biotite 1.0.1__cp312-cp312-macosx_11_0_arm64.whl → 1.1.0__cp312-cp312-macosx_11_0_arm64.whl

biotite/structure/info/misc.py

@@ -11,19 +11,13 @@ from biotite.structure.info.ccd import get_ccd, get_from_ccd
 
 def all_residues():
     """
-    Get a list of all residues/compound names in the
-    PDB chemical components dictionary.
+    Get a list of all residues/compound names in the PDB
+    *Chemical Component Dictionary* (CCD).
 
     Returns
     -------
     residues : list of str
-        A list of all available The up to 3-letter residue names.
-
-    Examples
-    --------
-
-    >>> print(all_residues()[1000 : 1010])
-    ['0V9', '0VA', '0VB', '0VC', '0VD', '0VE', '0VF', '0VG', '0VH', '0VI']
+        A list of all available residue names.
     """
     return get_ccd()["chem_comp"]["id"].as_array().tolist()
 
@@ -51,10 +45,10 @@ def full_name(res_name):
     >>> print(full_name("MAN"))
     alpha-D-mannopyranose
     """
-    array = get_from_ccd("chem_comp", res_name.upper(), "name")
-    if array is None:
+    column = get_from_ccd("chem_comp", res_name.upper(), "name")
+    if column is None:
         return None
-    return array.item()
+    return column.as_item()
 
 
 def link_type(res_name):
@@ -84,10 +78,10 @@ def link_type(res_name):
     >>> print(link_type("HOH"))
     NON-POLYMER
     """
-    array = get_from_ccd("chem_comp", res_name.upper(), "type")
-    if array is None:
+    column = get_from_ccd("chem_comp", res_name.upper(), "type")
+    if column is None:
         return None
-    return array.item()
+    return column.as_item()
 
 
 def one_letter_code(res_name):
@@ -107,7 +101,7 @@ def one_letter_code(res_name):
     -------
     one_letter_code : str or None
         The one-letter code.
-        None if the compound is not present in the CCD or if no
+        ``None`` if the compound is not present in the CCD or if no
         one-letter code is defined for this compound.
 
     Examples
@@ -135,10 +129,10 @@ def one_letter_code(res_name):
     None
 
     """
-    array = get_from_ccd("chem_comp", res_name.upper(), "one_letter_code")
-    if array is None:
+    column = get_from_ccd("chem_comp", res_name.upper(), "one_letter_code")
+    if column is None:
         return None
-    item = array.item()
-    if item == "":
+    if column.mask is not None:
+        # Value is masked, i.e. inapplicable or missing
         return None
-    return item
+    return column.as_item()

biotite/structure/info/standardize.py

@@ -121,8 +121,8 @@ def standardize_order(atoms):
         stop = starts[i + 1]
 
         res_name = atoms.res_name[start]
-        standard_atom_names = get_from_ccd("chem_comp_atom", res_name, "atom_id")
-        if standard_atom_names is None:
+        chem_comp_atom = get_from_ccd("chem_comp_atom", res_name, "atom_id")
+        if chem_comp_atom is None:
             # If the residue is not in the CCD, keep the current order
             warnings.warn(
                 f"Residue '{res_name}' is not in the CCD, "
@@ -131,6 +131,7 @@ def standardize_order(atoms):
             reordered_indices[start:stop] = np.arange(start, stop)
             continue
 
+        standard_atom_names = chem_comp_atom.as_array()
         reordered_indices[start:stop] = (
             _reorder(atoms.atom_name[start:stop], standard_atom_names) + start
         )

