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"""Tools for reading crystals from files, or from the CSD with ``csd-python-api``. |
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The readers return :class:`.periodicset.PeriodicSet` objects representing the |
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crystal which can be passed to :func:`.calculate.AMD` and :func:`.calculate.PDD` |
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to get their invariants. |
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""" |
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import os |
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import functools |
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import warnings |
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from typing import Callable, Iterable, Sequence, Tuple |
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import numpy as np |
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import numba |
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import ase.io.cif |
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import ase.data |
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from ase.spacegroup.spacegroup import parse_sitesym |
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from .utils import cellpar_to_cell |
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from .periodicset import PeriodicSet |
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try: |
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import ccdc.io |
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import ccdc.search |
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_CSD_PYTHON_API_ENABLED = True |
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except (ImportError, RuntimeError) as _: |
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_CSD_PYTHON_API_ENABLED = False |
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def _custom_warning(message, category, filename, lineno, *args, **kwargs): |
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return f'{category.__name__}: {message}\n' |
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warnings.formatwarning = _custom_warning |
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_EQUIV_SITE_TOL = 1e-3 |
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_DISORDER_OPTIONS = {'skip', 'ordered_sites', 'all_sites'} |
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_ATOM_SITE_FRACT_TAGS = [ |
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'_atom_site_fract_x', |
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'_atom_site_fract_y', |
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'_atom_site_fract_z', |
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] |
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_ATOM_SITE_CARTN_TAGS = [ |
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'_atom_site_cartn_x', |
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'_atom_site_cartn_y', |
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'_atom_site_cartn_z', |
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] |
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_SYMOP_TAGS = [ |
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'_space_group_symop_operation_xyz', |
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'_space_group_symop.operation_xyz', |
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'_symmetry_equiv_pos_as_xyz', |
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] |
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class _Reader: |
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def __init__( |
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self, |
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remove_hydrogens=False, |
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disorder='skip', |
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heaviest_component=False, |
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show_warnings=True, |
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): |
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if disorder not in _DISORDER_OPTIONS: |
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raise ValueError(f'disorder parameter {disorder} must be one of {_DISORDER_OPTIONS}') |
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self.remove_hydrogens = remove_hydrogens |
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self.disorder = disorder |
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self.heaviest_component = heaviest_component |
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self.show_warnings = show_warnings |
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self._generator = [] |
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def __iter__(self): |
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yield from self._generator |
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def read_one(self): |
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"""Read the first, and usually the only, item.""" |
