy',
        '_atom_site_fract_x',
        '_atom_site_fract_y',
        '_atom_site_fract_z',
        '_atom_site_adp_type',
        '_atom_site_thermal_displace_type',
        '_atom_site_B_iso_or_equiv',
        '_atom_site_U_iso_or_equiv',
        '_atom_site_B_equiv_geom_mean',
        '_atom_site_U_equiv_geom_mean',
        '_atom_site_type_symbol',
    ]
}

symmetry_tags = [
    '_symmetry_equiv_pos_site_id',
    '_symmetry_equiv_pos_as_xyz',
    '_symmetry_Int_Tables_number',
    '_symmetry_space_group_name_H-M',
    '_symmetry_space_group_name_Hall',
    '_space_group_symop_id',
    '_space_group_symop_operation_xyz',
    '_space_group_symop_sg_id',
    '_space_group_id',
    '_space_group_IT_number',
    '_space_group_name_H-M_alt',
    '_space_group_name_Hall',
]


def has_pycifrw():
    """
    :return: True if the PyCifRW module can be imported, False otherwise.
    """
    # pylint: disable=unused-variable
    try:
        import CifFile
        from CifFile import CifBlock
    except ImportError:
        return False
    return True


def symop_string_from_symop_matrix_tr(matrix, tr=(0, 0, 0), eps=0):
    """
    Construct a CIF representation of symmetry operator plus translation.
    See International Tables for Crystallography Vol. A. (2002) for
    definition.

    :param matrix: 3x3 matrix, representing the symmetry operator
    :param tr: translation vector of length 3 (default 0)
    :param eps: epsilon parameter for fuzzy comparison x == 0
    :return: CIF representation of symmetry operator
    """
    import re
    axes = ["x", "y", "z"]
    parts = ["", "", ""]
    for i in range(3):
        for j in range(3):
            sign = None
            if matrix[i][j] > eps:
                sign = "+"
            elif matrix[i][j] < -eps:
                sign = "-"
            if sign:
                parts[i] = format("{}{}{}".format(parts[i], sign, axes[j]))
        if tr[i] < -eps or tr[i] > eps:
            sign = "+"
            if tr[i] < -eps:
                sign = "-"
            parts[i] = format("{}{}{}".format(parts[i], sign, abs(tr[i])))
        parts[i] = re.sub(r'^\+', '', parts[i])
    return ",".join(parts)


@optional_inline
def _get_aiida_structure_ase_inline(cif, **kwargs):
    """
    Creates :py:class:`aiida.orm.data.structure.StructureData` using ASE.

    .. note:: unable to correctly import structures of alloys.
    .. note:: requires ASE module.
    """
    from aiida.orm.data.parameter import ParameterData
    from aiida.orm.data.structure import StructureData

    if 'parameters' in kwargs:
        parameters = kwargs['parameters']
    else:
        parameters = {}

    if isinstance(parameters, ParameterData):
        parameters = parameters.get_dict()

    parameters.pop('occupancy_tolerance', None)
    parameters.pop('site_tolerance', None)

    return {'structure': StructureData(ase=cif.get_ase(**parameters))}


@optional_inline
def _get_aiida_structure_pymatgen_inline(cif, **kwargs):
    """
    Creates :py:class:`aiida.orm.data.structure.StructureData` using pymatgen.

    :param occupancy_tolerance: If total occupancy of a site is between 1 and occupancy_tolerance,
        the occupancies will be scaled down to 1.
    :param site_tolerance: 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.