biotite/structure/io/mol/sdf.py

@@ -314,19 +314,19 @@ class SDRecord:
     >>> record = SDRecord(header=Header(mol_name="ALA", dimensions="3D"))
     >>> record.set_structure(atoms)
     >>> print(record.get_structure())
-            0             N        -0.970    0.490    1.500
-            0             C         0.260    0.420    0.690
-            0             C        -0.090    0.020   -0.720
-            0             O        -1.060   -0.680   -0.920
-            0             C         1.200   -0.620    1.300
-            0             O         0.660    0.440   -1.740
-            0             H        -1.380   -0.420    1.480
-            0             H        -0.680    0.660    2.450
-            0             H         0.750    1.390    0.680
-            0             H         1.460   -0.330    2.320
-            0             H         0.720   -1.590    1.310
-            0             H         2.110   -0.680    0.700
-            0             H         0.440    0.180   -2.650
+                0             N        -0.966    0.493    1.500
+                0             C         0.257    0.418    0.692
+                0             C        -0.094    0.017   -0.716
+                0             O        -1.056   -0.682   -0.923
+                0             C         1.204   -0.620    1.296
+                0             O         0.661    0.439   -1.742
+                0             H        -1.383   -0.425    1.482
+                0             H        -0.676    0.661    2.452
+                0             H         0.746    1.392    0.682
+                0             H         1.459   -0.330    2.316
+                0             H         0.715   -1.594    1.307
+                0             H         2.113   -0.676    0.697
+                0             H         0.435    0.182   -2.647
     >>> # Add the record to an SD file
     >>> file = SDFile()
     >>> file["ALA"] = record
@@ -335,19 +335,19 @@ class SDRecord:
                         3D
     <BLANKLINE>
      13 12  0     0  0  0  0  0  0  1 V2000
-       -0.9700    0.4900    1.5000 N   0  0  0  0  0  0  0  0  0  0  0  0
-        0.2600    0.4200    0.6900 C   0  0  0  0  0  0  0  0  0  0  0  0
-       -0.0900    0.0200   -0.7200 C   0  0  0  0  0  0  0  0  0  0  0  0
-       -1.0600   -0.6800   -0.9200 O   0  0  0  0  0  0  0  0  0  0  0  0
-        1.2000   -0.6200    1.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
-        0.6600    0.4400   -1.7400 O   0  0  0  0  0  0  0  0  0  0  0  0
-       -1.3800   -0.4200    1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
-       -0.6800    0.6600    2.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
-        0.7500    1.3900    0.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
-        1.4600   -0.3300    2.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
-        0.7200   -1.5900    1.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
-        2.1100   -0.6800    0.7000 H   0  0  0  0  0  0  0  0  0  0  0  0
-        0.4400    0.1800   -2.6500 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.9660    0.4930    1.5000 N   0  0  0  0  0  0  0  0  0  0  0  0
+        0.2570    0.4180    0.6920 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.0940    0.0170   -0.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.0560   -0.6820   -0.9230 O   0  0  0  0  0  0  0  0  0  0  0  0
+        1.2040   -0.6200    1.2960 C   0  0  0  0  0  0  0  0  0  0  0  0
+        0.6610    0.4390   -1.7420 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.3830   -0.4250    1.4820 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.6760    0.6610    2.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7460    1.3920    0.6820 H   0  0  0  0  0  0  0  0  0  0  0  0
+        1.4590   -0.3300    2.3160 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7150   -1.5940    1.3070 H   0  0  0  0  0  0  0  0  0  0  0  0
+        2.1130   -0.6760    0.6970 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.4350    0.1820   -2.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
       1  2  1  0  0  0  0
       1  7  1  0  0  0  0
       1  8  1  0  0  0  0
@@ -362,6 +362,7 @@ class SDRecord:
       6 13  1  0  0  0  0
     M  END
     $$$$
+    <BLANKLINE>
     """
 
     def __init__(self, header=None, ctab=None, metadata=None):
@@ -542,7 +543,7 @@ class SDFile(File, MutableMapping):
     ----------
     record : CIFBlock
         The sole record of the file.
-        If the file contains multiple blocks, an exception is raised.
+        If the file contains multiple records, an exception is raised.
 
