biotite 1.0.0__cp312-cp312-macosx_11_0_arm64.whl → 1.1.0__cp312-cp312-macosx_11_0_arm64.whl

biotite/structure/io/pdbx/convert.py

@@ -24,6 +24,10 @@ 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,
@@ -36,32 +40,38 @@ from biotite.structure.io.pdbx.bcif import (
 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_starts_for
+from biotite.structure.residues import (
+    get_residue_count,
+    get_residue_positions,
+    get_residue_starts_for,
+)
 from biotite.structure.util import matrix_rotate
 
-# Cond types in `struct_conn` category that refer to covalent bonds
-PDBX_COVALENT_TYPES = [
-    "covale",
-    "covale_base",
-    "covale_phosphate",
-    "covale_sugar",
-    "disulf",
-    "modres",
-    "modres_link",
-    "metalc",
-]
-# Map 'struct_conn' bond orders to 'BondType'...
-PDBX_BOND_ORDER_TO_TYPE = {
-    "": BondType.ANY,
-    "sing": BondType.SINGLE,
-    "doub": BondType.DOUBLE,
-    "trip": BondType.TRIPLE,
-    "quad": BondType.QUADRUPLE,
+# 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",
 }
-# ...and vice versa
 PDBX_BOND_TYPE_TO_ORDER = {
-    # 'ANY' is masked later, it is merely added here to avoid a KeyError
-    BondType.ANY: "",
     BondType.SINGLE: "sing",
     BondType.DOUBLE: "doub",
     BondType.TRIPLE: "trip",
@@ -69,6 +79,9 @@ PDBX_BOND_TYPE_TO_ORDER = {
     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 = {
@@ -84,6 +97,7 @@ COMP_BOND_ORDER_TO_TYPE = {
 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 = [
@@ -450,7 +464,7 @@ def _fill_annotations(array, atom_site, extra_fields, use_author_fields):
         "chain_id",
         _get_or_fallback(
             atom_site, f"{prefix}_asym_id", f"{alt_prefix}_asym_id"
-        ).as_array("U4"),
+        ).as_array(str),
     )
     array.set_annotation(
         "res_id",
@@ -458,33 +472,70 @@ def _fill_annotations(array, atom_site, extra_fields, use_author_fields):
             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("U1", ""))
+    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("U5"),
+        ).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("U6"),
+        ).as_array(str),
     )
-    array.set_annotation("element", atom_site["type_symbol"].as_array("U2"))
+    array.set_annotation("element", atom_site["type_symbol"].as_array(str))
 
     if "atom_id" in extra_fields:
-        array.set_annotation("atom_id", atom_site["id"].as_array(int))
+        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:
-        array.set_annotation("b_factor", atom_site["B_iso_or_equiv"].as_array(float))
+        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:
-        array.set_annotation("occupancy", atom_site["occupancy"].as_array(float))
+        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:
-        array.set_annotation("charge", atom_site["pdbx_formal_charge"].as_array(int, 0))
+        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
@@ -536,7 +587,8 @@ def _parse_inter_residue_bonds(atom_site, struct_conn):
     ]
 
     covale_mask = np.isin(
-        struct_conn["conn_type_id"].as_array(str), PDBX_COVALENT_TYPES
+        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
@@ -576,13 +628,14 @@ def _parse_inter_residue_bonds(atom_site, struct_conn):
     atoms_indices_1 = atoms_indices_1[mapping_exists_mask]
     atoms_indices_2 = atoms_indices_2[mapping_exists_mask]
 
-    # Interpret missing values as ANY bonds
-    bond_order = struct_conn["pdbx_value_order"].as_array("U4", "")
+    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_order = bond_order[covale_mask][mapping_exists_mask]
-    bond_types = [PDBX_BOND_ORDER_TO_TYPE[order] for order in bond_order]
+    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,
@@ -593,7 +646,7 @@ def _parse_inter_residue_bonds(atom_site, struct_conn):
 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 the reference counterpart.
+    `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(
@@ -703,7 +756,13 @@ def _get_box(block):
     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):
+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`.
@@ -737,6 +796,10 @@ def set_structure(pdbx_file, array, data_block=None, include_bonds=False):
         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
     -----
@@ -797,6 +860,32 @@ def set_structure(pdbx_file, array, data_block=None, include_bonds=False):
             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:
@@ -964,25 +1053,38 @@ def _set_intra_residue_bonds(array, atom_site):
         aromatic_flag[i] = aromatic
     any_mask = bond_array[:, 2] == BondType.ANY
 
