biotite 1.1.0__cp313-cp313-win_amd64.whl

biotite/structure/io/pdbx/convert.py

@@ -0,0 +1,1745 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.structure.io.pdbx"
+__author__ = "Fabrice Allain, Patrick Kunzmann"
+__all__ = [
+    "get_sequence",
+    "get_model_count",
+    "get_structure",
+    "set_structure",
+    "get_component",
+    "set_component",
+    "list_assemblies",
+    "get_assembly",
+]
+
+import itertools
+import warnings
+import numpy as np
+from biotite.file import InvalidFileError
+from biotite.sequence.seqtypes import NucleotideSequence, ProteinSequence
+from biotite.structure.atoms import AtomArray, AtomArrayStack, repeat
+from biotite.structure.bonds import BondList, BondType, connect_via_residue_names
+from biotite.structure.box import unitcell_from_vectors, vectors_from_unitcell
+from biotite.structure.error import BadStructureError
+from biotite.structure.filter import _canonical_aa_list as canonical_aa_list
+from biotite.structure.filter import (
+    _canonical_nucleotide_list as canonical_nucleotide_list,
+)
+from biotite.structure.filter import (
+    filter_first_altloc,
+    filter_highest_occupancy_altloc,
+)
+from biotite.structure.io.pdbx.bcif import (
+    BinaryCIFBlock,
+    BinaryCIFColumn,
+    BinaryCIFFile,
+)
+from biotite.structure.io.pdbx.cif import CIFBlock, CIFFile
+from biotite.structure.io.pdbx.component import MaskValue
+from biotite.structure.io.pdbx.encoding import StringArrayEncoding
+from biotite.structure.residues import (
+    get_residue_count,
+    get_residue_positions,
+    get_residue_starts_for,
+)
+from biotite.structure.util import matrix_rotate
+
+# Bond types in `struct_conn` category that refer to covalent bonds
+PDBX_BOND_TYPE_ID_TO_TYPE = {
+    # Although a covalent bond, could in theory have a higher bond order,
+    # practically inter-residue bonds are always single
+    "covale": BondType.SINGLE,
+    "covale_base": BondType.SINGLE,
+    "covale_phosphate": BondType.SINGLE,
+    "covale_sugar": BondType.SINGLE,
+    "disulf": BondType.SINGLE,
+    "modres": BondType.SINGLE,
+    "modres_link": BondType.SINGLE,
+    "metalc": BondType.COORDINATION,
+}
+PDBX_BOND_TYPE_TO_TYPE_ID = {
+    BondType.ANY: "covale",
+    BondType.SINGLE: "covale",
+    BondType.DOUBLE: "covale",
+    BondType.TRIPLE: "covale",
+    BondType.QUADRUPLE: "covale",
+    BondType.AROMATIC_SINGLE: "covale",
+    BondType.AROMATIC_DOUBLE: "covale",
+    BondType.AROMATIC_TRIPLE: "covale",
+    BondType.COORDINATION: "metalc",
+}
+PDBX_BOND_TYPE_TO_ORDER = {
+    BondType.SINGLE: "sing",
+    BondType.DOUBLE: "doub",
+    BondType.TRIPLE: "trip",
+    BondType.QUADRUPLE: "quad",
+    BondType.AROMATIC_SINGLE: "sing",
+    BondType.AROMATIC_DOUBLE: "doub",
+    BondType.AROMATIC_TRIPLE: "trip",
+    # These are masked later, it is merely added here to avoid a KeyError
+    BondType.ANY: "",
+    BondType.COORDINATION: "",
+}
+# Map 'chem_comp_bond' bond orders and aromaticity to 'BondType'...
+COMP_BOND_ORDER_TO_TYPE = {
+    ("SING", "N"): BondType.SINGLE,
+    ("DOUB", "N"): BondType.DOUBLE,
+    ("TRIP", "N"): BondType.TRIPLE,
+    ("QUAD", "N"): BondType.QUADRUPLE,
+    ("SING", "Y"): BondType.AROMATIC_SINGLE,
+    ("DOUB", "Y"): BondType.AROMATIC_DOUBLE,
+    ("TRIP", "Y"): BondType.AROMATIC_TRIPLE,
+}
+# ...and vice versa
+COMP_BOND_TYPE_TO_ORDER = {
+    bond_type: order for order, bond_type in COMP_BOND_ORDER_TO_TYPE.items()
+}
+CANONICAL_RESIDUE_LIST = canonical_aa_list + canonical_nucleotide_list
+
+_proteinseq_type_list = ["polypeptide(D)", "polypeptide(L)"]
+_nucleotideseq_type_list = [
+    "polydeoxyribonucleotide",
+    "polyribonucleotide",
+    "polydeoxyribonucleotide/polyribonucleotide hybrid",
+]
+_other_type_list = [
+    "cyclic-pseudo-peptide",
+    "other",
+    "peptide nucleic acid",
+    "polysaccharide(D)",
+    "polysaccharide(L)",
+]
+
+
+def _filter(category, index):
+    """
+    Reduce the ``atom_site`` category to the values for the given
+    model.
+    """
+    Category = type(category)
+    Column = Category.subcomponent_class()
+    Data = Column.subcomponent_class()
+
+    return Category(
+        {
+            key: Column(
+                Data(column.data.array[index]),
+                (Data(column.mask.array[index]) if column.mask is not None else None),
+            )
+            for key, column in category.items()
+        }
+    )
+
+
+def get_sequence(pdbx_file, data_block=None):
+    """
+    Get the protein and nucleotide sequences from the
+    ``entity_poly.pdbx_seq_one_letter_code_can`` entry.
+
+    Supported polymer types (``_entity_poly.type``) are:
+    ``'polypeptide(D)'``, ``'polypeptide(L)'``,
+    ``'polydeoxyribonucleotide'``, ``'polyribonucleotide'`` and
+    ``'polydeoxyribonucleotide/polyribonucleotide hybrid'``.
+    Uracil is converted to Thymine.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+
+    Returns
+    -------
+    sequence_dict : Dictionary of Sequences
+        Dictionary keys are derived from ``entity_poly.pdbx_strand_id``
+        (often equivalent to chain_id and atom_site.auth_asym_id
+        in most cases). Dictionary values are sequences.
+
+    Notes
+    -----
+    The ``entity_poly.pdbx_seq_one_letter_code_can`` field contains the initial
+    complete sequence. If the structure represents a truncated or spliced
+    version of this initial sequence, it will include only a subset of the
+    initial sequence. Use biotite.structure.get_residues to retrieve only
+    the residues that are represented in the structure.
+    """
+
+    block = _get_block(pdbx_file, data_block)
+    poly_category = block["entity_poly"]
+
+    seq_string = poly_category["pdbx_seq_one_letter_code_can"].as_array(str)
+    seq_type = poly_category["type"].as_array(str)
+
+    sequences = [
+        _convert_string_to_sequence(string, stype)
+        for string, stype in zip(seq_string, seq_type)
+    ]
+
+    strand_ids = poly_category["pdbx_strand_id"].as_array(str)
+    strand_ids = [strand_id.split(",") for strand_id in strand_ids]
+
+    sequence_dict = {
+        strand_id: sequence
+        for sequence, strand_ids in zip(sequences, strand_ids)
+        for strand_id in strand_ids
+        if sequence is not None
+    }
+
+    return sequence_dict
+
+
+def get_model_count(pdbx_file, data_block=None):
+    """
+    Get the number of models contained in a file.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+
+    Returns
+    -------
+    model_count : int
+        The number of models.
+    """
+    block = _get_block(pdbx_file, data_block)
+    return len(
+        _get_model_starts(block["atom_site"]["pdbx_PDB_model_num"].as_array(np.int32))
+    )
+
+
+def get_structure(
+    pdbx_file,
+    model=None,
+    data_block=None,
+    altloc="first",
+    extra_fields=None,
+    use_author_fields=True,
+    include_bonds=False,
+):
+    """
+    Create an :class:`AtomArray` or :class:`AtomArrayStack` from the
+    ``atom_site`` category in a file.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    model : int, optional
+        If this parameter is given, the function will return an
+        :class:`AtomArray` from the atoms corresponding to the given
+        model number (starting at 1).
