amd.io.CifReader._generate_from_dir() - Code Metrics - Inspection of "Revert "1.3.2"" - dwiddo/average-minimum-distance - Measure and Improve Code Quality continuously with Scrutinizer

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by Daniel
created 2022-09-01 14:24 UTC
amd.io.CifReader._generate_from_dir() A

↳ Parent: amd.io
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"""Tools for reading crystals from files, or from the CSD with ``csd-python-api``. 

The readers return :class:`.periodicset.PeriodicSet` objects representing the 

crystal which can be passed to :func:`.calculate.AMD` and :func:`.calculate.PDD` 

to get their invariants.
"""

import os
import functools
import warnings
from typing import Callable, Iterable, Sequence, Tuple

import numpy as np
import numba
import ase.io.cif
import ase.data
from ase.spacegroup.spacegroup import parse_sitesym

from .utils import cellpar_to_cell
from .periodicset import PeriodicSet

try:
    import ccdc.io
    import ccdc.search
    _CSD_PYTHON_API_ENABLED = True
except (ImportError, RuntimeError) as _:
    _CSD_PYTHON_API_ENABLED = False

def _custom_warning(message, category, filename, lineno, *args, **kwargs):

    return f'{category.__name__}: {message}\n'

warnings.formatwarning = _custom_warning

_EQUIV_SITE_TOL = 1e-3
_DISORDER_OPTIONS = {'skip', 'ordered_sites', 'all_sites'}
_ATOM_SITE_FRACT_TAGS = [
    '_atom_site_fract_x',
    '_atom_site_fract_y',
    '_atom_site_fract_z',
]
_ATOM_SITE_CARTN_TAGS = [
    '_atom_site_cartn_x',
    '_atom_site_cartn_y',
    '_atom_site_cartn_z',
]
_SYMOP_TAGS = [
    '_space_group_symop_operation_xyz',
    '_space_group_symop.operation_xyz',
    '_symmetry_equiv_pos_as_xyz',
]


class _Reader:

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

        if disorder not in _DISORDER_OPTIONS:
            raise ValueError(f'disorder parameter {disorder} must be one of {_DISORDER_OPTIONS}')

        self.remove_hydrogens = remove_hydrogens
        self.disorder = disorder
        self.heaviest_component = heaviest_component
        self.show_warnings = show_warnings
        self._generator = []

    def __iter__(self):
        yield from self._generator

    def read_one(self):
        """Read the first, and usually the only, item."""
        try:
            return next(iter(self._generator))
        except StopIteration:
            return None


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:`.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 for parsing. Default is :code:`ase`,
        to use csd-python-api change to :code:`ccdc`. 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 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 sites with disorder or 

        :code:`all_sites` include all sites regardless.
    heaviest_component : bool, optional
        csd-python-api only. Removes all but the heaviest molecule in the asymmeric unit,
        intended for removing solvents. 

    show_warnings : bool, optional
        Controls whether warnings that arise during reading are printed.

    Yields
    ------
    :class:`.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 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_one()

            # 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,
            show_warnings=True,
    ):

        super().__init__(
            remove_hydrogens=remove_hydrogens,
            disorder=disorder,
            heaviest_component=heaviest_component,
            show_warnings=show_warnings,
        )

        if reader in ('ase', 'pycodcif'):
            if heaviest_component:
                raise NotImplementedError('Parameter heaviest_component only implimented for reader="ccdc".')

            extensions = {'cif'}
            file_parser = functools.partial(ase.io.cif.parse_cif, reader=reader)
            converter = functools.partial(cifblock_to_periodicset,
                                          remove_hydrogens=remove_hydrogens,
                                          disorder=disorder)

        elif reader == 'ccdc':
            if not _CSD_PYTHON_API_ENABLED:
                raise ImportError("Failed to import csd-python-api; check it is installed and licensed.")
            extensions = ccdc.io.EntryReader.known_suffixes
            file_parser = ccdc.io.EntryReader
            converter = functools.partial(entry_to_periodicset,
                                          remove_hydrogens=remove_hydrogens,
                                          disorder=disorder,
                                          heaviest_component=heaviest_component)

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

        if os.path.isfile(path):
            generator = file_parser(path)
        elif os.path.isdir(path):
            generator = self._generate_from_dir(path, file_parser, extensions)
        else:
            raise FileNotFoundError(f'No such file or directory: {path}')

        self._generator = _map(converter, generator, self.show_warnings)

    def _generate_from_dir(self, path, file_parser, extensions):
class Foo:
    def some_method(self, x, y):
        return x + y;
        for file in os.listdir(path):
            suff = os.path.splitext(file)[1][1:]
            if suff.lower() in extensions:
                yield from file_parser(os.path.join(path, file))


class CSDReader(_Reader):
    """Read structures from the CSD with csd-python-api, yielding 

    :class:`.periodicset.PeriodicSet` s.