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try: |
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return next(iter(self._generator)) |
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except StopIteration: |
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return None |
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class CifReader(_Reader): |
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"""Read all structures in a .cif file or all files in a folder |
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with ase or csd-python-api (if installed), yielding |
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:class:`.periodicset.PeriodicSet` s. |
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Parameters |
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---------- |
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path : str |
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Path to a .cif file or directory. (Other files are accepted when using |
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``reader='ccdc'``, if csd-python-api is installed.) |
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reader : str, optional |
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The backend package used for parsing. Default is :code:`ase`, |
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to use csd-python-api change to :code:`ccdc`. The ccdc reader should |
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be able to read any format accepted by :class:`ccdc.io.EntryReader`, |
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though only cifs have been tested. |
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remove_hydrogens : bool, optional |
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Remove Hydrogens from the crystal. |
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disorder : str, optional |
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Controls how disordered structures are handled. Default is ``skip`` which skips any crystal |
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with disorder, since disorder conflicts with the periodic set model. To read disordered |
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structures anyway, choose either :code:`ordered_sites` to remove sites with disorder or |
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:code:`all_sites` include all sites regardless. |
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heaviest_component : bool, optional |
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csd-python-api only. Removes all but the heaviest molecule in the asymmeric unit, |
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intended for removing solvents. |
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show_warnings : bool, optional |
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Controls whether warnings that arise during reading are printed. |
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Yields |
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------ |
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:class:`.periodicset.PeriodicSet` |
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Represents the crystal as a periodic set, consisting of a finite set of points (motif) |
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and lattice (unit cell). Contains other useful data, e.g. the crystal's name and |
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information about the asymmetric unit for calculation. |
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Examples |
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-------- |
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:: |
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# Put all crystals in a .CIF in a list |
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structures = list(amd.CifReader('mycif.cif')) |
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# Can also accept path to a directory, reading all files inside |
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structures = list(amd.CifReader('path/to/folder')) |
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# Reads just one if the .CIF has just one crystal |
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periodic_set = amd.CifReader('mycif.cif').read_one() |
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# List of AMDs (k=100) of crystals in a .CIF |
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amds = [amd.AMD(periodic_set, 100) for periodic_set in amd.CifReader('mycif.cif')] |
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""" |
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def __init__( |
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self, |
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path, |
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reader='ase', |
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remove_hydrogens=False, |
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disorder='skip', |
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heaviest_component=False, |