+        Negative values are used to index models starting from the last
+        model insted of the first model.
+        If this parameter is omitted, an :class:`AtomArrayStack`
+        containing all models will be returned, even if the structure
+        contains only one model.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+    altloc : {'first', 'occupancy', 'all'}
+        This parameter defines how *altloc* IDs are handled:
+            - ``'first'`` - Use atoms that have the first *altloc* ID
+              appearing in a residue.
+            - ``'occupancy'`` - Use atoms that have the *altloc* ID
+              with the highest occupancy for a residue.
+            - ``'all'`` - Use all atoms.
+              Note that this leads to duplicate atoms.
+              When this option is chosen, the ``altloc_id`` annotation
+              array is added to the returned structure.
+    extra_fields : list of str, optional
+        The strings in the list are entry names, that are
+        additionally added as annotation arrays.
+        The annotation category name will be the same as the PDBx
+        subcategory name.
+        The array type is always `str`.
+        An exception are the special field identifiers:
+        ``'atom_id'``, ``'b_factor'``, ``'occupancy'`` and ``'charge'``.
+        These will convert the fitting subcategory into an
+        annotation array with reasonable type.
+    use_author_fields : bool, optional
+        Some fields can be read from two alternative sources,
+        for example both, ``label_seq_id`` and ``auth_seq_id`` describe
+        the ID of the residue.
+        While, the ``label_xxx`` fields can be used as official pointers
+        to other categories in the file, the ``auth_xxx``
+        fields are set by the author(s) of the structure and are
+        consistent with the corresponding values in PDB files.
+        If `use_author_fields` is true, the annotation arrays will be
+        read from the ``auth_xxx`` fields (if applicable),
+        otherwise from the the ``label_xxx`` fields.
+        If the requested field is not available, the respective other
+        field is taken as fallback.
+    include_bonds : bool, optional
+        If set to true, a :class:`BondList` will be created for the
+        resulting :class:`AtomArray` containing the bond information
+        from the file.
+        Inter-residue bonds, will be read from the ``struct_conn``
+        category.
+        Intra-residue bonds will be read from the ``chem_comp_bond``, if
+        available, otherwise they will be derived from the Chemical
+        Component Dictionary.
+
+    Returns
+    -------
+    array : AtomArray or AtomArrayStack
+        The return type depends on the `model` parameter.
+
+    Examples
+    --------
+
+    >>> import os.path
+    >>> file = CIFFile.read(os.path.join(path_to_structures, "1l2y.cif"))
+    >>> arr = get_structure(file, model=1)
+    >>> print(len(arr))
+    304
+
+    """
+    block = _get_block(pdbx_file, data_block)
+
+    extra_fields = set() if extra_fields is None else set(extra_fields)
+
+    atom_site = block.get("atom_site")
+    if atom_site is None:
+        raise InvalidFileError("Missing 'atom_site' category in file")
+
+    models = atom_site["pdbx_PDB_model_num"].as_array(np.int32)
+    model_starts = _get_model_starts(models)
+    model_count = len(model_starts)
+    atom_count = len(models)
+
+    if model is None:
+        # For a stack, the annotations are derived from the first model
+        model_atom_site = _filter_model(atom_site, model_starts, 1)
+        # Any field of the category would work here to get the length
+        model_length = model_atom_site.row_count
+        atoms = AtomArrayStack(model_count, model_length)
+
+        # Check if each model has the same amount of atoms
+        # If not, raise exception
+        if model_length * model_count != atom_count:
+            raise InvalidFileError(
+                "The models in the file have unequal "
+                "amount of atoms, give an explicit model "
+                "instead"
+            )
+
+        atoms.coord[:, :, 0] = (
+            atom_site["Cartn_x"]
+            .as_array(np.float32)
+            .reshape((model_count, model_length))
+        )
+        atoms.coord[:, :, 1] = (
+            atom_site["Cartn_y"]
+            .as_array(np.float32)
+            .reshape((model_count, model_length))
+        )
+        atoms.coord[:, :, 2] = (
+            atom_site["Cartn_z"]
+            .as_array(np.float32)
+            .reshape((model_count, model_length))
+        )
+
+        box = _get_box(block)
+        if box is not None:
+            # Duplicate same box for each model
+            atoms.box = np.repeat(box[np.newaxis, ...], model_count, axis=0)
+
+    else:
+        if model == 0:
+            raise ValueError("The model index must not be 0")
+        # Negative models mean model indexing starting from last model
+        model = model_count + model + 1 if model < 0 else model
+        if model > model_count:
+            raise ValueError(
+                f"The file has {model_count} models, "
+                f"the given model {model} does not exist"
+            )
+
+        model_atom_site = _filter_model(atom_site, model_starts, model)
+        # Any field of the category would work here to get the length
+        model_length = model_atom_site.row_count
+        atoms = AtomArray(model_length)
+
+        atoms.coord[:, 0] = model_atom_site["Cartn_x"].as_array(np.float32)
+        atoms.coord[:, 1] = model_atom_site["Cartn_y"].as_array(np.float32)
+        atoms.coord[:, 2] = model_atom_site["Cartn_z"].as_array(np.float32)
+
+        atoms.box = _get_box(block)
+
+    # The below part is the same for both, AtomArray and AtomArrayStack
+    _fill_annotations(atoms, model_atom_site, extra_fields, use_author_fields)
+    if include_bonds:
+        if "chem_comp_bond" in block:
+            try:
+                custom_bond_dict = _parse_intra_residue_bonds(block["chem_comp_bond"])
+            except KeyError:
+                warnings.warn(
+                    "The 'chem_comp_bond' category has missing columns, "
+                    "falling back to using Chemical Component Dictionary",
+                    UserWarning,
+                )
+                custom_bond_dict = None
+            bonds = connect_via_residue_names(atoms, custom_bond_dict=custom_bond_dict)
+        else:
+            bonds = connect_via_residue_names(atoms)
+        if "struct_conn" in block:
+            bonds = bonds.merge(
+                _parse_inter_residue_bonds(model_atom_site, block["struct_conn"])
+            )
+        atoms.bonds = bonds
+    atoms = _filter_altloc(atoms, model_atom_site, altloc)
+
+    return atoms
+
+
+def _get_block(pdbx_component, block_name):
+    if not isinstance(pdbx_component, (CIFBlock, BinaryCIFBlock)):
+        # Determine block
+        if block_name is None:
+            return pdbx_component.block
+        else:
+            return pdbx_component[block_name]
+    else:
+        return pdbx_component
+
+
+def _get_or_fallback(category, key, fallback_key):
+    """
+    Return column related to key in category if it exists,
+    otherwise try to get the column related to fallback key.
+    """
+    if key not in category:
+        warnings.warn(
+            f"Attribute '{key}' not found within 'atom_site' category. "
+            f"The fallback attribute '{fallback_key}' will be used instead",
+            UserWarning,
+        )
+        try:
+            return category[fallback_key]
+        except KeyError as key_exc:
+            raise InvalidFileError(
+                f"Fallback attribute '{fallback_key}' not found within "
+                "'atom_site' category"
+            ) from key_exc
+    return category[key]
+
+
+def _fill_annotations(array, atom_site, extra_fields, use_author_fields):
+    """Fill atom_site annotations in atom array or atom array stack.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        Atom array or stack which will be annotated.
+    atom_site : CIFCategory or BinaryCIFCategory
+        ``atom_site`` category with values for one model.
+    extra_fields : list of str
+        Entry names, that are additionally added as annotation arrays.
+    use_author_fields : bool
+        Define if alternate fields prefixed with ``auth_`` should be used
+        instead of ``label_``.