     Examples
     --------
@@ -678,19 +679,19 @@ class SDFile(File, MutableMapping):
     <BLANKLINE>
     <BLANKLINE>
      13 12  0     0  0  0  0  0  0  1 V2000
-       -0.9700    0.4900    1.5000 N   0  0  0  0  0  0  0  0  0  0  0  0
-        0.2600    0.4200    0.6900 C   0  0  0  0  0  0  0  0  0  0  0  0
-       -0.0900    0.0200   -0.7200 C   0  0  0  0  0  0  0  0  0  0  0  0
-       -1.0600   -0.6800   -0.9200 O   0  0  0  0  0  0  0  0  0  0  0  0
-        1.2000   -0.6200    1.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
-        0.6600    0.4400   -1.7400 O   0  0  0  0  0  0  0  0  0  0  0  0
-       -1.3800   -0.4200    1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
-       -0.6800    0.6600    2.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
-        0.7500    1.3900    0.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
-        1.4600   -0.3300    2.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
-        0.7200   -1.5900    1.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
-        2.1100   -0.6800    0.7000 H   0  0  0  0  0  0  0  0  0  0  0  0
-        0.4400    0.1800   -2.6500 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.9660    0.4930    1.5000 N   0  0  0  0  0  0  0  0  0  0  0  0
+        0.2570    0.4180    0.6920 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.0940    0.0170   -0.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.0560   -0.6820   -0.9230 O   0  0  0  0  0  0  0  0  0  0  0  0
+        1.2040   -0.6200    1.2960 C   0  0  0  0  0  0  0  0  0  0  0  0
+        0.6610    0.4390   -1.7420 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.3830   -0.4250    1.4820 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.6760    0.6610    2.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7460    1.3920    0.6820 H   0  0  0  0  0  0  0  0  0  0  0  0
+        1.4590   -0.3300    2.3160 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7150   -1.5940    1.3070 H   0  0  0  0  0  0  0  0  0  0  0  0
+        2.1130   -0.6760    0.6970 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.4350    0.1820   -2.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
       1  2  1  0  0  0  0
       1  7  1  0  0  0  0
       1  8  1  0  0  0  0

biotite/structure/io/pdb/convert.py

@@ -218,6 +218,8 @@ def get_assembly(
     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
     --------

biotite/structure/io/pdb/file.py

@@ -7,6 +7,7 @@ __author__ = "Patrick Kunzmann, Daniel Bauer, Claude J. Rogers"
 __all__ = ["PDBFile"]
 
 import warnings
+from collections import namedtuple
 import numpy as np
 from biotite.file import InvalidFileError, TextFile
 from biotite.structure.atoms import AtomArray, AtomArrayStack, repeat
@@ -53,6 +54,8 @@ _c = slice(24, 33)
 _alpha = slice(33, 40)
 _beta = slice(40, 47)
 _gamma = slice(47, 54)
+_space = slice(55, 66)
+_z = slice(66, 70)
 
 
 class PDBFile(TextFile):
@@ -545,6 +548,38 @@ class PDBFile(TextFile):
 
         return array
 
+    def get_space_group(self):
+        """
+        Extract the space group and Z value from the CRYST1 record.
+
+        Returns
+        -------
+        space_group : str
+            The extracted space group.
+        z_val : int
+            The extracted Z value.
+        """
+        # Initialize the namedtuple
+        SpaceGroupInfo = namedtuple("SpaceGroupInfo", ["space_group", "z_val"])
+
+        # CRYST1 is a one-time record so we can extract it directly
+        for line in self.lines:
+            if line.startswith("CRYST1"):
+                try:
+                    # Extract space group and Z value
+                    space_group = str(line[_space])
+                    z_val = int(line[_z])
+                except ValueError:
+                    # File contains invalid 'CRYST1' record
+                    raise InvalidFileError(
+                        "File does not contain valid space group and/or Z values"
+                    )
+                    # Set default values
+                    space_group = "P 1"
+                    z_val = 1
+                break
+        return SpaceGroupInfo(space_group=space_group, z_val=z_val)
+
     def set_structure(self, array, hybrid36=False):
         """
         Set the :class:`AtomArray` or :class:`AtomArrayStack` for the
@@ -700,6 +735,32 @@ class PDBFile(TextFile):
 
         self._index_models_and_atoms()
 