    .. note:: requires pymatgen module.
    """
    from pymatgen.io.cif import CifParser
    from aiida.orm.data.parameter import ParameterData
    from aiida.orm.data.structure import StructureData

    if 'parameters' in kwargs:
        parameters = kwargs['parameters']
    else:
        parameters = {}

    if isinstance(parameters, ParameterData):
        parameters = parameters.get_dict()

    constructor_kwargs = {}

    parameters['primitive'] = parameters.pop('primitive_cell', False)

    for argument in ['occupancy_tolerance', 'site_tolerance']:
        if argument in parameters:
            constructor_kwargs[argument] = parameters.pop(argument)

    parser = CifParser(cif.get_file_abs_path(), **constructor_kwargs)

    try:
        structures = parser.get_structures(**parameters)
    except ValueError:

        # Verify whether the failure was due to wrong occupancy numbers
        try:
            constructor_kwargs['occupancy_tolerance'] = 1E10
            parser = CifParser(cif.get_file_abs_path(), **constructor_kwargs)
            structures = parser.get_structures(**parameters)
        except ValueError:
            # If it still fails, the occupancies were not the reason for failure
            raise ValueError('pymatgen failed to provide a structure from the cif file')
        else:
            # If it now succeeds, non-unity occupancies were the culprit
            raise InvalidOccupationsError(
                'detected atomic sites with an occupation number larger than the occupation tolerance')

    return {'structure': StructureData(pymatgen_structure=structures[0])}


def cif_from_ase(ase, full_occupancies=False, add_fake_biso=False):
    """
    Construct a CIF datablock from the ASE structure. The code is taken
    from
    https://wiki.fysik.dtu.dk/ase/epydoc/ase.io.cif-pysrc.html#write_cif,
    as the original ASE code contains a bug in printing the
    Hermann-Mauguin symmetry space group symbol.

    :param ase: ASE "images"
    :return: array of CIF datablocks
    """
    from numpy import arccos, pi, dot
    from numpy.linalg import norm

    if not isinstance(ase, (list, tuple)):
        ase = [ase]

    datablocks = []
    for _, atoms in enumerate(ase):
        datablock = dict()

        cell = atoms.cell
        a = norm(cell[0])
        b = norm(cell[1])
        c = norm(cell[2])
        alpha = arccos(dot(cell[1], cell[2]) / (b * c)) * 180. / pi
        beta = arccos(dot(cell[0], cell[2]) / (a * c)) * 180. / pi
        gamma = arccos(dot(cell[0], cell[1]) / (a * b)) * 180. / pi

        datablock['_cell_length_a'] = str(a)
        datablock['_cell_length_b'] = str(b)
        datablock['_cell_length_c'] = str(c)
        datablock['_cell_angle_alpha'] = str(alpha)
        datablock['_cell_angle_beta'] = str(beta)
        datablock['_cell_angle_gamma'] = str(gamma)

        if atoms.pbc.all():
            datablock['_symmetry_space_group_name_H-M'] = 'P 1'
            datablock['_symmetry_int_tables_number'] = str(1)
            datablock['_symmetry_equiv_pos_as_xyz'] = ['x, y, z']

        datablock['_atom_site_label'] = []
        datablock['_atom_site_fract_x'] = []
        datablock['_atom_site_fract_y'] = []
        datablock['_atom_site_fract_z'] = []
        datablock['_atom_site_type_symbol'] = []

        if full_occupancies:
            datablock['_atom_site_occupancy'] = []
        if add_fake_biso:
            datablock['_atom_site_thermal_displace_type'] = []
            datablock['_atom_site_B_iso_or_equiv'] = []

        scaled = atoms.get_scaled_positions()
        no = {}
        for i, atom in enumerate(atoms):
            symbol = atom.symbol
            if symbol in no:
                no[symbol] += 1
            else:
                no[symbol] = 1
            datablock['_atom_site_label'].append(symbol + str(no[symbol]))
            datablock['_atom_site_fract_x'].append(str(scaled[i][0]))
            datablock['_atom_site_fract_y'].append(str(scaled[i][1]))
            datablock['_atom_site_fract_z'].append(str(scaled[i][2]))
            datablock['_atom_site_type_symbol'].append(symbol)

            if full_occupancies:
                datablock['_atom_site_occupancy'].append(str(1.0))
            if add_fake_biso:
                datablock['_atom_site_thermal_displace_type'].append('Biso')
                datablock['_atom_site_B_iso_or_equiv'].append(str(1.0))

        datablocks.append(datablock)
    return datablocks


# pylint: disable=too-many-branches
def pycifrw_from_cif(datablocks, loops=None, names=None):
    """
    Constructs PyCifRW's CifFile from an array of CIF datablocks.