+    """
+
+    prefix, alt_prefix = ("auth", "label") if use_author_fields else ("label", "auth")
+
+    array.set_annotation(
+        "chain_id",
+        _get_or_fallback(
+            atom_site, f"{prefix}_asym_id", f"{alt_prefix}_asym_id"
+        ).as_array(str),
+    )
+    array.set_annotation(
+        "res_id",
+        _get_or_fallback(
+            atom_site, f"{prefix}_seq_id", f"{alt_prefix}_seq_id"
+        ).as_array(int, -1),
+    )
+    array.set_annotation("ins_code", atom_site["pdbx_PDB_ins_code"].as_array(str, ""))
+    array.set_annotation(
+        "res_name",
+        _get_or_fallback(
+            atom_site, f"{prefix}_comp_id", f"{alt_prefix}_comp_id"
+        ).as_array(str),
+    )
+    array.set_annotation("hetero", atom_site["group_PDB"].as_array(str) == "HETATM")
+    array.set_annotation(
+        "atom_name",
+        _get_or_fallback(
+            atom_site, f"{prefix}_atom_id", f"{alt_prefix}_atom_id"
+        ).as_array(str),
+    )
+    array.set_annotation("element", atom_site["type_symbol"].as_array(str))
+
+    if "atom_id" in extra_fields:
+        if "id" in atom_site:
+            array.set_annotation("atom_id", atom_site["id"].as_array(int))
+        else:
+            warnings.warn(
+                "Missing 'id' in 'atom_site' category. 'atom_id' generated automatically.",
+                UserWarning,
+            )
+            array.set_annotation("atom_id", np.arange(array.array_length()))
+        extra_fields.remove("atom_id")
+    if "b_factor" in extra_fields:
+        if "B_iso_or_equiv" in atom_site:
+            array.set_annotation(
+                "b_factor", atom_site["B_iso_or_equiv"].as_array(float)
+            )
+        else:
+            warnings.warn(
+                "Missing 'B_iso_or_equiv' in 'atom_site' category. 'b_factor' will be set to `nan`.",
+                UserWarning,
+            )
+            array.set_annotation("b_factor", np.full(array.array_length(), np.nan))
+        extra_fields.remove("b_factor")
+    if "occupancy" in extra_fields:
+        if "occupancy" in atom_site:
+            array.set_annotation("occupancy", atom_site["occupancy"].as_array(float))
+        else:
+            warnings.warn(
+                "Missing 'occupancy' in 'atom_site' category. 'occupancy' will be assumed to be 1.0",
+                UserWarning,
+            )
+            array.set_annotation(
+                "occupancy", np.ones(array.array_length(), dtype=float)
+            )
+        extra_fields.remove("occupancy")
+    if "charge" in extra_fields:
+        if "pdbx_formal_charge" in atom_site:
+            array.set_annotation(
+                "charge",
+                atom_site["pdbx_formal_charge"].as_array(
+                    int, 0
+                ),  # masked values are set to 0
+            )
+        else:
+            warnings.warn(
+                "Missing 'pdbx_formal_charge' in 'atom_site' category. 'charge' will be set to 0",
+                UserWarning,
+            )
+            array.set_annotation("charge", np.zeros(array.array_length(), dtype=int))
+        extra_fields.remove("charge")
+
+    # Handle all remaining custom fields
+    for field in extra_fields:
+        array.set_annotation(field, atom_site[field].as_array(str))
+
+
+def _parse_intra_residue_bonds(chem_comp_bond):
+    """
+    Create a :func:`connect_via_residue_names()` compatible
+    `custom_bond_dict` from the ``chem_comp_bond`` category.
+    """
+    custom_bond_dict = {}
+    for res_name, atom_1, atom_2, order, aromatic_flag in zip(
+        chem_comp_bond["comp_id"].as_array(str),
+        chem_comp_bond["atom_id_1"].as_array(str),
+        chem_comp_bond["atom_id_2"].as_array(str),
+        chem_comp_bond["value_order"].as_array(str),
+        chem_comp_bond["pdbx_aromatic_flag"].as_array(str),
+    ):
+        if res_name not in custom_bond_dict:
+            custom_bond_dict[res_name] = {}
+        bond_type = COMP_BOND_ORDER_TO_TYPE.get(
+            (order.upper(), aromatic_flag), BondType.ANY
+        )
+        custom_bond_dict[res_name][atom_1.item(), atom_2.item()] = bond_type
+    return custom_bond_dict
+
+
+def _parse_inter_residue_bonds(atom_site, struct_conn):
+    """
+    Create inter-residue bonds by parsing the ``struct_conn`` category.
+    The atom indices of each bond are found by matching the bond labels
+    to the ``atom_site`` category.
+    """
+    # Identity symmetry operation
+    IDENTITY = "1_555"
+    # Columns in 'atom_site' that should be matched by 'struct_conn'
+    COLUMNS = [
+        "label_asym_id",
+        "label_comp_id",
+        "label_seq_id",
+        "label_atom_id",
+        "label_alt_id",
+        "auth_asym_id",
+        "auth_comp_id",
+        "auth_seq_id",
+        "pdbx_PDB_ins_code",
+    ]
+
+    covale_mask = np.isin(
+        struct_conn["conn_type_id"].as_array(str),
+        list(PDBX_BOND_TYPE_ID_TO_TYPE.keys()),
+    )
+    if "ptnr1_symmetry" in struct_conn:
+        covale_mask &= struct_conn["ptnr1_symmetry"].as_array(str, IDENTITY) == IDENTITY
+    if "ptnr2_symmetry" in struct_conn:
+        covale_mask &= struct_conn["ptnr2_symmetry"].as_array(str, IDENTITY) == IDENTITY
+
+    atom_indices = [None] * 2
+    for i in range(2):
+        reference_arrays = []
+        query_arrays = []
+        for col_name in COLUMNS:
+            struct_conn_col_name = _get_struct_conn_col_name(col_name, i + 1)
+            if col_name not in atom_site or struct_conn_col_name not in struct_conn:
+                continue
+            # Ensure both arrays have the same dtype to allow comparison
+            reference = atom_site[col_name].as_array()
+            dtype = reference.dtype
+            query = struct_conn[struct_conn_col_name].as_array(dtype)
+            if np.issubdtype(reference.dtype, str):
+                # The mask value is not necessarily consistent
+                # between query and reference
+                # -> make it consistent
+                reference[reference == "?"] = "."
+                query[query == "?"] = "."
+            reference_arrays.append(reference)
+            query_arrays.append(query[covale_mask])
+        # Match the combination of 'label_asym_id', 'label_comp_id', etc.
+        # in 'atom_site' and 'struct_conn'
+        atom_indices[i] = _find_matches(query_arrays, reference_arrays)
+    atoms_indices_1 = atom_indices[0]
+    atoms_indices_2 = atom_indices[1]
+
+    # Some bonds in 'struct_conn' may not be found in 'atom_site'
+    # This is okay,
+    # as 'atom_site' might already be reduced to a single model
+    mapping_exists_mask = (atoms_indices_1 != -1) & (atoms_indices_2 != -1)
+    atoms_indices_1 = atoms_indices_1[mapping_exists_mask]
+    atoms_indices_2 = atoms_indices_2[mapping_exists_mask]
+
+    bond_type_id = struct_conn["conn_type_id"].as_array()
+    # Consecutively apply the same masks as applied to the atom indices
+    # Logical combination does not work here,
+    # as the second mask was created based on already filtered data
+    bond_type_id = bond_type_id[covale_mask][mapping_exists_mask]
+    # The type ID is always present in the dictionary,
+    # as it was used to filter the applicable bonds
+    bond_types = [PDBX_BOND_TYPE_ID_TO_TYPE[type_id] for type_id in bond_type_id]
+
+    return BondList(
+        atom_site.row_count,
+        np.stack([atoms_indices_1, atoms_indices_2, bond_types], axis=-1),
+    )
+
+
+def _find_matches(query_arrays, reference_arrays):
+    """
+    For each index in the `query_arrays` find the indices in the
+    `reference_arrays` where all query values match the reference counterpart.
+    If no match is found for a query, the corresponding index is -1.