+    def set_space_group(self, info):
+        """
+        Update the CRYST1 record with the provided space group and Z value.
+
+        Parameters
+        ----------
+        info : tuple(str, int) or SpaceGroupInfo
+            Contains the space group and Z-value.
+        """
+        for i, line in enumerate(self.lines):
+            if line.startswith("CRYST1"):
+                try:
+                    # Format the replacement string
+                    space_group_str = info.space_group.ljust(11)
+                    z_val_str = str(info.z_val).rjust(4)
+
+                    # Replace the existing CRYST1 record
+                    self.lines[i] = line[:55] + space_group_str + z_val_str + line[70:]
+                except (ValueError, AttributeError) as e:
+                    # Raise an exception with context
+                    raise AttributeError(
+                        f"Failed to update CRYST1 record. "
+                        f"Line: {line.strip()} | Error: {e}"
+                    )
+                break
+
     def list_assemblies(self):
         """
         List the biological assemblies that are available for the
@@ -790,6 +851,8 @@ class PDBFile(TextFile):
         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
         --------
@@ -853,8 +916,12 @@ class PDBFile(TextFile):
             affected_chain_ids = []
             transform_start = None
             for j, line in enumerate(assembly_lines[start:stop]):
-                if line.startswith("APPLY THE FOLLOWING TO CHAINS:") or line.startswith(
-                    "                   AND CHAINS:"
+                if any(
+                    line.startswith(chain_signal_string)
+                    for chain_signal_string in [
+                        "APPLY THE FOLLOWING TO CHAINS:",
+                        "                   AND CHAINS:",
+                    ]
                 ):
                     affected_chain_ids += [
                         chain_id.strip() for chain_id in line[30:].split(",")
@@ -1148,7 +1215,11 @@ def _apply_transformations(structure, rotations, translations):
         coord += translation
         assembly_coord[i] = coord
 
-    return repeat(structure, assembly_coord)
+    assembly = repeat(structure, assembly_coord)
+    assembly.set_annotation(
+        "sym_id", np.repeat(np.arange(len(rotations)), structure.array_length())
+    )
+    return assembly
 
 
 def _check_pdb_compatibility(array, hybrid36):