    Parameters
    ----------
    refcodes : List[str], optional
        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 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 sites with disorder or 

        :code:`all_sites` include all sites regardless.
    heaviest_component : bool, optional
        csd-python-api only. Removes all but the heaviest molecule in the asymmeric unit,
        intended for removing solvents. 

    show_warnings : bool, optional
        Controls whether warnings that arise during reading are printed.

    Yields
    ------
    :class:`.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.
            reader = amd.CSDReader()
            

            # looping over this generic reader will yield all CSD entries
            for periodic_set in reader:
                ...
            

            # or, read structures by refcode on demand
            debxit01 = reader.entry('DEBXIT01')
    """

    def __init__(

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

        super().__init__(
            remove_hydrogens=remove_hydrogens,
            disorder=disorder,
            heaviest_component=heaviest_component,
            show_warnings=show_warnings,
        )

        if not _CSD_PYTHON_API_ENABLED:
            raise ImportError('Failed to import csd-python-api; check it is installed and licensed.')

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

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

        if families:
            refcodes = _refcodes_from_families(refcodes)

        self._entry_reader = ccdc.io.EntryReader('CSD')
        converter = functools.partial(entry_to_periodicset,
                                      remove_hydrogens=self.remove_hydrogens,
                                      disorder=self.disorder,
                                      heaviest_component=self.heaviest_component)

        generator = self._ccdc_generator(refcodes)
        self._generator = _map(converter, generator, self.show_warnings)

    def entry(self, refcode: str, **kwargs) -> PeriodicSet:
        """Read a crystal given a CSD refcode, returning a :class:`.periodicset.PeriodicSet`.
        If given kwargs, overrides the kwargs given to the Reader."""

        try:
            entry = self._entry_reader.entry(refcode)
        except RuntimeError:
            warnings.warn(f'{refcode} not found in database')

        kwargs_ = {
            'remove_hydrogens': self.remove_hydrogens,
            'disorder': self.disorder,
            'heaviest_component': self.heaviest_component
        }
        kwargs_.update(kwargs)
        converter = functools.partial(entry_to_periodicset, **kwargs_)

        if 'show_warnings' in kwargs:

            show_warnings = kwargs['show_warnings']
        else:
            show_warnings = self.show_warnings

        try:
            periodic_set = next(iter(_map(converter, [entry], show_warnings)))
        except StopIteration:
            periodic_set = None

        return periodic_set

    def family(self, refcode_family: str, **kwargs):

        

        kwargs_ = {
            'remove_hydrogens': self.remove_hydrogens,
            'disorder': self.disorder,
            'heaviest_component': self.heaviest_component
        }
        kwargs_.update(kwargs)
        converter = functools.partial(entry_to_periodicset, **kwargs_)
        refcodes = _refcodes_from_families([refcode_family])
        generator = self._ccdc_generator(refcodes)

        if 'show_warnings' in kwargs:

            show_warnings = kwargs['show_warnings']
        else:
            show_warnings = self.show_warnings

        yield from _map(converter, generator, show_warnings)

    def _ccdc_generator(self, refcodes):
        """Generates ccdc Entries from CSD refcodes."""

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


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



def entry_to_periodicset(
        entry,
        remove_hydrogens=False,
        disorder='skip',
        heaviest_component=False
) -> PeriodicSet:
    """:class:`ccdc.entry.Entry` --> :class:`amd.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 sites with disorder or 

        :code:`all_sites` include all sites regardless.
    heaviest_component : bool, optional
        Removes all but the heaviest molecule in the asymmeric unit,
        intended for removing solvents. 