    :param datablocks: an array of CIF datablocks
    :param loops: optional dict of lists of CIF tag loops.
    :param names: optional list of datablock names
    :return: CifFile
    """
    try:
        import CifFile
        from CifFile import CifBlock
    except ImportError as exc:
        raise ImportError(str(exc) + '. You need to install the PyCifRW package.')

    if loops is None:
        loops = dict()

    cif = CifFile.CifFile()  # pylint: disable=no-member
    try:
        cif.set_grammar("1.1")
    except AttributeError:
        # if no grammar can be set, we assume it's 1.1 (widespread standard)
        pass

    if names and len(names) < len(datablocks):
        raise ValueError("Not enough names supplied for "
                         "datablocks: {} (names) < "
                         "{} (datablocks)".format(len(names), len(datablocks)))
    for i, values in enumerate(datablocks):
        name = str(i)
        if names:
            name = names[i]
        datablock = CifBlock()
        cif[name] = datablock
        tags_in_loops = []
        for loopname in loops.keys():
            row_size = None
            tags_seen = []
            for tag in loops[loopname]:
                if tag in values:
                    tag_values = values.pop(tag)
                    if not isinstance(tag_values, list):
                        tag_values = [tag_values]
                    if row_size is None:
                        row_size = len(tag_values)
                    elif row_size != len(tag_values):
                        raise ValueError("Number of values for tag "
                                         "'{}' is different from "
                                         "the others in the same "
                                         "loop".format(tag))
                    if row_size == 0:
                        continue
                    datablock.AddItem(tag, tag_values)
                    tags_seen.append(tag)
                    tags_in_loops.append(tag)
            if row_size is not None and row_size > 0:
                datablock.CreateLoop(datanames=tags_seen)
        for tag in sorted(values.keys()):
            if not tag in tags_in_loops:
                datablock.AddItem(tag, values[tag])
                # create automatically a loop for non-scalar values
                if isinstance(values[tag], (tuple, list)) and tag not in loops.keys():
                    datablock.CreateLoop([tag])
    return cif


@optional_inline
def refine_inline(node):
    """
    Refine (reduce) the cell of :py:class:`aiida.orm.data.cif.CifData`,
    find and remove symmetrically equivalent atoms.

    :param node: a :py:class:`aiida.orm.data.cif.CifData` instance.
    :return: dict with :py:class:`aiida.orm.data.cif.CifData`

    .. note:: can be used as inline calculation.
    """
    from aiida.orm.data.structure import StructureData, ase_refine_cell

    if len(node.values.keys()) > 1:
        raise ValueError("CifData seems to contain more than one data "
                         "block -- multiblock CIF files are not "
                         "supported yet")

    name = list(node.values.keys())[0]

    original_atoms = node.get_ase(index=None)
    if len(original_atoms) > 1:
        raise ValueError("CifData seems to contain more than one crystal "
                         "structure -- such refinement is not supported "
                         "yet")

    original_atoms = original_atoms[0]

    refined_atoms, symmetry = ase_refine_cell(original_atoms)

    cif = CifData(ase=refined_atoms)
    if name != str(0):
        cif.values.rename(str(0), name)

    # Remove all existing symmetry tags before overwriting:
    for tag in symmetry_tags:
        cif.values[name].RemoveCifItem(tag)

    cif.values[name]['_symmetry_space_group_name_H-M'] = symmetry['hm']
    cif.values[name]['_symmetry_space_group_name_Hall'] = symmetry['hall']
    cif.values[name]['_symmetry_Int_Tables_number'] = symmetry['tables']
    cif.values[name]['_symmetry_equiv_pos_as_xyz'] = \
        [symop_string_from_symop_matrix_tr(symmetry['rotations'][i],
                                           symmetry['translations'][i])
         for i in range(len(symmetry['rotations']))]