biotite/structure/io/pdbqt/file.py

@@ -58,48 +58,48 @@ class PDBQTFile(TextFile):
     >>> mask = file.set_structure(ligand, rotatable_bonds="all")
     >>> # Print removed nonpolar hydrogen atoms
     >>> print(ligand[~mask])
-    HET         0  BTN H101   H         3.740    1.170    0.970
-    HET         0  BTN H102   H         4.070    1.340   -0.770
-    HET         0  BTN H91    H         2.800   -0.740   -1.210
-    HET         0  BTN H92    H         2.480   -0.910    0.530
-    HET         0  BTN H81    H         1.290    1.260    0.520
-    HET         0  BTN H82    H         1.620    1.440   -1.220
-    HET         0  BTN H71    H         0.350   -0.650   -1.660
-    HET         0  BTN H72    H         0.020   -0.820    0.080
-    HET         0  BTN H2     H        -0.840    1.580   -1.630
-    HET         0  BTN H61    H        -3.800    1.840    1.290
-    HET         0  BTN H62    H        -3.370    2.740   -0.200
-    HET         0  BTN H5     H        -4.310    0.810   -1.210
-    HET         0  BTN H4     H        -2.450   -0.040   -2.250
+    HET         0  BTN H101   H         3.745    1.171    0.974
+    HET         0  BTN H102   H         4.071    1.343   -0.767
+    HET         0  BTN H91    H         2.802   -0.740   -1.211
+    HET         0  BTN H92    H         2.476   -0.912    0.530
+    HET         0  BTN H81    H         1.289    1.265    0.523
+    HET         0  BTN H82    H         1.616    1.437   -1.218
+    HET         0  BTN H71    H         0.346   -0.646   -1.662
+    HET         0  BTN H72    H         0.020   -0.818    0.079
+    HET         0  BTN H2     H        -0.838    1.576   -1.627
+    HET         0  BTN H61    H        -3.797    1.837    1.286
+    HET         0  BTN H62    H        -3.367    2.738   -0.205
+    HET         0  BTN H5     H        -4.307    0.812   -1.205
+    HET         0  BTN H4     H        -2.451   -0.038   -2.252
     >>> print(file)
     ROOT
-    HETATM    1 C11  BTN     0       5.090  -0.280   0.170  1.00  0.00     0.258 C
-    HETATM    2 O11  BTN     0       4.960  -1.470   0.030  1.00  0.00    -0.264 OA
+    HETATM    1 C11  BTN     0       5.089  -0.280   0.173  1.00  0.00     0.258 C
+    HETATM    2 O11  BTN     0       4.956  -1.473   0.030  1.00  0.00    -0.264 OA
     ENDROOT
     BRANCH   1   3
-    HETATM    3 O12  BTN     0       6.300   0.230   0.440  1.00  0.00    -0.331 OA
-    HETATM   17 HO2  BTN     0       7.030  -0.390   0.520  1.00  0.00     0.221 HD
+    HETATM    3 O12  BTN     0       6.299   0.233   0.444  1.00  0.00    -0.331 OA
+    HETATM   17 HO2  BTN     0       7.034  -0.391   0.517  1.00  0.00     0.221 HD
     ENDBRANCH   1   3
     BRANCH   1   4
-    HETATM    4 C10  BTN     0       3.900   0.630   0.040  1.00  0.00     0.105 C
+    HETATM    4 C10  BTN     0       3.896   0.631   0.039  1.00  0.00     0.105 C
     BRANCH   4   5
-    HETATM    5 C9   BTN     0       2.650  -0.200  -0.280  1.00  0.00     0.010 C
+    HETATM    5 C9   BTN     0       2.651  -0.200  -0.276  1.00  0.00     0.010 C
     BRANCH   5   6
-    HETATM    6 C8   BTN     0       1.440   0.720  -0.410  1.00  0.00     0.002 C
+    HETATM    6 C8   BTN     0       1.440   0.725  -0.412  1.00  0.00     0.002 C
     BRANCH   6   7
-    HETATM    7 C7   BTN     0       0.200  -0.110  -0.730  1.00  0.00     0.016 C
+    HETATM    7 C7   BTN     0       0.196  -0.106  -0.727  1.00  0.00     0.016 C
     BRANCH   7   8
-    HETATM    8 C2   BTN     0      -1.020   0.820  -0.860  1.00  0.00     0.065 C
-    HETATM    9 S1   BTN     0      -1.420   1.600   0.750  1.00  0.00    -0.154 SA
-    HETATM   10 C6   BTN     0      -3.200   1.830   0.370  1.00  0.00     0.090 C
-    HETATM   11 C5   BTN     0      -3.530   0.580  -0.480  1.00  0.00     0.091 C
-    HETATM   12 N1   BTN     0      -3.970  -0.510   0.410  1.00  0.00    -0.239 NA
-    HETATM   13 C3   BTN     0      -3.140  -1.550   0.270  1.00  0.00     0.272 C
-    HETATM   14 O3   BTN     0      -3.270  -2.590   0.890  1.00  0.00    -0.259 OA
-    HETATM   15 N2   BTN     0      -2.150  -1.340  -0.610  1.00  0.00    -0.239 NA
-    HETATM   16 C4   BTN     0      -2.290   0.010  -1.170  1.00  0.00     0.093 C
-    HETATM   18 HN1  BTN     0      -4.740  -0.470   1.000  1.00  0.00     0.132 HD
-    HETATM   19 HN2  BTN     0      -1.460  -1.980  -0.840  1.00  0.00     0.132 HD
+    HETATM    8 C2   BTN     0      -1.015   0.819  -0.863  1.00  0.00     0.065 C
+    HETATM    9 S1   BTN     0      -1.419   1.604   0.751  1.00  0.00    -0.154 SA
+    HETATM   10 C6   BTN     0      -3.205   1.827   0.371  1.00  0.00     0.090 C
+    HETATM   11 C5   BTN     0      -3.530   0.581  -0.476  1.00  0.00     0.091 C
+    HETATM   12 N1   BTN     0      -3.970  -0.507   0.412  1.00  0.00    -0.239 NA
+    HETATM   13 C3   BTN     0      -3.141  -1.549   0.271  1.00  0.00     0.272 C
+    HETATM   14 O3   BTN     0      -3.271  -2.589   0.888  1.00  0.00    -0.259 OA
+    HETATM   15 N2   BTN     0      -2.154  -1.343  -0.612  1.00  0.00    -0.239 NA
+    HETATM   16 C4   BTN     0      -2.289   0.010  -1.175  1.00  0.00     0.093 C
+    HETATM   18 HN1  BTN     0      -4.738  -0.474   1.004  1.00  0.00     0.132 HD
+    HETATM   19 HN2  BTN     0      -1.462  -1.982  -0.843  1.00  0.00     0.132 HD
     ENDBRANCH   7   8
     ENDBRANCH   6   7
     ENDBRANCH   5   6

