biotite 1.0.0__cp312-cp312-macosx_10_9_x86_64.whl → 1.0.1__cp312-cp312-macosx_10_9_x86_64.whl

biotite/structure/atoms.py

@@ -99,9 +99,24 @@ class _AtomArrayBase(Copyable, metaclass=abc.ABCMeta):
         See Also
         --------
         set_annotation
+
+        Notes
+        -----
+        If the annotation category already exists, a compatible dtype is chosen,
+        that is also able to represent the old values.
         """
         if category not in self._annot:
             self._annot[str(category)] = np.zeros(self._array_length, dtype=dtype)
+        elif np.can_cast(self._annot[str(category)].dtype, dtype):
+            self._annot[str(category)] = self._annot[str(category)].astype(dtype)
+        elif np.can_cast(dtype, self._annot[str(category)].dtype):
+            # The existing dtype is more general
+            pass
+        else:
+            raise ValueError(
+                f"Cannot cast '{str(category)}' "
+                f"with dtype '{self._annot[str(category)].dtype}' into '{dtype}'"
+            )
 
     def del_annotation(self, category):
         """
@@ -145,16 +160,25 @@ class _AtomArrayBase(Copyable, metaclass=abc.ABCMeta):
         array : ndarray or None
             The new value of the annotation category. The size of the
             array must be the same as the array length.
+
+        Notes
+        -----
+        If the annotation category already exists, a compatible dtype is chosen,
+        that is able to represent the old and new array values.
         """
+        array = np.asarray(array)
         if len(array) != self._array_length:
             raise IndexError(
                 f"Expected array length {self._array_length}, " f"but got {len(array)}"
             )
         if category in self._annot:
-            # Keep the dtype if the annotation already exists
-            self._annot[category] = np.asarray(array, dtype=self._annot[category].dtype)
+            # If the annotation already exists, find the compatible dtype
+            self._annot[category] = array.astype(
+                dtype=np.promote_types(self._annot[category].dtype, array.dtype),
+                copy=False,
+            )
         else:
-            self._annot[category] = np.asarray(array)
+            self._annot[category] = array
 
     def get_annotation_categories(self):
         """

biotite/structure/filter.py

@@ -577,7 +577,7 @@ def filter_highest_occupancy_altloc(atoms, altloc_ids, occupancies):
         if len(letter_altloc_ids) > 0:
             highest = -1.0
             highest_id = None
-            for id in set(letter_altloc_ids):
+            for id in sorted(set(letter_altloc_ids)):
                 occupancy_sum = np.sum(occupancies_in_res[altloc_ids_in_res == id])
                 if occupancy_sum > highest:
                     highest = occupancy_sum

biotite/structure/io/pdbx/cif.py

@@ -370,7 +370,7 @@ class CIFCategory(_Component, MutableMapping):
         if category_name is None:
             raise DeserializationError("Failed to parse category name")
 
-        lines = _to_single(lines, is_looped)
+        lines = _to_single(lines)
         if is_looped:
             category_dict = CIFCategory._deserialize_looped(lines, expect_whitespace)
         else:
@@ -439,11 +439,28 @@ class CIFCategory(_Component, MutableMapping):
         Process a category where each field has a single value.
         """
         category_dict = {}
-        for line in lines:
+        line_i = 0
+        while line_i < len(lines):
+            line = lines[line_i]
             parts = _split_one_line(line)
-            column_name = parts[0].split(".")[1]
-            column = parts[1]
-            category_dict[column_name] = CIFColumn(column)
+            if len(parts) == 2:
+                # Standard case -> name and value in one line
+                name_part, value_part = parts
+                line_i += 1
+            elif len(parts) == 1:
+                # Value is a multiline value on the next line
+                name_part = parts[0]
+                parts = _split_one_line(lines[line_i + 1])
+                if len(parts) == 1:
+                    value_part = parts[0]
+                else:
+                    raise DeserializationError(f"Failed to parse line '{line}'")
+                line_i += 2
+            elif len(parts) == 0:
+                raise DeserializationError("Empty line within category")
+            else:
+                raise DeserializationError(f"Failed to parse line '{line}'")
+            category_dict[name_part.split(".")[1]] = CIFColumn(value_part)
         return category_dict
 