    # Summary formula has to be calculated from non-reduced set of atoms.
    cif.values[name]['_chemical_formula_sum'] = \
        StructureData(ase=original_atoms).get_formula(mode='hill',
                                                      separator=' ')

    # If the number of reduced atoms multiplies the number of non-reduced
    # atoms, the new Z value can be calculated.
    if '_cell_formula_units_Z' in node.values[name].keys():
        old_Z = node.values[name]['_cell_formula_units_Z']
        if len(original_atoms) % len(refined_atoms):
            new_Z = old_Z * len(original_atoms) // len(refined_atoms)
            cif.values[name]['_cell_formula_units_Z'] = new_Z

    return {'cif': cif}


def parse_formula(formula):
    """
    Parses the Hill formulae, written with spaces for separators.
    """
    import re

    contents = {}
    for part in re.split(r'\s+', formula):
        m = re.match(r'(\D+)([\.\d]+)?', part)
        specie = m.group(1)
        quantity = m.group(2)
        if quantity is None:
            quantity = 1
        else:
            if re.match(r'^\d+$', quantity):
                quantity = int(quantity)
            else:
                quantity = float(quantity)
        contents[specie] = quantity
    return contents


# pylint: disable=abstract-method
# Note:  Method 'query' is abstract in class 'Node' but is not overridden
class CifData(SinglefileData):
    """
    Wrapper for Crystallographic Interchange File (CIF)

    .. note:: the file (physical) is held as the authoritative source of
        information, so all conversions are done through the physical file:
        when setting ``ase`` or ``values``, a physical CIF file is generated
        first, the values are updated from the physical CIF file.
    """
    _set_incompatibilities = [('ase', 'file'), ('ase', 'values'), ('file', 'values')]
    _scan_types = ['standard', 'flex']
    _parse_policies = ['eager', 'lazy']

    @property
    def _set_defaults(self):
        """
        Add defaults for some attributes.

        """
        parent_dict = super(CifData, self)._set_defaults
        parent_dict.update({
            'scan_type': self._scan_types[0],
            'parse_policy': 'eager',
        })

        return parent_dict

    @staticmethod
    def read_cif(fileobj, index=-1, **kwargs):
        """
        A wrapper method that simulates the behavior of the old
        function ase.io.cif.read_cif by using the new generic ase.io.read
        function.
        """
        from ase.io import read

        # the read function returns a list as a cif file might contain multiple
        # structures
        struct_list = read(fileobj, index=':', format='cif', **kwargs)

        if index is None:
            # If index is explicitely set to None, the list is returned as such.
            return struct_list
        # otherwise return the desired structure specified by index.
        # If no index is specified, the last structure is assumed by default
        return struct_list[index]

    @classmethod
    def from_md5(cls, md5):
        """
        Return a list of all CIF files that match a given MD5 hash.

        .. note:: the hash has to be stored in a ``_md5`` attribute,
            otherwise the CIF file will not be found.
        """
        from aiida.orm.querybuilder import QueryBuilder
        qb = QueryBuilder()
        qb.append(cls, filters={'attributes.md5': {'==': md5}})
        return [_ for [_] in qb.all()]

    @classmethod
    def get_or_create(cls, filename, use_first=False, store_cif=True):
        """
        Pass the same parameter of the init; if a file with the same md5
        is found, that CifData is returned.

        :param filename: an absolute filename on disk
        :param use_first: if False (default), raise an exception if more than \
                one CIF file is found.\
                If it is True, instead, use the first available CIF file.
        :param bool store_cif: If false, the CifData objects are not stored in
                the database. default=True.
        :return (cif, created): where cif is the CifData object, and create is either\
            True if the object was created, or False if the object was retrieved\
            from the DB.
        """
        import aiida.common.utils
        import os

        if not os.path.abspath(filename):
            raise ValueError("filename must be an absolute path")
        md5 = aiida.common.utils.md5_file(filename)

        cifs = cls.from_md5(md5)
        if not cifs:
            if store_cif:
                instance = cls(file=filename).store()
                return (instance, True)
            instance = cls(file=filename)
            return (instance, True)
        else:
            if len(cifs) > 1:
                if use_first:
                    return (cifs[0], False)
                else:
                    raise ValueError("More than one copy of a CIF file "
                                     "with the same MD5 has been found in "
                                     "the DB. pks={}".format(",".join([str(i.pk) for i in cifs])))
            else:
                return cifs[0], False

    # pylint: disable=attribute-defined-outside-init
    @property
    def ase(self):
        """
        ASE object, representing the CIF.