biotite/structure/io/pdbx/__init__.py

@@ -18,5 +18,6 @@ __author__ = "Patrick Kunzmann"
 from .bcif import *
 from .cif import *
 from .component import *
+from .compress import *
 from .convert import *
 from .encoding import *

biotite/structure/io/pdbx/bcif.py

@@ -38,8 +38,9 @@ class BinaryCIFData(_Component):
     array : array_like or int or float or str
         The data array to be stored.
         If a single item is given, it is converted into an array.
-    encoding : list of Encoding
+    encoding : list of Encoding , optional
         The encoding steps that are successively applied to the data.
+        By default, the data is stored uncompressed directly as bytes.
 
     Attributes
     ----------
@@ -61,7 +62,7 @@ class BinaryCIFData(_Component):
     >>> print(data.array)
     ['apple']
 
-    Well-chosen encoding can significantly reduce the serialized data
+    A well-chosen encoding can significantly reduce the serialized data
     size:
 
     >>> # Default uncompressed encoding
@@ -457,7 +458,12 @@ class BinaryCIFBlock(_HierarchicalContainer):
     """
 
     def __init__(self, categories=None):
-        super().__init__(categories)
+        if categories is None:
+            categories = {}
+        super().__init__(
+            # Actual bcif files use leading '_' as category names
+            {"_" + name: category for name, category in categories.items()}
+        )
 
     @staticmethod
     def subcomponent_class():
@@ -470,25 +476,43 @@ class BinaryCIFBlock(_HierarchicalContainer):
     @staticmethod
     def deserialize(content):
         return BinaryCIFBlock(
-            BinaryCIFBlock._deserialize_elements(content["categories"], "name")
+            {
+                # The superclass uses leading '_' in category names,
+                # but on the level of this class, the leading '_' is omitted
+                name.lstrip("_"): category
+                for name, category in BinaryCIFBlock._deserialize_elements(
+                    content["categories"], "name"
+                ).items()
+            }
         )
 
     def serialize(self):
         return {"categories": self._serialize_elements("name")}
 
     def __getitem__(self, key):
-        # Actual bcif files use leading '_' as categories
-        return super().__getitem__("_" + key)
+        try:
+            return super().__getitem__("_" + key)
+        except KeyError:
+            raise KeyError(key)
 
     def __setitem__(self, key, element):
-        return super().__setitem__("_" + key, element)
+        try:
+            return super().__setitem__("_" + key, element)
+        except KeyError:
+            raise KeyError(key)
 
     def __delitem__(self, key):
-        return super().__setitem__("_" + key)
+        try:
+            return super().__setitem__("_" + key)
+        except KeyError:
+            raise KeyError(key)
 
     def __iter__(self):
         return (key.lstrip("_") for key in super().__iter__())
 
+    def __contains__(self, key):
+        return super().__contains__("_" + key)
+
 
 class BinaryCIFFile(File, _HierarchicalContainer):
     """