+    """
+    match_masks_for_all_columns = np.stack(
+        [
+            query[:, np.newaxis] == reference[np.newaxis, :]
+            for query, reference in zip(query_arrays, reference_arrays)
+        ],
+        axis=-1,
+    )
+    match_masks = np.all(match_masks_for_all_columns, axis=-1)
+    query_matches, reference_matches = np.where(match_masks)
+
+    # Duplicate matches indicate that an atom from the query cannot
+    # be uniquely matched to an atom in the reference
+    unique_query_matches, counts = np.unique(query_matches, return_counts=True)
+    if np.any(counts > 1):
+        ambiguous_query = unique_query_matches[np.where(counts > 1)[0][0]]
+        raise InvalidFileError(
+            f"The covalent bond in the 'struct_conn' category at index "
+            f"{ambiguous_query} cannot be unambiguously assigned to atoms in "
+            f"the 'atom_site' category"
+        )
+
+    # -1 indicates that no match was found in the reference
+    match_indices = np.full(len(query_arrays[0]), -1, dtype=int)
+    match_indices[query_matches] = reference_matches
+    return match_indices
+
+
+def _get_struct_conn_col_name(col_name, partner):
+    """
+    For a column name in ``atom_site`` get the corresponding column name
+    in ``struct_conn``.
+    """
+    if col_name == "label_alt_id":
+        return f"pdbx_ptnr{partner}_label_alt_id"
+    elif col_name.startswith("pdbx_"):
+        # Move 'pdbx_' to front
+        return f"pdbx_ptnr{partner}_{col_name[5:]}"
+    else:
+        return f"ptnr{partner}_{col_name}"
+
+
+def _filter_altloc(array, atom_site, altloc):
+    altloc_ids = atom_site.get("label_alt_id")
+    occupancy = atom_site.get("occupancy")
+
+    # Filter altloc IDs and return
+    if altloc_ids is None:
+        return array
+    elif altloc == "occupancy" and occupancy is not None:
+        return array[
+            ...,
+            filter_highest_occupancy_altloc(
+                array, altloc_ids.as_array(str), occupancy.as_array(float)
+            ),
+        ]
+    # 'first' is also fallback if file has no occupancy information
+    elif altloc == "first":
+        return array[..., filter_first_altloc(array, altloc_ids.as_array(str))]
+    elif altloc == "all":
+        array.set_annotation("altloc_id", altloc_ids.as_array(str))
+        return array
+    else:
+        raise ValueError(f"'{altloc}' is not a valid 'altloc' option")
+
+
+def _get_model_starts(model_array):
+    """
+    Get the start index for each model in the arrays of the
+    ``atom_site`` category.
+    """
+    _, indices = np.unique(model_array, return_index=True)
+    indices.sort()
+    return indices
+
+
+def _filter_model(atom_site, model_starts, model):
+    """
+    Reduce the ``atom_site`` category to the values for the given
+    model.
+    """
+    # Append exclusive stop
+    model_starts = np.append(model_starts, [atom_site.row_count])
+    # Indexing starts at 0, but model number starts at 1
+    model_index = model - 1
+    index = slice(model_starts[model_index], model_starts[model_index + 1])
+    return _filter(atom_site, index)
+
+
+def _get_box(block):
+    cell = block.get("cell")
+    if cell is None:
+        return None
+    try:
+        len_a, len_b, len_c = [
+            float(cell[length].as_item())
+            for length in ["length_a", "length_b", "length_c"]
+        ]
+        alpha, beta, gamma = [
+            np.deg2rad(float(cell[angle].as_item()))
+            for angle in ["angle_alpha", "angle_beta", "angle_gamma"]
+        ]
+    except ValueError:
+        # 'cell_dict' has no proper unit cell values, e.g. '?'
+        return None
+    return vectors_from_unitcell(len_a, len_b, len_c, alpha, beta, gamma)
+
+
+def set_structure(
+    pdbx_file,
+    array,
+    data_block=None,
+    include_bonds=False,
+    extra_fields=[],
+):
+    """
+    Set the ``atom_site`` category with atom information from an
+    :class:`AtomArray` or :class:`AtomArrayStack`.
+
+    This will save the coordinates, the mandatory annotation categories
+    and the optional annotation categories
+    ``atom_id``, ``b_factor``, ``occupancy`` and ``charge``.
+    If the atom array (stack) contains the annotation ``'atom_id'``,
+    these values will be used for atom numbering instead of continuous
+    numbering.
+    Furthermore, inter-residue bonds will be written into the
+    ``struct_conn`` category.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    array : AtomArray or AtomArrayStack
+        The structure to be written. If a stack is given, each array in
+        the stack will be in a separate model.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+        If the file is empty, a new data block will be created.
+    include_bonds : bool, optional
+        If set to true and `array` has associated ``bonds`` , the
+        intra-residue bonds will be written into the ``chem_comp_bond``
+        category.
+        Inter-residue bonds will be written into the ``struct_conn``
+        independent of this parameter.
+    extra_fields : list of str, optional
+        List of additional fields from the ``atom_site`` category
+        that should be written into the file.
+        Default is an empty list.
+
+    Notes
+    -----
+    In some cases, the written inter-residue bonds cannot be read again
+    due to ambiguity to which atoms the bond refers.
+    This is the case, when two equal residues in the same chain have
+    the same (or a masked) `res_id`.
+
+    Examples
+    --------
+
+    >>> import os.path
+    >>> file = CIFFile()
+    >>> set_structure(file, atom_array)
+    >>> file.write(os.path.join(path_to_directory, "structure.cif"))
+
+    """
+    _check_non_empty(array)
+
+    block = _get_or_create_block(pdbx_file, data_block)
+    Category = block.subcomponent_class()
+    Column = Category.subcomponent_class()
+
+    # Fill PDBx columns from information
+    # in structures' attribute arrays as good as possible
+    atom_site = Category()
+    atom_site["group_PDB"] = np.where(array.hetero, "HETATM", "ATOM")
+    atom_site["type_symbol"] = np.copy(array.element)
+    atom_site["label_atom_id"] = np.copy(array.atom_name)
+    atom_site["label_alt_id"] = Column(
+        # AtomArrays do not store altloc atoms
+        np.full(array.array_length(), "."),
+        np.full(array.array_length(), MaskValue.INAPPLICABLE),
+    )
+    atom_site["label_comp_id"] = np.copy(array.res_name)
+    atom_site["label_asym_id"] = np.copy(array.chain_id)
+    atom_site["label_entity_id"] = _determine_entity_id(array.chain_id)
+    atom_site["label_seq_id"] = np.copy(array.res_id)
+    atom_site["pdbx_PDB_ins_code"] = Column(
+        np.copy(array.ins_code),
+        np.where(array.ins_code == "", MaskValue.INAPPLICABLE, MaskValue.PRESENT),
+    )
+    atom_site["auth_seq_id"] = atom_site["label_seq_id"]
+    atom_site["auth_comp_id"] = atom_site["label_comp_id"]
+    atom_site["auth_asym_id"] = atom_site["label_asym_id"]
+    atom_site["auth_atom_id"] = atom_site["label_atom_id"]
+
+    annot_categories = array.get_annotation_categories()
+    if "atom_id" in annot_categories:
+        atom_site["id"] = np.copy(array.atom_id)
+    if "b_factor" in annot_categories:
+        atom_site["B_iso_or_equiv"] = np.copy(array.b_factor)
+    if "occupancy" in annot_categories:
+        atom_site["occupancy"] = np.copy(array.occupancy)
+    if "charge" in annot_categories:
+        atom_site["pdbx_formal_charge"] = Column(
+            np.array([f"{c:+d}" if c != 0 else "?" for c in array.charge]),
+            np.where(array.charge == 0, MaskValue.MISSING, MaskValue.PRESENT),
+        )
+
+    # Handle all remaining custom fields
+    if len(extra_fields) > 0:
+        # ... check to avoid clashes with standard annotations
+        _standard_annotations = [
+            "hetero",
+            "element",
+            "atom_name",
+            "res_name",
+            "chain_id",
+            "res_id",
+            "ins_code",
+            "atom_id",
+            "b_factor",
+            "occupancy",
+            "charge",
+        ]
+        _reserved_annotation_names = list(atom_site.keys()) + _standard_annotations
+
+        for annot in extra_fields:
+            if annot in _reserved_annotation_names:
+                raise ValueError(
+                    f"Annotation name '{annot}' is reserved and cannot be written to as extra field. "
+                    "Please choose another name."