     @staticmethod
@@ -468,7 +485,7 @@ class CIFCategory(_Component, MutableMapping):
         data_lines = lines[i:]
         # Rows may be split over multiple lines -> do not rely on
         # row-line-alignment at all and simply cycle through columns
-        column_names = itertools.cycle(column_names)
+        column_indices = itertools.cycle(range(len(column_names)))
         for data_line in data_lines:
             # If whitespace is expected in quote protected values,
             # use regex-based _split_one_line() to split
@@ -485,9 +502,18 @@ class CIFCategory(_Component, MutableMapping):
                     ):
                         values[k] = values[k][1:-1]
             for val in values:
-                column_name = next(column_names)
+                column_index = next(column_indices)
+                column_name = column_names[column_index]
                 category_dict[column_name].append(val)
 
+        # Check if all columns have the same length
+        # Otherwise, this would indicate a parsing error or an invalid CIF file
+        column_index = next(column_indices)
+        if column_index != 0:
+            raise DeserializationError(
+                "Category contains columns with different lengths"
+            )
+
         return category_dict
 
     def _serialize_single(self):
@@ -496,7 +522,8 @@ class CIFCategory(_Component, MutableMapping):
         # "+3" Because of three whitespace chars after longest key
         req_len = max_len + 3
         return [
-            key.ljust(req_len) + _multiline(_quote(column.as_item()))
+            # Remove potential terminal newlines from multiline values
+            (key.ljust(req_len) + _escape(column.as_item())).strip()
             for key, column in zip(keys, self.values())
         ]
 
@@ -508,7 +535,7 @@ class CIFCategory(_Component, MutableMapping):
             array = column.as_array(str)
             # Quote before measuring the number of chars,
             # as the quote characters modify the length
-            array = np.array([_multiline(_quote(element)) for element in array])
+            array = np.array([_escape(element) for element in array])
             column_arrays.append(array)
 
         # Number of characters the longest string in the column needs
@@ -522,7 +549,8 @@ class CIFCategory(_Component, MutableMapping):
             for j, array in enumerate(column_arrays):
                 value_lines[i] += array[i].ljust(column_n_chars[j])
             # Remove trailing justification of last column
-            value_lines[i].rstrip()
+            # and potential terminal newlines from multiline values
+            value_lines[i] = value_lines[i].strip()
 
         return ["loop_"] + key_lines + value_lines
 
@@ -927,52 +955,50 @@ def _is_loop_start(line):
     return line.startswith("loop_")
 
 
-def _to_single(lines, is_looped):
-    """
+def _to_single(lines):
+    r"""
     Convert multiline values into singleline values
     (in terms of 'lines' list elements).
-    Linebreaks are preserved.
+    Linebreaks are preserved as ``'\n'`` characters within a list element.
+    The initial ``';'`` character is also preserved, while the final ``';'`` character
+    is removed.
     """
-    processed_lines = [None] * len(lines)
-    in_i = 0
-    out_i = 0
-    while in_i < len(lines):
-        if lines[in_i][0] == ";":
-            # Multiline value
-            multi_line_str = lines[in_i][1:]
-            j = in_i + 1
-            while lines[j] != ";":
-                # Preserve linebreaks
-                multi_line_str += "\n" + lines[j]
-                j += 1
-            if is_looped:
-                # Create a line for the multiline string only
-                processed_lines[out_i] = f"'{multi_line_str}'"
-                out_i += 1
+    processed_lines = []
+    in_multi_line = False
+    mutli_line_value = []
+    for line in lines:
+        # Multiline value are enclosed by ';' at the start of the beginning and end line
+        if line[0] == ";":
+            if not in_multi_line:
+                # Start of multiline value
+                in_multi_line = True
+                mutli_line_value.append(line)
             else:
-                # Append multiline string to previous line
-                processed_lines[out_i - 1] += " " + f"'{multi_line_str}'"
-            in_i = j + 1
-
-        elif not is_looped and lines[in_i][0] != "_":
-            # Singleline value in the line after the corresponding key
-            processed_lines[out_i - 1] += " " + lines[in_i]
-            in_i += 1
-
+                # End of multiline value
+                in_multi_line = False
+                # The current line contains only the end character ';'
+                # Hence this line is not added to the processed lines
+                processed_lines.append("\n".join(mutli_line_value))
+                mutli_line_value = []
         else:
-            # Normal singleline value in the same row as the key
-            processed_lines[out_i] = lines[in_i]
-            in_i += 1
-            out_i += 1
-
-    return [line for line in processed_lines if line is not None]
+            if in_multi_line:
+                mutli_line_value.append(line)
+            else:
+                processed_lines.append(line)
+    return processed_lines
 