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show_warnings=True, |
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): |
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super().__init__( |
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remove_hydrogens=remove_hydrogens, |
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disorder=disorder, |
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heaviest_component=heaviest_component, |
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show_warnings=show_warnings, |
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) |
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if reader in ('ase', 'pycodcif'): |
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if heaviest_component: |
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raise NotImplementedError('Parameter heaviest_component only implimented for reader="ccdc".') |
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extensions = {'cif'} |
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file_parser = functools.partial(ase.io.cif.parse_cif, reader=reader) |
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converter = functools.partial(cifblock_to_periodicset, |
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remove_hydrogens=remove_hydrogens, |
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disorder=disorder) |
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elif reader == 'ccdc': |
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if not _CSD_PYTHON_API_ENABLED: |
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raise ImportError("Failed to import csd-python-api; check it is installed and licensed.") |
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extensions = ccdc.io.EntryReader.known_suffixes |
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file_parser = ccdc.io.EntryReader |
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converter = functools.partial(entry_to_periodicset, |
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remove_hydrogens=remove_hydrogens, |
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disorder=disorder, |
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heaviest_component=heaviest_component) |
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else: |
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raise ValueError(f'Invalid reader {reader}.') |
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if os.path.isfile(path): |
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generator = file_parser(path) |
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elif os.path.isdir(path): |
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generator = self._generate_from_dir(path, file_parser, extensions) |
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else: |
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raise FileNotFoundError(f'No such file or directory: {path}') |
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self._generator = _map(converter, generator, self.show_warnings) |
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def _generate_from_dir(self, path, file_parser, extensions): |
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for file in os.listdir(path): |
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suff = os.path.splitext(file)[1][1:] |
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if suff.lower() in extensions: |
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yield from file_parser(os.path.join(path, file)) |
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class CSDReader(_Reader): |
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"""Read structures from the CSD with csd-python-api, yielding |
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:class:`.periodicset.PeriodicSet` s. |
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Parameters |
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---------- |
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refcodes : List[str], optional |
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List of CSD refcodes to read. If None or 'CSD', iterates over the whole CSD. |
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families : bool, optional |
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Read all entries whose refcode starts with the given strings, or 'families' |
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(e.g. giving 'DEBXIT' reads all entries starting with DEBXIT). |
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remove_hydrogens : bool, optional |
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Remove hydrogens from the crystal. |
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disorder : str, optional |
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Controls how disordered structures are handled. Default is ``skip`` which skips any crystal |
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with disorder, since disorder conflicts with the periodic set model. To read disordered |
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structures anyway, choose either :code:`ordered_sites` to remove sites with disorder or |