        .. note:: requires ASE module.
        """
        if self._ase is None:
            self._ase = self.get_ase()
        return self._ase

    def get_ase(self, **kwargs):
        """
        Returns ASE object, representing the CIF. This function differs
        from the property ``ase`` by the possibility to pass the keyworded
        arguments (kwargs) to ase.io.cif.read_cif().

        .. note:: requires ASE module.
        """
        if not kwargs and self._ase:
            return self.ase
        return CifData.read_cif(self._get_folder_pathsubfolder.open(self.filename), **kwargs)

    def set_ase(self, aseatoms):
        """
        Set the contents of the CifData starting from an ASE atoms object

        :param aseatoms: the ASE atoms object
        """
        import tempfile
        cif = cif_from_ase(aseatoms)
        with tempfile.NamedTemporaryFile(mode='w+') as f:
            with HiddenPrints():
                f.write(pycifrw_from_cif(cif, loops=ase_loops).WriteOut())
            f.flush()
            self.set_file(f.name)

    @ase.setter
    def ase(self, aseatoms):
        self.set_ase(aseatoms)

    @property
    def values(self):
        """
        PyCifRW structure, representing the CIF datablocks.

        .. note:: requires PyCifRW module.
        """
        if self._values is None:
            import CifFile
            from CifFile import CifBlock  # pylint: disable=no-name-in-module

            c = CifFile.ReadCif(self.get_file_abs_path(), scantype=self.get_attr('scan_type'))  # pylint: disable=no-member
            for k, v in c.items():
                c.dictionary[k] = CifBlock(v)
            self._values = c
        return self._values

    def set_values(self, values):
        """
        Set internal representation to `values`.

        Warning: This also writes a new CIF file.

        :param values: PyCifRW CifFile object

        .. note:: requires PyCifRW module.
        """
        import tempfile
        with tempfile.NamedTemporaryFile(mode='w+') as f:
            with HiddenPrints():
                f.write(values.WriteOut())
            f.flush()
            self.set_file(f.name)

        self._values = values

    @values.setter
    def values(self, values):
        self.set_values(values)

    def __init__(self, **kwargs):
        """
        Initialises an instance of CifData.
        """
        # Note: this will set attributes, if specified as kwargs
        super(CifData, self).__init__(**kwargs)
        self._values = None
        self._ase = None

        if not self.is_stored and 'file' in kwargs \
                and self.get_attr('parse_policy') == 'eager':
            self.parse()

    def parse(self, scan_type=None):
        """
        Parses CIF file and sets attributes.

        :param scan_type:  See set_scan_type
        """
        if scan_type is not None:
            self.set_scan_type(scan_type)

        # Note: this causes parsing, if not already parsed
        self._set_attr('formulae', self.get_formulae())
        self._set_attr('spacegroup_numbers', self.get_spacegroup_numbers())

    # pylint: disable=arguments-differ
    def store(self, *args, **kwargs):
        """
        Store the node.
        """
        if not self.is_stored:
            self._set_attr('md5', self.generate_md5())

        return super(CifData, self).store(*args, **kwargs)

    # pylint: disable=attribute-defined-outside-init
    def set_file(self, filename):
        """
        Set the file.

        If the source is set and the MD5 checksum of new file
        is different from the source, the source has to be deleted.
        """
        super(CifData, self).set_file(filename)
        md5sum = self.generate_md5()
        if isinstance(self.source, dict) and \
                self.source.get('source_md5', None) is not None and \
                self.source['source_md5'] != md5sum:
            self.source = {}
        self._set_attr('md5', md5sum)

        self._values = None
        self._ase = None
        self._set_attr('formulae', None)
        self._set_attr('spacegroup_numbers', None)

    def set_scan_type(self, scan_type):
        """
        Set the scan_type for PyCifRW.