+                )
+            atom_site[annot] = np.copy(array.get_annotation(annot))
+
+    if array.bonds is not None:
+        struct_conn = _set_inter_residue_bonds(array, atom_site)
+        if struct_conn is not None:
+            block["struct_conn"] = struct_conn
+        if include_bonds:
+            chem_comp_bond = _set_intra_residue_bonds(array, atom_site)
+            if chem_comp_bond is not None:
+                block["chem_comp_bond"] = chem_comp_bond
+
+    # In case of a single model handle each coordinate
+    # simply like a flattened array
+    if isinstance(array, AtomArray) or (
+        isinstance(array, AtomArrayStack) and array.stack_depth() == 1
+    ):
+        # 'ravel' flattens coord without copy
+        # in case of stack with stack_depth = 1
+        atom_site["Cartn_x"] = np.copy(np.ravel(array.coord[..., 0]))
+        atom_site["Cartn_y"] = np.copy(np.ravel(array.coord[..., 1]))
+        atom_site["Cartn_z"] = np.copy(np.ravel(array.coord[..., 2]))
+        atom_site["pdbx_PDB_model_num"] = np.ones(array.array_length(), dtype=np.int32)
+    # In case of multiple models repeat annotations
+    # and use model specific coordinates
+    else:
+        atom_site = _repeat(atom_site, array.stack_depth())
+        coord = np.reshape(array.coord, (array.stack_depth() * array.array_length(), 3))
+        atom_site["Cartn_x"] = np.copy(coord[:, 0])
+        atom_site["Cartn_y"] = np.copy(coord[:, 1])
+        atom_site["Cartn_z"] = np.copy(coord[:, 2])
+        atom_site["pdbx_PDB_model_num"] = np.repeat(
+            np.arange(1, array.stack_depth() + 1, dtype=np.int32),
+            repeats=array.array_length(),
+        )
+    if "atom_id" not in annot_categories:
+        # Count from 1
+        atom_site["id"] = np.arange(1, len(atom_site["group_PDB"]) + 1)
+    block["atom_site"] = atom_site
+
+    # Write box into file
+    if array.box is not None:
+        # PDBx files can only store one box for all models
+        # -> Use first box
+        if array.box.ndim == 3:
+            box = array.box[0]
+        else:
+            box = array.box
+        len_a, len_b, len_c, alpha, beta, gamma = unitcell_from_vectors(box)
+        cell = Category()
+        cell["length_a"] = len_a
+        cell["length_b"] = len_b
+        cell["length_c"] = len_c
+        cell["angle_alpha"] = np.rad2deg(alpha)
+        cell["angle_beta"] = np.rad2deg(beta)
+        cell["angle_gamma"] = np.rad2deg(gamma)
+        block["cell"] = cell
+
+
+def _check_non_empty(array):
+    if isinstance(array, AtomArray):
+        if array.array_length() == 0:
+            raise BadStructureError("Structure must not be empty")
+    elif isinstance(array, AtomArrayStack):
+        if array.array_length() == 0 or array.stack_depth() == 0:
+            raise BadStructureError("Structure must not be empty")
+    else:
+        raise ValueError(
+            "Structure must be AtomArray or AtomArrayStack, "
+            f"but got {type(array).__name__}"
+        )
+
+
+def _get_or_create_block(pdbx_component, block_name):
+    Block = pdbx_component.subcomponent_class()
+
+    if isinstance(pdbx_component, (CIFFile, BinaryCIFFile)):
+        if block_name is None:
+            if len(pdbx_component) > 0:
+                block_name = next(iter(pdbx_component.keys()))
+            else:
+                # File is empty -> invent a new block name
+                block_name = "structure"
+
+        if block_name not in pdbx_component:
+            block = Block()
+            pdbx_component[block_name] = block
+        return pdbx_component[block_name]
+    else:
+        # Already a block
+        return pdbx_component
+
+
+def _determine_entity_id(chain_id):
+    entity_id = np.zeros(len(chain_id), dtype=int)
+    # Dictionary that translates chain_id to entity_id
+    id_translation = {}
+    id = 1
+    for i in range(len(chain_id)):
+        try:
+            entity_id[i] = id_translation[chain_id[i]]
+        except KeyError:
+            # chain_id is not in dictionary -> new entry
+            id_translation[chain_id[i]] = id
+            entity_id[i] = id_translation[chain_id[i]]
+            id += 1
+    return entity_id
+
+
+def _repeat(category, repetitions):
+    Category = type(category)
+    Column = Category.subcomponent_class()
+    Data = Column.subcomponent_class()
+
+    category_dict = {}
+    for key, column in category.items():
+        if isinstance(column, BinaryCIFColumn):
+            data_encoding = column.data.encoding
+            # Optimization: The repeated string array has the same
+            # unique values, as the original string array
+            # -> Use same unique values (faster due to shorter array)
+            if isinstance(data_encoding[0], StringArrayEncoding):
+                data_encoding[0].strings = np.unique(column.data.array)
+            data = Data(np.tile(column.data.array, repetitions), data_encoding)
+        else:
+            data = Data(np.tile(column.data.array, repetitions))
+        mask = (
+            Data(np.tile(column.mask.array, repetitions))
+            if column.mask is not None
+            else None
+        )
+        category_dict[key] = Column(data, mask)
+    return Category(category_dict)
+
+
+def _set_intra_residue_bonds(array, atom_site):
+    """
+    Create the ``chem_comp_bond`` category containing the intra-residue
+    bonds.
+    ``atom_site`` is only used to infer the right :class:`Category` type
+    (either :class:`CIFCategory` or :class:`BinaryCIFCategory`).
+    """
+    if (array.res_name == "").any():
+        raise BadStructureError(
+            "Structure contains atoms with empty residue name, "
+            "but it is required to write intra-residue bonds"
+        )
+    if (array.atom_name == "").any():
+        raise BadStructureError(
+            "Structure contains atoms with empty atom name, "
+            "but it is required to write intra-residue bonds"
+        )
+
+    Category = type(atom_site)
+    Column = Category.subcomponent_class()
+
+    bond_array = _filter_bonds(array, "intra")
+    if len(bond_array) == 0:
+        return None
+    value_order = np.zeros(len(bond_array), dtype="U4")
+    aromatic_flag = np.zeros(len(bond_array), dtype="U1")
+    for i, bond_type in enumerate(bond_array[:, 2]):
+        if bond_type == BondType.ANY:
+            # ANY bonds will be masked anyway, no need to set the value
+            continue
+        order, aromatic = COMP_BOND_TYPE_TO_ORDER[bond_type]
+        value_order[i] = order
+        aromatic_flag[i] = aromatic
+    any_mask = bond_array[:, 2] == BondType.ANY
+
+    # Remove already existing residue and atom name combinations
+    # These appear when the structure contains a residue multiple times
+    atom_id_1 = array.atom_name[bond_array[:, 0]]
+    atom_id_2 = array.atom_name[bond_array[:, 1]]
+    # Take the residue name from the first atom index, as the residue
+    # name is the same for both atoms, since we have only intra bonds
+    comp_id = array.res_name[bond_array[:, 0]]
+    _, unique_indices = np.unique(
+        np.stack([comp_id, atom_id_1, atom_id_2], axis=-1), axis=0, return_index=True
+    )
+    unique_indices.sort()
+
+    chem_comp_bond = Category()
+    n_bonds = len(unique_indices)
+    chem_comp_bond["pdbx_ordinal"] = np.arange(1, n_bonds + 1, dtype=np.int32)
+    chem_comp_bond["comp_id"] = comp_id[unique_indices]
+    chem_comp_bond["atom_id_1"] = atom_id_1[unique_indices]
+    chem_comp_bond["atom_id_2"] = atom_id_2[unique_indices]
+    chem_comp_bond["value_order"] = Column(
+        value_order[unique_indices],
+        np.where(any_mask[unique_indices], MaskValue.MISSING, MaskValue.PRESENT),
+    )
+    chem_comp_bond["pdbx_aromatic_flag"] = Column(
+        aromatic_flag[unique_indices],
+        np.where(any_mask[unique_indices], MaskValue.MISSING, MaskValue.PRESENT),
+    )
+    # BondList does not contain stereo information
+    # -> all values are missing
+    chem_comp_bond["pdbx_stereo_config"] = Column(
+        np.zeros(n_bonds, dtype="U1"),
+        np.full(n_bonds, MaskValue.MISSING),
+    )
+    return chem_comp_bond
+
+
+def _set_inter_residue_bonds(array, atom_site):
+    """
+    Create the ``struct_conn`` category containing the inter-residue
+    bonds.