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:code:`all_sites` include all sites regardless. |
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heaviest_component : bool, optional |
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csd-python-api only. Removes all but the heaviest molecule in the asymmeric unit, |
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intended for removing solvents. |
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show_warnings : bool, optional |
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Controls whether warnings that arise during reading are printed. |
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Yields |
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------ |
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:class:`.periodicset.PeriodicSet` |
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Represents the crystal as a periodic set, consisting of a finite set of points (motif) |
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and lattice (unit cell). Contains other useful data, e.g. the crystal's name and |
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information about the asymmetric unit for calculation. |
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Examples |
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-------- |
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:: |
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# Put these entries in a list |
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refcodes = ['DEBXIT01', 'DEBXIT05', 'HXACAN01'] |
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structures = list(amd.CSDReader(refcodes)) |
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# Read refcode families (any whose refcode starts with strings in the list) |
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refcode_families = ['ACSALA', 'HXACAN'] |
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structures = list(amd.CSDReader(refcode_families, families=True)) |
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# Get AMDs (k=100) for crystals in these families |
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refcodes = ['ACSALA', 'HXACAN'] |
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amds = [] |
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for periodic_set in amd.CSDReader(refcodes, families=True): |
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amds.append(amd.AMD(periodic_set, 100)) |
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# Giving the reader nothing reads from the whole CSD. |
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reader = amd.CSDReader() |
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# looping over this generic reader will yield all CSD entries |
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for periodic_set in reader: |
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... |
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# or, read structures by refcode on demand |
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debxit01 = reader.entry('DEBXIT01') |
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""" |
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def __init__( |
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self, |
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refcodes=None, |
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families=False, |
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remove_hydrogens=False, |
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disorder='skip', |
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heaviest_component=False, |
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show_warnings=True, |
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): |
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super().__init__( |
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remove_hydrogens=remove_hydrogens, |
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disorder=disorder, |
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heaviest_component=heaviest_component, |
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show_warnings=show_warnings, |
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) |
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if not _CSD_PYTHON_API_ENABLED: |
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raise ImportError('Failed to import csd-python-api; check it is installed and licensed.') |
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if isinstance(refcodes, str) and refcodes.lower() == 'csd': |
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refcodes = None |
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if refcodes is None: |
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families = False |
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else: |
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refcodes = [refcodes] if isinstance(refcodes, str) else list(refcodes) |