    Returns
    -------
    :class:`.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. entry.has_3d_structure is False,
        2. disorder == 'skip' and any of:
            (a) any disorder flag is True,
            (b) any atom has fractional occupancy,
            (c) any atom's label ends with '?',
        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. motif is empty after removing H, disordered sites or solvents.
    """

    crystal = entry.crystal

    if not entry.has_3d_structure:
        raise _ParseError(f'{crystal.identifier} has no 3D structure')

    molecule = crystal.disordered_molecule

    if disorder == 'skip':
        if crystal.has_disorder or entry.has_disorder or \
            any(_atom_has_disorder(a.label, a.occupancy) for a in molecule.atoms):
            raise _ParseError(f'{crystal.identifier} has disorder')

    elif disorder == 'ordered_sites':
        molecule.remove_atoms(a for a in molecule.atoms
                              if _atom_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(molecule)

    # nonsensical results are likely if not all atoms have sites, but attempt to read anyway
    if any(a.fractional_coordinates is None for a in molecule.atoms):
        warnings.warn(f'has atoms without sites')

        molecule.remove_atoms(a for a in molecule.atoms if a.fractional_coordinates is None)
        # raise _ParseError(f'{crystal.identifier} has atoms without sites')

    if not molecule.all_atoms_have_sites:
        raise _ParseError(f'{crystal.identifier} has atoms without sites')

    crystal.molecule = molecule
    asym_atoms = crystal.asymmetric_unit_molecule.atoms
    asym_unit = np.array([tuple(a.fractional_coordinates) for a in asym_atoms])
    asym_unit = np.mod(asym_unit, 1)
    asym_types = [a.atomic_number for a in asym_atoms]
    cell = cellpar_to_cell(*crystal.cell_lengths, *crystal.cell_angles)

    sitesym = crystal.symmetry_operators
    if not sitesym:
        sitesym = ['x,y,z']

    if disorder != 'all_sites':
        keep_sites = _unique_sites(asym_unit)
        if not np.all(keep_sites):
            warnings.warn(f'may have overlapping sites; duplicates will be removed')

        asym_unit = asym_unit[keep_sites]
        asym_types = [sym for sym, keep in zip(asym_types, keep_sites) if keep]

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

    frac_motif, asym_inds, multiplicities, inverses = _expand_asym_unit(asym_unit, sitesym)
    full_types = np.array([asym_types[i] for i in inverses])
    motif = frac_motif @ cell

    kwargs = {
        'name': crystal.identifier,
        'asymmetric_unit': asym_inds,
        'wyckoff_multiplicities': multiplicities,
        'types': full_types
    }

    return PeriodicSet(motif, cell, **kwargs)


def cifblock_to_periodicset(
        block,
        remove_hydrogens=False,
        disorder='skip'
) -> PeriodicSet:
    """:class:`ase.io.cif.CIFBlock` --> :class:`amd.periodicset.PeriodicSet`. 

    CIFBlock is the type returned by :class:`ase.io.cif.parse_cif`.

    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 sites with disorder or 

        :code:`all_sites` include all sites regardless.

    Returns
    -------
    :class:`.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 H or disordered sites,
        2. a site has missing coordinates,
        3. disorder == 'skip' and any of:
            (a) any atom has fractional occupancy,
            (b) any atom's label ends with '?'.
    """

    cell = block.get_cell().array

    # asymmetric unit fractional coords
    asym_unit = [block.get(name) for name in _ATOM_SITE_FRACT_TAGS]
    if None in asym_unit:
        asym_motif = [block.get(name) for name in _ATOM_SITE_CARTN_TAGS]
        if None in asym_motif:
            raise _ParseError(f'{block.name} has no sites')
        asym_unit = np.array(asym_motif) @ np.linalg.inv(cell)

    if any(None in coords for coords in asym_unit):
        raise _ParseError(f'{block.name} has atoms without sites')

    asym_unit = np.mod(np.array(asym_unit).T, 1)

    try:
        asym_types = [ase.data.atomic_numbers[s] for s in block.get_symbols()]
    except ase.io.cif.NoStructureData as _:
        asym_types = [0 for _ in range(len(asym_unit))]

    sitesym = ['x,y,z', ]
    for tag in _SYMOP_TAGS:
        if tag in block:
            sitesym = block[tag]
            break
    if isinstance(sitesym, str):
        sitesym = [sitesym]

    remove_sites = []

    occupancies = block.get('_atom_site_occupancy')
    labels = block.get('_atom_site_label')
    if occupancies is not None:
        if disorder == 'skip':
            if any(_atom_has_disorder(lab, occ) for lab, occ in zip(labels, occupancies)):
                raise _ParseError(f'{block.name} has disorder')
        elif disorder == 'ordered_sites':
            remove_sites.extend(
                (i for i, (lab, occ) in enumerate(zip(labels, occupancies))

                 if _atom_has_disorder(lab, occ)))