-    chem_comp_bond = Category()
+    # 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
-    chem_comp_bond["comp_id"] = array.res_name[bond_array[:, 0]]
-    chem_comp_bond["atom_id_1"] = array.atom_name[bond_array[:, 0]]
-    chem_comp_bond["atom_id_2"] = array.atom_name[bond_array[:, 1]]
+    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, np.where(any_mask, MaskValue.MISSING, MaskValue.PRESENT)
+        value_order[unique_indices],
+        np.where(any_mask[unique_indices], MaskValue.MISSING, MaskValue.PRESENT),
     )
     chem_comp_bond["pdbx_aromatic_flag"] = Column(
-        aromatic_flag, np.where(any_mask, MaskValue.MISSING, MaskValue.PRESENT)
+        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(len(bond_array), dtype="U1"),
-        np.full(len(bond_array), MaskValue.MISSING),
+        np.zeros(n_bonds, dtype="U1"),
+        np.full(n_bonds, MaskValue.MISSING),
     )
-    chem_comp_bond["pdbx_ordinal"] = np.arange(1, len(bond_array) + 1, dtype=np.int32)
     return chem_comp_bond
 
 
@@ -1007,13 +1109,22 @@ def _set_inter_residue_bonds(array, atom_site):
     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"] = np.full(len(bond_array), "covale")
+    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(
-            bond_array[:, 2] == BondType.ANY,
+            np.isin(bond_array[:, 2], (BondType.ANY, BondType.COORDINATION)),
             MaskValue.MISSING,
             MaskValue.PRESENT,
         ),
@@ -1049,6 +1160,27 @@ def _filter_bonds(array, connection):
         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
@@ -1135,12 +1267,11 @@ def get_component(pdbx_file, data_block=None, use_ideal_coord=True, res_name=Non
 
     array = AtomArray(atom_category.row_count)
 
-    array.hetero[:] = True
-    array.res_name = atom_category["comp_id"].as_array("U5")
-    array.atom_name = atom_category["atom_id"].as_array("U6")
-    array.element = atom_category["type_symbol"].as_array("U2")
-    array.add_annotation("charge", int)
-    array.charge = atom_category["charge"].as_array(int, 0)
+    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")]
@@ -1148,17 +1279,28 @@ def get_component(pdbx_file, data_block=None, use_ideal_coord=True, res_name=Non
         # Swap with the fallback option
         coord_fields, alt_coord_fields = alt_coord_fields, coord_fields
     try:
-        for i, field in enumerate(coord_fields):
-            array.coord[:, i] = atom_category[field].as_array(np.float32)
-    except KeyError as err:
-        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,
+        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]
         )
-        for i, field in enumerate(alt_coord_fields):
-            array.coord[:, i] = atom_category[field].as_array(np.float32)
 
     try:
         bond_category = block["chem_comp_bond"]
@@ -1188,6 +1330,17 @@ def get_component(pdbx_file, data_block=None, use_ideal_coord=True, res_name=Non
     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,
@@ -1404,7 +1557,10 @@ def get_assembly(
     Returns
     -------
     assembly : AtomArray or AtomArrayStack
-        The assembly. The return type depends on the `model` parameter.
+        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
     --------
@@ -1493,7 +1649,6 @@ def _apply_transformations(structure, transformation_dict, operations):
     """
     # 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
@@ -1507,7 +1662,11 @@ def _apply_transformations(structure, transformation_dict, operations):
             coord += translation_vector
         assembly_coord[i] = coord
 
-    return repeat(structure, assembly_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):