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if families: |
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refcodes = _refcodes_from_families(refcodes) |
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283
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self._entry_reader = ccdc.io.EntryReader('CSD') |
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converter = functools.partial(entry_to_periodicset, |
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remove_hydrogens=self.remove_hydrogens, |
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286
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disorder=self.disorder, |
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287
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heaviest_component=self.heaviest_component) |
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288
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289
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generator = self._ccdc_generator(refcodes) |
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290
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self._generator = _map(converter, generator, self.show_warnings) |
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291
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292
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def entry(self, refcode: str, **kwargs) -> PeriodicSet: |
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293
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"""Read a crystal given a CSD refcode, returning a :class:`.periodicset.PeriodicSet`. |
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294
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If given kwargs, overrides the kwargs given to the Reader.""" |
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295
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296
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try: |
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297
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entry = self._entry_reader.entry(refcode) |
|
298
|
|
|
except RuntimeError: |
|
299
|
|
|
warnings.warn(f'{refcode} not found in database') |
|
300
|
|
|
|
|
301
|
|
|
kwargs_ = { |
|
302
|
|
|
'remove_hydrogens': self.remove_hydrogens, |
|
303
|
|
|
'disorder': self.disorder, |
|
304
|
|
|
'heaviest_component': self.heaviest_component |
|
305
|
|
|
} |
|
306
|
|
|
kwargs_.update(kwargs) |
|
307
|
|
|
converter = functools.partial(entry_to_periodicset, **kwargs_) |
|
308
|
|
|
|
|
309
|
|
|
if 'show_warnings' in kwargs: |
|
|
|
|
|
|
310
|
|
|
show_warnings = kwargs['show_warnings'] |
|
311
|
|
|
else: |
|
312
|
|
|
show_warnings = self.show_warnings |
|
313
|
|
|
|
|
314
|
|
|
try: |
|
315
|
|
|
periodic_set = next(iter(_map(converter, [entry], show_warnings))) |
|
316
|
|
|
except StopIteration: |
|
317
|
|
|
periodic_set = None |
|
318
|
|
|
|
|
319
|
|
|
return periodic_set |
|
320
|
|
|
|
|
321
|
|
|
def family(self, refcode_family: str, **kwargs): |
|
|
|
|
|
|
322
|
|
|
|
|
|
|
|
|
|
323
|
|
|
kwargs_ = { |
|
324
|
|
|
'remove_hydrogens': self.remove_hydrogens, |
|
325
|
|
|
'disorder': self.disorder, |
|
326
|
|
|
'heaviest_component': self.heaviest_component |
|
327
|
|
|
} |
|
328
|
|
|
kwargs_.update(kwargs) |
|
329
|
|
|
converter = functools.partial(entry_to_periodicset, **kwargs_) |
|
330
|
|
|
refcodes = _refcodes_from_families([refcode_family]) |
|
331
|
|
|
generator = self._ccdc_generator(refcodes) |
|
332
|
|
|
|
|
333
|
|
|
if 'show_warnings' in kwargs: |
|
|
|
|
|
|
334
|
|
|
show_warnings = kwargs['show_warnings'] |
|
335
|
|
|
else: |
|
336
|
|
|
show_warnings = self.show_warnings |
|
337
|
|
|
|
|
338
|
|
|
yield from _map(converter, generator, show_warnings) |
|
339
|
|
|
|
|
340
|
|
|
def _ccdc_generator(self, refcodes): |
|
341
|
|
|
"""Generates ccdc Entries from CSD refcodes.""" |
|
342
|
|
|
|
|
343
|
|
|
if refcodes is None: |
|
344
|
|
|
for entry in self._entry_reader: |
|
345
|
|
|
yield entry |
|
346
|
|
|
else: |
|
347
|
|
|
for refcode in refcodes: |
|
348
|
|
|
try: |
|
349
|
|
|
entry = self._entry_reader.entry(refcode) |
|
350
|
|
|
yield entry |
|
351
|
|
|
except RuntimeError: |
|
352
|
|
|
warnings.warn(f'{refcode} not found in database') |
|
353
|
|
|
|
|
354
|
|
|
|
|
355
|
|
|
class _ParseError(ValueError): |
|
356
|
|
|
"""Raised when an item cannot be parsed into a periodic set.""" |
|
357
|
|
|
pass |
|
|
|
|
|
|
358
|
|
|
|
|
359
|
|
|
|
|
360
|
|
|
def entry_to_periodicset( |
|
361
|
|
|
entry, |
|
362
|
|
|
remove_hydrogens=False, |
|
363
|
|
|
disorder='skip', |
|
364
|
|
|
heaviest_component=False |
|
365
|
|
|
) -> PeriodicSet: |
|
366
|
|
|
""":class:`ccdc.entry.Entry` --> :class:`amd.periodicset.PeriodicSet`. |
|
367
|
|
|
Entry is the type returned by :class:`ccdc.io.EntryReader`. |
|
368
|
|
|
|
|
369
|
|
|
Parameters |
|
370
|
|
|
---------- |
|
371
|
|
|
entry : :class:`ccdc.entry.Entry` |
|
372
|
|
|
A ccdc Entry object representing a database entry. |
|
373
|
|
|
remove_hydrogens : bool, optional |
|
374
|
|
|
Remove Hydrogens from the crystal. |
|
375
|
|
|
disorder : str, optional |