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

    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 disorder != 'all_sites':
        keep_sites = _unique_sites(asym_unit)
        if not np.all(keep_sites):
            warnings.warn(f'may have overlapping sites; duplicates will be removed')

        asym_unit = asym_unit[keep_sites]
        asym_types = [sym for sym, keep in zip(asym_types, keep_sites) if keep]

    if asym_unit.shape[0] == 0:
        raise _ParseError(f'{block.name} has no valid sites')

    frac_motif, asym_inds, multiplicities, inverses = _expand_asym_unit(asym_unit, sitesym)
    full_types = np.array([asym_types[i] for i in inverses])
    motif = frac_motif @ cell

    kwargs = {
        'name': block.name,
        'asymmetric_unit': asym_inds,
        'wyckoff_multiplicities': multiplicities,
        'types': full_types
    }

    return PeriodicSet(motif, cell, **kwargs)


def _expand_asym_unit(
        asym_unit: np.ndarray,
        sitesym: Sequence[str]
) -> Tuple[np.ndarray, ...]:
    """
    Asymmetric unit's fractional coords + site symmetries (as strings)
    -->
    fractional motif, asymmetric unit indices, multiplicities and inverses.
    """

    rotations, translations = parse_sitesym(sitesym)
    all_sites = []
    asym_inds = [0]
    multiplicities = []
    inverses = []

    for inv, site in enumerate(asym_unit):
        multiplicity = 0

        for rot, trans in zip(rotations, translations):
            site_ = np.mod(np.dot(rot, site) + trans, 1)

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

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

            if np.any(mask):
                where_equal = np.argwhere(mask).flatten()
                for ind in where_equal:
                    if inverses[ind] == inv:
                        pass
                    else:
                        warnings.warn(f'has equivalent sites at positions {inverses[ind]}, {inv}')
            else:
                all_sites.append(site_)
                inverses.append(inv)
                multiplicity += 1

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

    frac_motif = np.array(all_sites)
    asym_inds = np.array(asym_inds[:-1])
    multiplicities = np.array(multiplicities)
    return frac_motif, asym_inds, multiplicities, inverses


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


@numba.njit()
def _unique_sites(asym_unit):
    site_diffs1 = np.abs(np.expand_dims(asym_unit, 1) - asym_unit)
    site_diffs2 = np.abs(site_diffs1 - 1)
    sites_neq_mask = np.logical_and((site_diffs1 > _EQUIV_SITE_TOL), 

                                    (site_diffs2 > _EQUIV_SITE_TOL))
    overlapping = np.triu(sites_neq_mask.sum(axis=-1) == 0, 1)
    return overlapping.sum(axis=0) == 0


def _heaviest_component(molecule):
    """Heaviest component (removes all but the heaviest component of the asym unit).
    Intended for removing solvents. Probably doesn't play well with disorder"""
    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 _refcodes_from_families(refcode_families):
    """List of strings --> all CSD refcodes starting with one of the strings.
    Intended to be passed a list of families and return all refcodes in them."""
    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


def _map(func: Callable, iterable: Iterable, show_warnings: bool):
    """Iterates over iterable, passing items through func and yielding the result. 

    Catches _ParseError and warnings, optionally printing them.
    """

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

    for item in iterable:

        with warnings.catch_warnings(record=True) as warning_msgs:

            parse_failed = False
            try:
                periodic_set = func(item)
            except _ParseError as err:
                parse_failed = str(err)

        if parse_failed:
            warnings.warn(parse_failed)
            continue

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

        yield periodic_set

dwiddo / average-minimum-distance

Push — master ( 6f99a2...0038b7 )

amd.io.CifReader._generate_from_dir() A

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