+    The involved atoms are identified by annotations from the
+    ``atom_site`` category.
+    """
+    COLUMNS = [
+        "label_asym_id",
+        "label_comp_id",
+        "label_seq_id",
+        "label_atom_id",
+        "pdbx_PDB_ins_code",
+    ]
+
+    Category = type(atom_site)
+    Column = Category.subcomponent_class()
+
+    bond_array = _filter_bonds(array, "inter")
+    if len(bond_array) == 0:
+        return None
+
+    # Filter out 'standard' links, i.e. backbone bonds between adjacent canonical
+    # nucleotide/amino acid residues
+    bond_array = bond_array[~_filter_canonical_links(array, bond_array)]
+    if len(bond_array) == 0:
+        return None
+
+    struct_conn = Category()
+    struct_conn["id"] = np.arange(1, len(bond_array) + 1)
+    struct_conn["conn_type_id"] = [
+        PDBX_BOND_TYPE_TO_TYPE_ID[btype] for btype in bond_array[:, 2]
+    ]
+    struct_conn["pdbx_value_order"] = Column(
+        np.array([PDBX_BOND_TYPE_TO_ORDER[btype] for btype in bond_array[:, 2]]),
+        np.where(
+            np.isin(bond_array[:, 2], (BondType.ANY, BondType.COORDINATION)),
+            MaskValue.MISSING,
+            MaskValue.PRESENT,
+        ),
+    )
+    # Write the identifying annotation...
+    for col_name in COLUMNS:
+        annot = atom_site[col_name].as_array()
+        # ...for each bond partner
+        for i in range(2):
+            atom_indices = bond_array[:, i]
+            struct_conn[_get_struct_conn_col_name(col_name, i + 1)] = annot[
+                atom_indices
+            ]
+    return struct_conn
+
+
+def _filter_bonds(array, connection):
+    """
+    Get a bonds array, that contain either only intra-residue or
+    only inter-residue bonds.
+    """
+    bond_array = array.bonds.as_array()
+    # To save computation time call 'get_residue_starts_for()' only once
+    # with indices of the first and second atom of each bond
+    residue_starts_1, residue_starts_2 = (
+        get_residue_starts_for(array, bond_array[:, :2].flatten()).reshape(-1, 2).T
+    )
+    if connection == "intra":
+        return bond_array[residue_starts_1 == residue_starts_2]
+    elif connection == "inter":
+        return bond_array[residue_starts_1 != residue_starts_2]
+    else:
+        raise ValueError("Invalid 'connection' option")
+
+
+def _filter_canonical_links(array, bond_array):
+    """
+    Filter out peptide bonds between adjacent canonical amino acid residues.
+    """
+    # Get the residue index for each bonded atom
+    residue_indices = get_residue_positions(array, bond_array[:, :2].flatten()).reshape(
+        -1, 2
+    )
+
+    return (
+        # Must be canonical residues
+        np.isin(array.res_name[bond_array[:, 0]], CANONICAL_RESIDUE_LIST) &
+        np.isin(array.res_name[bond_array[:, 1]], CANONICAL_RESIDUE_LIST) &
+        # Must be backbone bond
+        np.isin(array.atom_name[bond_array[:, 0]], ("C", "O3'")) &
+        np.isin(array.atom_name[bond_array[:, 1]], ("N", "P")) &
+        # Must connect adjacent residues
+        residue_indices[:, 1] - residue_indices[:, 0] == 1
+    )  # fmt: skip
+
+
+def get_component(pdbx_file, data_block=None, use_ideal_coord=True, res_name=None):
+    """
+    Create an :class:`AtomArray` for a chemical component from the
+    ``chem_comp_atom`` and, if available, the ``chem_comp_bond``
+    category in a file.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+    use_ideal_coord : bool, optional
+        If true, the *ideal* coordinates are read from the file
+        (``pdbx_model_Cartn_<dim>_ideal`` fields), typically
+        originating from computations.
+        If set to false, alternative coordinates are read
+        (``model_Cartn_<dim>_`` fields).
+    res_name : str
+        In rare cases the categories may contain rows for multiple
+        components.
+        In this case, the component with the given residue name is
+        read.
+        By default, all rows would be read in this case.
+
+    Returns
+    -------
+    array : AtomArray
+        The parsed chemical component.
+
+    Examples
+    --------
+
+    >>> import os.path
+    >>> file = CIFFile.read(
+    ...     os.path.join(path_to_structures, "molecules", "TYR.cif")
+    ... )
+    >>> comp = get_component(file)
+    >>> print(comp)
+    HET         0  TYR N      N         1.320    0.952    1.428
+    HET         0  TYR CA     C        -0.018    0.429    1.734
+    HET         0  TYR C      C        -0.103    0.094    3.201
+    HET         0  TYR O      O         0.886   -0.254    3.799
+    HET         0  TYR CB     C        -0.274   -0.831    0.907
+    HET         0  TYR CG     C        -0.189   -0.496   -0.559
+    HET         0  TYR CD1    C         1.022   -0.589   -1.219
+    HET         0  TYR CD2    C        -1.324   -0.102   -1.244
+    HET         0  TYR CE1    C         1.103   -0.282   -2.563
+    HET         0  TYR CE2    C        -1.247    0.210   -2.587
+    HET         0  TYR CZ     C        -0.032    0.118   -3.252
+    HET         0  TYR OH     O         0.044    0.420   -4.574
+    HET         0  TYR OXT    O        -1.279    0.184    3.842
+    HET         0  TYR H      H         1.977    0.225    1.669
+    HET         0  TYR H2     H         1.365    1.063    0.426
+    HET         0  TYR HA     H        -0.767    1.183    1.489
+    HET         0  TYR HB2    H         0.473   -1.585    1.152
+    HET         0  TYR HB3    H        -1.268   -1.219    1.134
+    HET         0  TYR HD1    H         1.905   -0.902   -0.683
+    HET         0  TYR HD2    H        -2.269   -0.031   -0.727
+    HET         0  TYR HE1    H         2.049   -0.354   -3.078
+    HET         0  TYR HE2    H        -2.132    0.523   -3.121
+    HET         0  TYR HH     H        -0.123   -0.399   -5.059
+    HET         0  TYR HXT    H        -1.333   -0.030    4.784
+    """
+    block = _get_block(pdbx_file, data_block)
+
+    try:
+        atom_category = block["chem_comp_atom"]
+    except KeyError:
+        raise InvalidFileError("Missing 'chem_comp_atom' category in file")
+    if res_name is not None:
+        atom_category = _filter(
+            atom_category, atom_category["comp_id"].as_array() == res_name
+        )
+        if atom_category.row_count == 0:
+            raise KeyError(
+                f"No rows with residue name '{res_name}' found in "
+                f"'chem_comp_atom' category"
+            )
+
+    array = AtomArray(atom_category.row_count)
+
+    array.set_annotation("hetero", np.full(len(atom_category["comp_id"]), True))
+    array.set_annotation("res_name", atom_category["comp_id"].as_array(str))
+    array.set_annotation("atom_name", atom_category["atom_id"].as_array(str))
+    array.set_annotation("element", atom_category["type_symbol"].as_array(str))
+    array.set_annotation("charge", atom_category["charge"].as_array(int, 0))
+
+    coord_fields = [f"pdbx_model_Cartn_{dim}_ideal" for dim in ("x", "y", "z")]
+    alt_coord_fields = [f"model_Cartn_{dim}" for dim in ("x", "y", "z")]
+    if not use_ideal_coord:
+        # Swap with the fallback option
+        coord_fields, alt_coord_fields = alt_coord_fields, coord_fields
+    try:
+        array.coord = _parse_component_coordinates(
+            [atom_category[field] for field in coord_fields]
+        )
+    except Exception as err:
+        if isinstance(err, KeyError):
+            key = err.args[0]
+            warnings.warn(
+                f"Attribute '{key}' not found within 'chem_comp_atom' category. "
+                f"The fallback coordinates will be used instead",
+                UserWarning,
+            )
+        elif isinstance(err, ValueError):
+            warnings.warn(
+                "The coordinates are missing for some atoms. "
+                "The fallback coordinates will be used instead",
+                UserWarning,
+            )
+        else:
+            raise
+        array.coord = _parse_component_coordinates(
+            [atom_category[field] for field in alt_coord_fields]
+        )
+
+    try:
+        bond_category = block["chem_comp_bond"]
+        if res_name is not None:
+            bond_category = _filter(
+                bond_category, bond_category["comp_id"].as_array() == res_name
+            )
+    except KeyError:
+        warnings.warn(
+            "Category 'chem_comp_bond' not found. " "No bonds will be parsed",
+            UserWarning,
+        )
+    else:
+        bonds = BondList(array.array_length())
+        for atom1, atom2, order, aromatic_flag in zip(
+            bond_category["atom_id_1"].as_array(str),
+            bond_category["atom_id_2"].as_array(str),
+            bond_category["value_order"].as_array(str),
+            bond_category["pdbx_aromatic_flag"].as_array(str),
+        ):
+            atom_i = np.where(array.atom_name == atom1)[0][0]
+            atom_j = np.where(array.atom_name == atom2)[0][0]
+            bond_type = COMP_BOND_ORDER_TO_TYPE[order, aromatic_flag]
+            bonds.add_bond(atom_i, atom_j, bond_type)
+        array.bonds = bonds
+
+    return array
+
+
+def _parse_component_coordinates(coord_columns):
+    coord = np.zeros((len(coord_columns[0]), 3), dtype=np.float32)
+    for i, column in enumerate(coord_columns):
+        if column.mask is not None and column.mask.array.any():
+            raise ValueError(
+                "Missing coordinates for some atoms",
+            )
+        coord[:, i] = column.as_array(np.float32)
+    return coord
+
+
+def set_component(pdbx_file, array, data_block=None):
+    """
+    Set the ``chem_comp_atom`` and, if bonds are available,
+    ``chem_comp_bond`` category with atom information from an
+    :class:`AtomArray`.