|
376
|
|
|
Controls how disordered structures are handled. Default is ``skip`` which skips any crystal |
|
|
|
|
|
|
377
|
|
|
with disorder, since disorder conflicts with the periodic set model. To read disordered |
|
|
|
|
|
|
378
|
|
|
structures anyway, choose either :code:`ordered_sites` to remove sites with disorder or |
|
|
|
|
|
|
379
|
|
|
:code:`all_sites` include all sites regardless. |
|
380
|
|
|
heaviest_component : bool, optional |
|
381
|
|
|
Removes all but the heaviest molecule in the asymmeric unit, |
|
382
|
|
|
intended for removing solvents. |
|
|
|
|
|
|
383
|
|
|
|
|
384
|
|
|
Returns |
|
385
|
|
|
------- |
|
386
|
|
|
:class:`.periodicset.PeriodicSet` |
|
387
|
|
|
Represents the crystal as a periodic set, consisting of a finite set of points (motif) |
|
388
|
|
|
and lattice (unit cell). Contains other useful data, e.g. the crystal's name and |
|
389
|
|
|
information about the asymmetric unit for calculation. |
|
390
|
|
|
|
|
391
|
|
|
Raises |
|
392
|
|
|
------ |
|
393
|
|
|
_ParseError : |
|
394
|
|
|
Raised if the structure can/should not be parsed for the following reasons: |
|
395
|
|
|
1. entry.has_3d_structure is False, |
|
396
|
|
|
2. disorder == 'skip' and any of: |
|
397
|
|
|
(a) any disorder flag is True, |
|
398
|
|
|
(b) any atom has fractional occupancy, |
|
399
|
|
|
(c) any atom's label ends with '?', |
|
400
|
|
|
3. entry.crystal.molecule.all_atoms_have_sites is False, |
|
401
|
|
|
4. a.fractional_coordinates is None for any a in entry.crystal.disordered_molecule, |
|
402
|
|
|
5. motif is empty after removing H, disordered sites or solvents. |
|
403
|
|
|
""" |
|
404
|
|
|
|
|
405
|
|
|
crystal = entry.crystal |
|
406
|
|
|
|
|
407
|
|
|
if not entry.has_3d_structure: |
|
408
|
|
|
raise _ParseError(f'{crystal.identifier} has no 3D structure') |
|
409
|
|
|
|
|
410
|
|
|
molecule = crystal.disordered_molecule |
|
411
|
|
|
|
|
412
|
|
|
if disorder == 'skip': |
|
413
|
|
|
if crystal.has_disorder or entry.has_disorder or \ |
|
414
|
|
|
any(_atom_has_disorder(a.label, a.occupancy) for a in molecule.atoms): |
|
415
|
|
|
raise _ParseError(f'{crystal.identifier} has disorder') |
|
416
|
|
|
|
|
417
|
|
|
elif disorder == 'ordered_sites': |
|
418
|
|
|
molecule.remove_atoms(a for a in molecule.atoms |
|
419
|
|
|
if _atom_has_disorder(a.label, a.occupancy)) |
|
420
|
|
|
|
|
421
|
|
|
if remove_hydrogens: |
|
422
|
|
|
molecule.remove_atoms(a for a in molecule.atoms if a.atomic_symbol in 'HD') |
|
423
|
|
|
|
|
424
|
|
|
if heaviest_component and len(molecule.components) > 1: |
|
425
|
|
|
molecule = _heaviest_component(molecule) |
|
426
|
|
|
|
|
427
|
|
|
# nonsensical results are likely if not all atoms have sites, but attempt to read anyway |
|
428
|
|
|
if any(a.fractional_coordinates is None for a in molecule.atoms): |
|
429
|
|
|
warnings.warn(f'has atoms without sites') |
|
|
|
|
|
|
430
|
|
|
molecule.remove_atoms(a for a in molecule.atoms if a.fractional_coordinates is None) |
|
431
|
|
|
# raise _ParseError(f'{crystal.identifier} has atoms without sites') |
|
432
|
|
|
|
|
433
|
|
|
if not molecule.all_atoms_have_sites: |
|
434
|
|
|
raise _ParseError(f'{crystal.identifier} has atoms without sites') |
|
435
|
|
|
|
|
436
|
|
|
crystal.molecule = molecule |
|
437
|
|
|
asym_atoms = crystal.asymmetric_unit_molecule.atoms |
|
438
|
|
|
asym_unit = np.array([tuple(a.fractional_coordinates) for a in asym_atoms]) |
|
439
|
|
|
asym_unit = np.mod(asym_unit, 1) |
|
440
|
|
|
asym_types = [a.atomic_number for a in asym_atoms] |
|
441
|
|
|
cell = cellpar_to_cell(*crystal.cell_lengths, *crystal.cell_angles) |
|
442
|
|
|
|
|
443
|
|
|
sitesym = crystal.symmetry_operators |
|
444
|
|
|
if not sitesym: |
|
445
|
|
|
sitesym = ['x,y,z'] |
|
446
|
|
|
|
|
447
|
|
|
if disorder != 'all_sites': |
|
448
|
|
|
keep_sites = _unique_sites(asym_unit) |
|
449
|
|
|
if not np.all(keep_sites): |
|
450
|
|
|
warnings.warn(f'may have overlapping sites; duplicates will be removed') |
|
|
|
|
|
|
451
|
|
|
asym_unit = asym_unit[keep_sites] |
|
452
|
|
|
asym_types = [sym for sym, keep in zip(asym_types, keep_sites) if keep] |
|
453
|
|
|
|
|
454
|
|
|
if asym_unit.shape[0] == 0: |
|
455
|
|
|
raise _ParseError(f'{crystal.identifier} has no valid sites') |
|
456
|
|
|
|
|
457
|
|
|
frac_motif, asym_inds, multiplicities, inverses = _expand_asym_unit(asym_unit, sitesym) |
|
458
|
|
|
full_types = np.array([asym_types[i] for i in inverses]) |
|
459
|
|
|
motif = frac_motif @ cell |
|
460
|
|
|
|
|
461
|
|
|
kwargs = { |
|
462
|
|
|
'name': crystal.identifier, |
|
463
|
|
|
'asymmetric_unit': asym_inds, |
|
464
|
|
|
'wyckoff_multiplicities': multiplicities, |
|
465
|
|
|
'types': full_types |
|
466
|
|
|
} |
|
467
|
|
|
|
|
468
|
|
|
return PeriodicSet(motif, cell, **kwargs) |
|
469
|
|
|
|
|
470
|
|
|
|
|
471
|
|
|
def cifblock_to_periodicset( |
|
472
|
|
|
block, |
|
473
|
|
|
remove_hydrogens=False, |
|
474
|
|
|
disorder='skip' |
|
475
|
|
|
) -> PeriodicSet: |
|
476
|
|
|
""":class:`ase.io.cif.CIFBlock` --> :class:`amd.periodicset.PeriodicSet`. |
|
|
|
|
|
|
477
|
|
|
CIFBlock is the type returned by :class:`ase.io.cif.parse_cif`. |