        The 'flex' scan_type of PyCifRW is faster for large CIF files but
        does not yet support the CIF2 format as of 02/2018.
        See the CifFile.ReadCif function

        :param scan_type: Either 'standard' or 'flex' (see _scan_types)
        """
        if scan_type in self._scan_types:
            self._set_attr('scan_type', scan_type)
        else:
            raise ValueError("Got unknown scan_type {}".format(scan_type))

    def set_parse_policy(self, parse_policy):
        """
        Set the parse policy.

        :param parse_policy: Either 'eager' (parse CIF file on set_file)
            or 'lazy' (defer parsing until needed)
        """
        if parse_policy in self._parse_policies:
            self._set_attr('parse_policy', parse_policy)
        else:
            raise ValueError("Got unknown parse_policy {}".format(parse_policy))

    def get_formulae(self, mode='sum'):
        """
        Return chemical formulae specified in CIF file.

        Note: This does not compute the formula, it only reads it from the
        appropriate tag. Use refine_inline to compute formulae.
        """
        # note: If formulae are not None, they could be returned
        # directly (but the function is very cheap anyhow).
        formula_tag = "_chemical_formula_{}".format(mode)
        formulae = []
        for datablock in self.values.keys():
            formula = None
            if formula_tag in self.values[datablock].keys():
                formula = self.values[datablock][formula_tag]
            formulae.append(formula)

        return formulae

    def get_spacegroup_numbers(self):
        """
        Get the spacegroup international number.
        """
        # note: If spacegroup_numbers are not None, they could be returned
        # directly (but the function is very cheap anyhow).
        spg_tags = ["_space_group.it_number", "_space_group_it_number", "_symmetry_int_tables_number"]
        spacegroup_numbers = []
        for datablock in self.values.keys():
            spacegroup_number = None
            correct_tags = [tag for tag in spg_tags if tag in self.values[datablock].keys()]
            if correct_tags:
                try:
                    spacegroup_number = int(self.values[datablock][correct_tags[0]])
                except ValueError:
                    pass
            spacegroup_numbers.append(spacegroup_number)

        return spacegroup_numbers

    @property
    def has_partial_occupancies(self):
        """
        Check if there are float values in the atomic occupancies

        :returns: True if there are partial occupancies, False otherwise
        """
        epsilon = 1e-6
        tag = '_atom_site_occupancy'
        partial_occupancies = False
        for datablock in self.values.keys():
            if tag in self.values[datablock].keys():
                for site in self.values[datablock][tag]:
                    # find the float number in the string
                    bracket = site.find('(')
                    if bracket == -1:
                        # no bracket found
                        if abs(float(site) - 1) > epsilon:
                            partial_occupancies = True
                    else:
                        # bracket, cut string
                        if abs(float(site[0:bracket]) - 1) > epsilon:
                            partial_occupancies = True

        return partial_occupancies

    @property
    def has_attached_hydrogens(self):
        """
        Check if there are hydrogens without coordinates, specified as attached
        to the atoms of the structure.

        :returns: True if there are attached hydrogens, False otherwise.
        """
        tag = '_atom_site_attached_hydrogens'
        for datablock in self.values.keys():
            if tag in self.values[datablock].keys():
                for value in self.values[datablock][tag]:
                    if value != '.' and value != '?' and value != '0':
                        return True

        return False

    @property
    def has_atomic_sites(self):
        """
        Returns whether there are any atomic sites defined in the cif data. That
        is to say, it will check all the values for the `_atom_site_fract_*` tags
        and if they are all equal to `?` that means there are no relevant atomic
        sites defined and the function will return False. In all other cases the
        function will return True