+
+    This will save the coordinates, the mandatory annotation categories
+    and the optional ``charge`` category as well as an associated
+    :class:`BondList`, if available.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    array : AtomArray
+        The chemical component to be written.
+        Must contain only a single residue.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the file is empty, a new data will be created.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+    """
+    _check_non_empty(array)
+
+    block = _get_or_create_block(pdbx_file, data_block)
+    Category = block.subcomponent_class()
+
+    if get_residue_count(array) > 1:
+        raise BadStructureError("The input atom array must comprise only one residue")
+    res_name = array.res_name[0]
+
+    annot_categories = array.get_annotation_categories()
+    if "charge" in annot_categories:
+        charge = array.charge.astype("U2")
+    else:
+        charge = np.full(array.array_length(), "?", dtype="U2")
+
+    atom_cat = Category()
+    atom_cat["comp_id"] = np.full(array.array_length(), res_name)
+    atom_cat["atom_id"] = np.copy(array.atom_name)
+    atom_cat["alt_atom_id"] = atom_cat["atom_id"]
+    atom_cat["type_symbol"] = np.copy(array.element)
+    atom_cat["charge"] = charge
+    atom_cat["model_Cartn_x"] = np.copy(array.coord[:, 0])
+    atom_cat["model_Cartn_y"] = np.copy(array.coord[:, 1])
+    atom_cat["model_Cartn_z"] = np.copy(array.coord[:, 2])
+    atom_cat["pdbx_model_Cartn_x_ideal"] = atom_cat["model_Cartn_x"]
+    atom_cat["pdbx_model_Cartn_y_ideal"] = atom_cat["model_Cartn_y"]
+    atom_cat["pdbx_model_Cartn_z_ideal"] = atom_cat["model_Cartn_z"]
+    atom_cat["pdbx_component_atom_id"] = atom_cat["atom_id"]
+    atom_cat["pdbx_component_comp_id"] = atom_cat["comp_id"]
+    atom_cat["pdbx_ordinal"] = np.arange(1, array.array_length() + 1).astype(str)
+    block["chem_comp_atom"] = atom_cat
+
+    if array.bonds is not None and array.bonds.get_bond_count() > 0:
+        bond_array = array.bonds.as_array()
+        order_flags = []
+        aromatic_flags = []
+        for bond_type in bond_array[:, 2]:
+            order_flag, aromatic_flag = COMP_BOND_TYPE_TO_ORDER[bond_type]
+            order_flags.append(order_flag)
+            aromatic_flags.append(aromatic_flag)
+
+        bond_cat = Category()
+        bond_cat["comp_id"] = np.full(len(bond_array), res_name)
+        bond_cat["atom_id_1"] = array.atom_name[bond_array[:, 0]]
+        bond_cat["atom_id_2"] = array.atom_name[bond_array[:, 1]]
+        bond_cat["value_order"] = np.array(order_flags)
+        bond_cat["pdbx_aromatic_flag"] = np.array(aromatic_flags)
+        bond_cat["pdbx_ordinal"] = np.arange(1, len(bond_array) + 1).astype(str)
+        block["chem_comp_bond"] = bond_cat
+
+
+def list_assemblies(pdbx_file, data_block=None):
+    """
+    List the biological assemblies that are available for the structure
+    in the given file.
+
+    This function receives the data from the ``pdbx_struct_assembly``
+    category in the file.
+    Consequently, this category must be present in the file.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+
+    Returns
+    -------
+    assemblies : dict of str -> str
+        A dictionary that maps an assembly ID to a description of the
+        corresponding assembly.
+
+    Examples
+    --------
+    >>> import os.path
+    >>> file = CIFFile.read(os.path.join(path_to_structures, "1f2n.cif"))
+    >>> assembly_ids = list_assemblies(file)
+    >>> for key, val in assembly_ids.items():
+    ...     print(f"'{key}' : '{val}'")
+    '1' : 'complete icosahedral assembly'
+    '2' : 'icosahedral asymmetric unit'
+    '3' : 'icosahedral pentamer'
+    '4' : 'icosahedral 23 hexamer'
+    '5' : 'icosahedral asymmetric unit, std point frame'
+    '6' : 'crystal asymmetric unit, crystal frame'
+    """
+    block = _get_block(pdbx_file, data_block)
+
+    try:
+        assembly_category = block["pdbx_struct_assembly"]
+    except KeyError:
+        raise InvalidFileError("File has no 'pdbx_struct_assembly' category")
+    return {
+        id: details
+        for id, details in zip(
+            assembly_category["id"].as_array(str),
+            assembly_category["details"].as_array(str),
+        )
+    }
+
+
+def get_assembly(
+    pdbx_file,
+    assembly_id=None,
+    model=None,
+    data_block=None,
+    altloc="first",
+    extra_fields=None,
+    use_author_fields=True,
+    include_bonds=False,
+):
+    """
+    Build the given biological assembly.
+
+    This function receives the data from the
+    ``pdbx_struct_assembly_gen``, ``pdbx_struct_oper_list`` and
+    ``atom_site`` categories in the file.
+    Consequently, these categories must be present in the file.
+
+    Parameters
+    ----------
+    pdbx_file : CIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock
+        The file object.
+    assembly_id : str
+        The assembly to build.
+        Available assembly IDs can be obtained via
+        :func:`list_assemblies()`.
+    model : int, optional
+        If this parameter is given, the function will return an
+        :class:`AtomArray` from the atoms corresponding to the given
+        model number (starting at 1).
+        Negative values are used to index models starting from the last
+        model insted of the first model.
+        If this parameter is omitted, an :class:`AtomArrayStack`
+        containing all models will be returned, even if the structure
+        contains only one model.
+    data_block : str, optional
+        The name of the data block.
+        Default is the first (and most times only) data block of the
+        file.
+        If the data block object is passed directly to `pdbx_file`,
+        this parameter is ignored.
+    altloc : {'first', 'occupancy', 'all'}
+        This parameter defines how *altloc* IDs are handled:
+            - ``'first'`` - Use atoms that have the first *altloc* ID
+              appearing in a residue.
+            - ``'occupancy'`` - Use atoms that have the *altloc* ID
+              with the highest occupancy for a residue.
+            - ``'all'`` - Use all atoms.
+              Note that this leads to duplicate atoms.
+              When this option is chosen, the ``altloc_id`` annotation
+              array is added to the returned structure.