|
478
|
|
|
|
|
479
|
|
|
Parameters |
|
480
|
|
|
---------- |
|
481
|
|
|
block : :class:`ase.io.cif.CIFBlock` |
|
482
|
|
|
An ase CIFBlock object representing a crystal. |
|
483
|
|
|
remove_hydrogens : bool, optional |
|
484
|
|
|
Remove Hydrogens from the crystal. |
|
485
|
|
|
disorder : str, optional |
|
486
|
|
|
Controls how disordered structures are handled. Default is ``skip`` which skips any crystal |
|
|
|
|
|
|
487
|
|
|
with disorder, since disorder conflicts with the periodic set model. To read disordered |
|
|
|
|
|
|
488
|
|
|
structures anyway, choose either :code:`ordered_sites` to remove sites with disorder or |
|
|
|
|
|
|
489
|
|
|
:code:`all_sites` include all sites regardless. |
|
490
|
|
|
|
|
491
|
|
|
Returns |
|
492
|
|
|
------- |
|
493
|
|
|
:class:`.periodicset.PeriodicSet` |
|
494
|
|
|
Represents the crystal as a periodic set, consisting of a finite set of points (motif) |
|
495
|
|
|
and lattice (unit cell). Contains other useful data, e.g. the crystal's name and |
|
496
|
|
|
information about the asymmetric unit for calculation. |
|
497
|
|
|
|
|
498
|
|
|
Raises |
|
499
|
|
|
------ |
|
500
|
|
|
_ParseError |
|
501
|
|
|
Raised if the structure can/should not be parsed for the following reasons: |
|
502
|
|
|
1. no sites found or motif is empty after removing H or disordered sites, |
|
503
|
|
|
2. a site has missing coordinates, |
|
504
|
|
|
3. disorder == 'skip' and any of: |
|
505
|
|
|
(a) any atom has fractional occupancy, |
|
506
|
|
|
(b) any atom's label ends with '?'. |
|
507
|
|
|
""" |
|
508
|
|
|
|
|
509
|
|
|
cell = block.get_cell().array |
|
510
|
|
|
|
|
511
|
|
|
# asymmetric unit fractional coords |
|
512
|
|
|
asym_unit = [block.get(name) for name in _ATOM_SITE_FRACT_TAGS] |
|
513
|
|
|
if None in asym_unit: |
|
514
|
|
|
asym_motif = [block.get(name) for name in _ATOM_SITE_CARTN_TAGS] |
|
515
|
|
|
if None in asym_motif: |
|
516
|
|
|
raise _ParseError(f'{block.name} has no sites') |
|
517
|
|
|
asym_unit = np.array(asym_motif) @ np.linalg.inv(cell) |
|
518
|
|
|
|
|
519
|
|
|
if any(None in coords for coords in asym_unit): |
|
520
|
|
|
raise _ParseError(f'{block.name} has atoms without sites') |
|
521
|
|
|
|
|
522
|
|
|
asym_unit = np.mod(np.array(asym_unit).T, 1) |
|
523
|
|
|
|
|
524
|
|
|
try: |
|
525
|
|
|
asym_types = [ase.data.atomic_numbers[s] for s in block.get_symbols()] |
|
526
|
|
|
except ase.io.cif.NoStructureData as _: |
|
527
|
|
|
asym_types = [0 for _ in range(len(asym_unit))] |
|
528
|
|
|
|
|
529
|
|
|
sitesym = ['x,y,z', ] |
|
530
|
|
|
for tag in _SYMOP_TAGS: |
|
531
|
|
|
if tag in block: |
|
532
|
|
|
sitesym = block[tag] |
|
533
|
|
|
break |
|
534
|
|
|
if isinstance(sitesym, str): |
|
535
|
|
|
sitesym = [sitesym] |
|
536
|
|
|
|
|
537
|
|
|
remove_sites = [] |
|
538
|
|
|
|
|
539
|
|
|
occupancies = block.get('_atom_site_occupancy') |
|
540
|
|
|
labels = block.get('_atom_site_label') |
|
541
|
|
|
if occupancies is not None: |
|
542
|
|
|
if disorder == 'skip': |
|
543
|
|
|
if any(_atom_has_disorder(lab, occ) for lab, occ in zip(labels, occupancies)): |
|
544
|
|
|
raise _ParseError(f'{block.name} has disorder') |
|
545
|
|
|
elif disorder == 'ordered_sites': |
|
546
|
|
|
remove_sites.extend( |
|
547
|
|
|
(i for i, (lab, occ) in enumerate(zip(labels, occupancies)) |
|
|
|
|
|
|
548
|
|
|
if _atom_has_disorder(lab, occ))) |
|
549
|
|
|
|
|
550
|
|
|
if remove_hydrogens: |
|
551
|
|
|
remove_sites.extend((i for i, num in enumerate(asym_types) if num == 1)) |
|
552
|
|
|
|
|
553
|
|
|
asym_unit = np.delete(asym_unit, remove_sites, axis=0) |
|
554
|
|
|
asym_types = [s for i, s in enumerate(asym_types) if i not in remove_sites] |
|
555
|
|
|
|
|
556
|
|
|
if disorder != 'all_sites': |
|
557
|
|
|
keep_sites = _unique_sites(asym_unit) |
|
558
|
|
|
if not np.all(keep_sites): |
|
559
|
|
|
warnings.warn(f'may have overlapping sites; duplicates will be removed') |
|
|
|
|
|
|
560
|
|
|
asym_unit = asym_unit[keep_sites] |
|
561
|
|
|
asym_types = [sym for sym, keep in zip(asym_types, keep_sites) if keep] |
|
562
|
|
|
|
|
563
|
|
|
if asym_unit.shape[0] == 0: |
|
564
|
|
|
raise _ParseError(f'{block.name} has no valid sites') |
|
565
|
|
|
|
|
566
|
|
|
frac_motif, asym_inds, multiplicities, inverses = _expand_asym_unit(asym_unit, sitesym) |
|
567
|
|
|
full_types = np.array([asym_types[i] for i in inverses]) |
|
568
|
|
|
motif = frac_motif @ cell |
|
569
|
|
|
|
|
570
|
|
|
kwargs = { |
|
571
|
|
|
'name': block.name, |
|
572
|
|
|
'asymmetric_unit': asym_inds, |
|
573
|
|
|
'wyckoff_multiplicities': multiplicities, |
|
574
|
|
|
'types': full_types |
|
575
|
|
|
} |
|
576
|
|
|
|
|
577
|
|
|
return PeriodicSet(motif, cell, **kwargs) |
|
578
|
|
|
|
|
579
|
|
|
|
|
580
|
|
|
def _expand_asym_unit( |
|
581
|
|
|
asym_unit: np.ndarray, |
|
582
|
|
|
sitesym: Sequence[str] |
|
583
|
|
|
) -> Tuple[np.ndarray, ...]: |
|
584
|
|
|
""" |
|
585
|
|
|
Asymmetric unit's fractional coords + site symmetries (as strings) |
|
586
|
|
|
--> |
|
587
|
|
|
fractional motif, asymmetric unit indices, multiplicities and inverses. |
|
588
|
|
|
""" |
|
589
|
|
|
|
|
590
|
|
|