        :returns: False when at least one atomic site fractional coordinate is not
            equal to `?` and True otherwise
        """
        tag_x = '_atom_site_fract_x'
        tag_y = '_atom_site_fract_y'
        tag_z = '_atom_site_fract_z'
        coords = []
        for datablock in self.values.keys():
            for tag in [tag_x, tag_y, tag_z]:
                if tag in self.values[datablock].keys():
                    coords.extend(self.values[datablock][tag])

        return not all([coord == '?' for coord in coords])

    @property
    def has_unknown_species(self):
        """
        Returns whether the cif contains atomic species that are not recognized by AiiDA.
        The known species are taken from the elements dictionary in aiida.common.constants.
        If any of the formula of the cif data contain species that are not in that elements
        dictionary, the function will return True and False in all other cases. If there is
        no formulae to be found, it will return None

        :returns: True when there are unknown species in any of the formulae, False if not, None if no formula found
        """
        from aiida.common.constants import elements

        known_species = [element['symbol'] for element in elements.values()]

        for formula in self.get_formulae():

            if formula is None:
                return None

            species = parse_formula(formula).keys()
            if any([specie not in known_species for specie in species]):
                return True

        return False

    def generate_md5(self):
        """
        Computes and returns MD5 hash of the CIF file.
        """
        import aiida.common.utils
        from aiida.common.exceptions import ValidationError

        abspath = self.get_file_abs_path()
        if not abspath:
            raise ValidationError("No valid CIF was passed!")

        return aiida.common.utils.md5_file(abspath)

    def _get_aiida_structure(self, converter='pymatgen', store=False, **kwargs):
        """
        Creates :py:class:`aiida.orm.data.structure.StructureData`.

        :param converter: specify the converter. Default 'pymatgen'.
        :param store: if True, intermediate calculation gets stored in the
            AiiDA database for record. Default False.
        :param primitive_cell: if True, primitive cell is returned,
            conventional cell if False. Default False.
        :param occupancy_tolerance: If total occupancy of a site is between 1 and occupancy_tolerance,
            the occupancies will be scaled down to 1. (pymatgen only)
        :param site_tolerance: 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. (pymatgen only)
        :return: :py:class:`aiida.orm.data.structure.StructureData` node.
        """
        from . import cif  # pylint: disable=import-self
        from aiida.orm.data.parameter import ParameterData

        parameters = ParameterData(dict=kwargs)

        try:
            convert_function = getattr(cif, '_get_aiida_structure_{}_inline'.format(converter))
        except AttributeError:
            raise ValueError("No such converter '{}' available".format(converter))

        result = convert_function(cif=self, parameters=parameters, store=store)

        return result['structure']

    # pylint: disable=unused-argument
    def _prepare_cif(self, main_file_name=""):
        """
        Return CIF string of CifData object.

        If parsed values are present, a CIF string is created
        and written to file.
        If no parsed values are present, the CIF string is read
        from file.
        """
        if self._values and not self.is_stored:
            # Note: this overwrites the CIF file!
            self.set_values(self._values)

        with self._get_folder_pathsubfolder.open(self.filename) as f:
            return f.read().encode('utf-8'), {}

    # pylint: disable=unused-argument
    def _prepare_tcod(self, main_file_name="", **kwargs):
        """
        Write the given CIF to a string of format TCOD CIF.
        """
        from aiida.tools.dbexporters.tcod import export_cif
        return export_cif(self, **kwargs), {}

    def _get_object_ase(self):
        """
        Converts CifData to ase.Atoms

        :return: an ase.Atoms object
        """
        return self.ase

    def _get_object_pycifrw(self):
        """
        Converts CifData to PyCIFRW.CifFile

        :return: a PyCIFRW.CifFile object
        """
        return self.values

    def _validate(self):
        """
        Validates MD5 hash of CIF file.
        """
        from aiida.common.exceptions import ValidationError

        super(CifData, self)._validate()

        try:
            attr_md5 = self.get_attr('md5')
        except AttributeError:
            raise ValidationError("attribute 'md5' not set.")
        md5 = self.generate_md5()
        if attr_md5 != md5:
            raise ValidationError("Attribute 'md5' says '{}' but '{}' was " "parsed instead.".format(attr_md5, md5))