+    extra_fields : list of str, optional
+        The strings in the list are entry names, that are
+        additionally added as annotation arrays.
+        The annotation category name will be the same as the PDBx
+        subcategory name.
+        The array type is always `str`.
+        An exception are the special field identifiers:
+        ``'atom_id'``, ``'b_factor'``, ``'occupancy'`` and ``'charge'``.
+        These will convert the fitting subcategory into an
+        annotation array with reasonable type.
+    use_author_fields : bool, optional
+        Some fields can be read from two alternative sources,
+        for example both, ``label_seq_id`` and ``auth_seq_id`` describe
+        the ID of the residue.
+        While, the ``label_xxx`` fields can be used as official pointers
+        to other categories in the file, the ``auth_xxx``
+        fields are set by the author(s) of the structure and are
+        consistent with the corresponding values in PDB files.
+        If `use_author_fields` is true, the annotation arrays will be
+        read from the ``auth_xxx`` fields (if applicable),
+        otherwise from the the ``label_xxx`` fields.
+    include_bonds : bool, optional
+        If set to true, a :class:`BondList` will be created for the
+        resulting :class:`AtomArray` containing the bond information
+        from the file.
+        Bonds, whose order could not be determined from the
+        *Chemical Component Dictionary*
+        (e.g. especially inter-residue bonds),
+        have :attr:`BondType.ANY`, since the PDB format itself does
+        not support bond orders.
+
+    Returns
+    -------
+    assembly : AtomArray or AtomArrayStack
+        The assembly.
+        The return type depends on the `model` parameter.
+        Contains the `sym_id` annotation, which enumerates the copies of the asymmetric
+        unit in the assembly.
+
+    Examples
+    --------
+
+    >>> import os.path
+    >>> file = CIFFile.read(os.path.join(path_to_structures, "1f2n.cif"))
+    >>> assembly = get_assembly(file, model=1)
+    """
+    block = _get_block(pdbx_file, data_block)
+
+    try:
+        assembly_gen_category = block["pdbx_struct_assembly_gen"]
+    except KeyError:
+        raise InvalidFileError("File has no 'pdbx_struct_assembly_gen' category")
+
+    try:
+        struct_oper_category = block["pdbx_struct_oper_list"]
+    except KeyError:
+        raise InvalidFileError("File has no 'pdbx_struct_oper_list' category")
+
+    assembly_ids = assembly_gen_category["assembly_id"].as_array(str)
+    if assembly_id is None:
+        assembly_id = assembly_ids[0]
+    elif assembly_id not in assembly_ids:
+        raise KeyError(f"File has no Assembly ID '{assembly_id}'")
+
+    ### Calculate all possible transformations
+    transformations = _get_transformations(struct_oper_category)
+
+    ### Get structure according to additional parameters
+    # Include 'label_asym_id' as annotation array
+    # for correct asym ID filtering
+    extra_fields = [] if extra_fields is None else extra_fields
+    if "label_asym_id" in extra_fields:
+        extra_fields_and_asym = extra_fields
+    else:
+        # The operations apply on asym IDs
+        # -> they need to be included to select the correct atoms
+        extra_fields_and_asym = extra_fields + ["label_asym_id"]
+    structure = get_structure(
+        pdbx_file,
+        model,
+        data_block,
+        altloc,
+        extra_fields_and_asym,
+        use_author_fields,
+        include_bonds,
+    )
+
+    ### Get transformations and apply them to the affected asym IDs
+    assembly = None
+    for id, op_expr, asym_id_expr in zip(
+        assembly_gen_category["assembly_id"].as_array(str),
+        assembly_gen_category["oper_expression"].as_array(str),
+        assembly_gen_category["asym_id_list"].as_array(str),
+    ):
+        # Find the operation expressions for given assembly ID
+        # We already asserted that the ID is actually present
+        if id == assembly_id:
+            operations = _parse_operation_expression(op_expr)
+            asym_ids = asym_id_expr.split(",")
+            # Filter affected asym IDs
+            sub_structure = structure[..., np.isin(structure.label_asym_id, asym_ids)]
+            sub_assembly = _apply_transformations(
+                sub_structure, transformations, operations
+            )
+            # Merge the chains with asym IDs for this operation
+            # with chains from other operations
+            if assembly is None:
+                assembly = sub_assembly
+            else:
+                assembly += sub_assembly
+
+    # Remove 'label_asym_id', if it was not included in the original
+    # user-supplied 'extra_fields'
+    if "label_asym_id" not in extra_fields:
+        assembly.del_annotation("label_asym_id")
+
+    return assembly
+
+
+def _apply_transformations(structure, transformation_dict, operations):
+    """
+    Get subassembly by applying the given operations to the input
+    structure containing affected asym IDs.
+    """
+    # Additional first dimesion for 'structure.repeat()'
+    assembly_coord = np.zeros((len(operations),) + structure.coord.shape)
+    # Apply corresponding transformation for each copy in the assembly
+    for i, operation in enumerate(operations):
+        coord = structure.coord
+        # Execute for each transformation step
+        # in the operation expression
+        for op_step in operation:
+            rotation_matrix, translation_vector = transformation_dict[op_step]
+            # Rotate
+            coord = matrix_rotate(coord, rotation_matrix)
+            # Translate
+            coord += translation_vector
+        assembly_coord[i] = coord
+
+    assembly = repeat(structure, assembly_coord)
+    assembly.set_annotation(
+        "sym_id", np.repeat(np.arange(len(operations)), structure.array_length())
+    )
+    return assembly
+
+
+def _get_transformations(struct_oper):
+    """
+    Get transformation operation in terms of rotation matrix and
+    translation for each operation ID in ``pdbx_struct_oper_list``.
+    """
+    transformation_dict = {}
+    for index, id in enumerate(struct_oper["id"].as_array(str)):
+        rotation_matrix = np.array(
+            [
+                [
+                    struct_oper[f"matrix[{i}][{j}]"].as_array(float)[index]
+                    for j in (1, 2, 3)
+                ]
+                for i in (1, 2, 3)
+            ]
+        )
+        translation_vector = np.array(
+            [struct_oper[f"vector[{i}]"].as_array(float)[index] for i in (1, 2, 3)]
+        )
+        transformation_dict[id] = (rotation_matrix, translation_vector)
+    return transformation_dict
+
+
+def _parse_operation_expression(expression):
+    """
+    Get successive operation steps (IDs) for the given
+    ``oper_expression``.
+    Form the cartesian product, if necessary.
+    """
+    # Split groups by parentheses:
+    # use the opening parenthesis as delimiter
+    # and just remove the closing parenthesis
+    # example: '(X0)(1-10,21-25)' from 1a34
+    expressions_per_step = expression.replace(")", "").split("(")
+    expressions_per_step = [e for e in expressions_per_step if len(e) > 0]
+    # Important: Operations are applied from right to left
+    expressions_per_step.reverse()
+
+    operations = []
+    for one_step_expr in expressions_per_step:
+        one_step_op_ids = []
+        for expr in one_step_expr.split(","):
+            if "-" in expr:
+                # Range of operation IDs, they must be integers
+                first, last = expr.split("-")
+                one_step_op_ids.extend(
+                    [str(id) for id in range(int(first), int(last) + 1)]
+                )
+            else:
+                # Single operation ID
+                one_step_op_ids.append(expr)
+        operations.append(one_step_op_ids)
+
+    # Cartesian product of operations
+    return list(itertools.product(*operations))
+
+
+def _convert_string_to_sequence(string, stype):
+    """
+    Convert strings to `ProteinSequence` if `stype` is contained in
+    ``proteinseq_type_list`` or to ``NucleotideSequence`` if `stype` is
+    contained in ``_nucleotideseq_type_list``.
+    """
+    # sequence may be stored as multiline string
+    string = string.replace("\n", "")
+    if stype in _proteinseq_type_list:
+        return ProteinSequence(string)
+    elif stype in _nucleotideseq_type_list:
+        string = string.replace("U", "T")
+        return NucleotideSequence(string)
+    elif stype in _other_type_list:
+        return None
+    else:
+        raise InvalidFileError("mmCIF _entity_poly.type unsupported" " type: " + stype)