rotations, translations = parse_sitesym(sitesym) |
|
591
|
|
|
all_sites = [] |
|
592
|
|
|
asym_inds = [0] |
|
593
|
|
|
multiplicities = [] |
|
594
|
|
|
inverses = [] |
|
595
|
|
|
|
|
596
|
|
|
for inv, site in enumerate(asym_unit): |
|
597
|
|
|
multiplicity = 0 |
|
598
|
|
|
|
|
599
|
|
|
for rot, trans in zip(rotations, translations): |
|
600
|
|
|
site_ = np.mod(np.dot(rot, site) + trans, 1) |
|
601
|
|
|
|
|
602
|
|
|
if not all_sites: |
|
603
|
|
|
all_sites.append(site_) |
|
604
|
|
|
inverses.append(inv) |
|
605
|
|
|
multiplicity += 1 |
|
606
|
|
|
continue |
|
607
|
|
|
|
|
608
|
|
|
# check if site_ overlaps with existing sites |
|
609
|
|
|
diffs1 = np.abs(site_ - all_sites) |
|
610
|
|
|
diffs2 = np.abs(diffs1 - 1) |
|
611
|
|
|
mask = np.all((diffs1 <= _EQUIV_SITE_TOL) | (diffs2 <= _EQUIV_SITE_TOL), axis=-1) |
|
612
|
|
|
|
|
613
|
|
|
if np.any(mask): |
|
614
|
|
|
where_equal = np.argwhere(mask).flatten() |
|
615
|
|
|
for ind in where_equal: |
|
616
|
|
|
if inverses[ind] == inv: |
|
617
|
|
|
pass |
|
618
|
|
|
else: |
|
619
|
|
|
warnings.warn(f'has equivalent sites at positions {inverses[ind]}, {inv}') |
|
620
|
|
|
else: |
|
621
|
|
|
all_sites.append(site_) |
|
622
|
|
|
inverses.append(inv) |
|
623
|
|
|
multiplicity += 1 |
|
624
|
|
|
|
|
625
|
|
|
if multiplicity > 0: |
|
626
|
|
|
multiplicities.append(multiplicity) |
|
627
|
|
|
asym_inds.append(len(all_sites)) |
|
628
|
|
|
|
|
629
|
|
|
frac_motif = np.array(all_sites) |
|
630
|
|
|
asym_inds = np.array(asym_inds[:-1]) |
|
631
|
|
|
multiplicities = np.array(multiplicities) |
|
632
|
|
|
return frac_motif, asym_inds, multiplicities, inverses |
|
633
|
|
|
|
|
634
|
|
|
|
|
635
|
|
|
def _atom_has_disorder(label, occupancy): |
|
636
|
|
|
"""Return True if label ends with ? or occupancy < 1.""" |
|
637
|
|
|
return label.endswith('?') or (np.isscalar(occupancy) and occupancy < 1) |
|
638
|
|
|
|
|
639
|
|
|
|
|
640
|
|
|
@numba.njit() |
|
641
|
|
|
def _unique_sites(asym_unit): |
|
642
|
|
|
site_diffs1 = np.abs(np.expand_dims(asym_unit, 1) - asym_unit) |
|
643
|
|
|
site_diffs2 = np.abs(site_diffs1 - 1) |
|
644
|
|
|
sites_neq_mask = np.logical_and((site_diffs1 > _EQUIV_SITE_TOL), |
|
|
|
|
|
|
645
|
|
|
(site_diffs2 > _EQUIV_SITE_TOL)) |
|
646
|
|
|
overlapping = np.triu(sites_neq_mask.sum(axis=-1) == 0, 1) |
|
647
|
|
|
return overlapping.sum(axis=0) == 0 |
|
648
|
|
|
|
|
649
|
|
|
|
|
650
|
|
|
def _heaviest_component(molecule): |
|
651
|
|
|
"""Heaviest component (removes all but the heaviest component of the asym unit). |
|
652
|
|
|
Intended for removing solvents. Probably doesn't play well with disorder""" |
|
653
|
|
|
component_weights = [] |
|
654
|
|
|
for component in molecule.components: |
|
655
|
|
|
weight = 0 |
|
656
|
|
|
for a in component.atoms: |
|
657
|
|
|
if isinstance(a.atomic_weight, (float, int)): |
|
658
|
|
|
if isinstance(a.occupancy, (float, int)): |
|
659
|
|
|
weight += a.occupancy * a.atomic_weight |
|
660
|
|
|
else: |
|
661
|
|
|
weight += a.atomic_weight |
|
662
|
|
|
component_weights.append(weight) |
|
663
|
|
|
largest_component_ind = np.argmax(np.array(component_weights)) |
|
664
|
|
|
molecule = molecule.components[largest_component_ind] |
|
665
|
|
|
return molecule |
|
666
|
|
|
|
|
667
|
|
|
|
|
668
|
|
|
def _refcodes_from_families(refcode_families): |
|
669
|
|
|
"""List of strings --> all CSD refcodes starting with one of the strings. |
|
670
|
|
|
Intended to be passed a list of families and return all refcodes in them.""" |
|
671
|
|
|
all_refcodes = [] |
|
672
|
|
|
for refcode in refcode_families: |
|
673
|
|
|
query = ccdc.search.TextNumericSearch() |
|
674
|
|
|
query.add_identifier(refcode) |
|
675
|
|
|
hits = [hit.identifier for hit in query.search()] |
|
676
|
|
|
all_refcodes.extend(hits) |
|
677
|
|
|
|
|
678
|
|
|
# filter to unique refcodes |
|
679
|
|
|
seen = set() |
|
680
|
|
|
seen_add = seen.add |
|
681
|
|
|
refcodes = [ |
|
682
|
|
|
refcode for refcode in all_refcodes |
|
683
|
|
|
if not (refcode in seen or seen_add(refcode))] |
|
684
|
|
|
|
|
685
|
|
|
return refcodes |
|
686
|
|
|
|
|
687
|
|
|
|
|
688
|
|
|
def _map(func: Callable, iterable: Iterable, show_warnings: bool): |
|
689
|
|
|
"""Iterates over iterable, passing items through func and yielding the result. |
|
|
|
|
|
|
690
|
|
|
Catches _ParseError and warnings, optionally printing them. |
|
691
|
|
|
""" |
|
692
|
|
|
|
|
693
|
|
|
if not show_warnings: |
|
694
|
|
|
warnings.simplefilter('ignore') |
|
695
|
|
|
|
|
696
|
|
|
for item in iterable: |
|
697
|
|
|
|
|
698
|
|
|
with warnings.catch_warnings(record=True) as warning_msgs: |
|
699
|
|
|
|
|
700
|
|
|
parse_failed = False |
|
701
|
|
|
try: |
|
702
|
|
|
periodic_set = func(item) |
|
703
|
|
|
except _ParseError as err: |
|
704
|
|
|
parse_failed = str(err) |
|
705
|
|
|
|
|
706
|
|
|
if parse_failed: |
|
707
|
|
|
warnings.warn(parse_failed) |
|
708
|
|
|
continue |
|
709
|
|
|
|
|
710
|
|
|
for warning in warning_msgs: |
|
711
|
|
|
msg = f'{periodic_set.name} {warning.message}' |
|
712
|
|
|
warnings.warn(msg, category=warning.category) |
|
713
|
|
|
|
|
714
|
|
|
yield periodic_set |
|
715
|
|
|
|