 
-def _quote(value):
+def _escape(value):
     """
-    A less secure but much quicker version of ``shlex.quote()``.
+    Escape special characters in a value to make it compatible with CIF.
     """
-    if len(value) == 0:
+    if "\n" in value:
+        # A value with linebreaks must be represented as multiline value
+        return _multiline(value)
+    elif "'" in value and '"' in value:
+        # If both quote types are present, you cannot use them for escaping
+        return _multiline(value)
+    elif len(value) == 0:
         return "''"
     elif value[0] == "_":
         return "'" + value + "'"
@@ -990,12 +1016,10 @@ def _quote(value):
 
 def _multiline(value):
     """
-    Convert a string containing linebreaks into CIF-compatible
+    Convert a string that may contain linebreaks into CIF-compatible
     multiline string.
     """
-    if "\n" in value:
-        return "\n;" + value + "\n;\n"
-    return value
+    return "\n;" + value + "\n;\n"
 
 
 def _split_one_line(line):
@@ -1003,6 +1027,10 @@ def _split_one_line(line):
     Split a line into its fields.
     Supporting embedded quotes (' or "), like `'a dog's life'` to  `a dog's life`
     """
+    # Special case of multiline value, where the line starts with ';'
+    if line[0] == ";":
+        return [line[1:]]
+
     # Define the patterns for different types of fields
     single_quote_pattern = r"('(?:'(?! )|[^'])*')(?:\s|$)"
     double_quote_pattern = r'("(?:"(?! )|[^"])*")(?:\s|$)'

biotite/structure/io/pdbx/convert.py

@@ -450,7 +450,7 @@ 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",
@@ -458,21 +458,21 @@ 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))
@@ -577,7 +577,7 @@ def _parse_inter_residue_bonds(atom_site, struct_conn):
     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_order = struct_conn["pdbx_value_order"].as_array(str, "")
     # 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
@@ -964,25 +964,38 @@ 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
 
 
@@ -1007,6 +1020,7 @@ def _set_inter_residue_bonds(array, atom_site):
     bond_array = _filter_bonds(array, "inter")
     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")
@@ -1135,12 +1149,11 @@ 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")]

biotite/structure/io/trajfile.py

@@ -54,9 +54,9 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
 
         Parameters
         ----------
-        file_name : str
+        file_name : str or Path
             The path of the file to be read.
-            A file-like-object cannot be used.
+            Any other file-like object cannot be used.
         start : int, optional
             The frame index, where file parsing is started. If no value
             is given, parsing starts at the first frame.
@@ -101,7 +101,7 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
                 chunk_size = ((chunk_size // step) + 1) * step
 
         traj_type = cls.traj_type()
-        with traj_type(file_name, "r") as f:
+        with traj_type(str(file_name), "r") as f:
             if start is None:
                 start = 0
             # Discard atoms before start
@@ -153,9 +153,9 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
 
         Parameters
         ----------
-        file_name : str
+        file_name : str or Path
             The path of the file to be read.
-            A file-like-object cannot be used.
+            Any other file-like object cannot be used.
         start : int, optional
             The frame index, where file parsing is started. If no value
             is given, parsing starts at the first frame.
@@ -196,7 +196,7 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
         The `step` parameter does currently not work for *DCD* files.
         """
         traj_type = cls.traj_type()
-        with traj_type(file_name, "r") as f:
+        with traj_type(str(file_name), "r") as f:
             if start is None:
                 start = 0
             # Discard atoms before start
@@ -280,9 +280,9 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
 
         Parameters
         ----------
-        file_name : str
+        file_name : str or Path
             The path of the file to be read.
-            A file-like-object cannot be used.
+            Any other file-like object cannot be used.
         template : AtomArray or AtomArrayStack
             The template array or stack, where the atom annotation data
             is taken from.
@@ -354,13 +354,13 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
 
         Parameters
         ----------
-        file_name : str
-            The path of the file to be written to.
-            A file-like-object cannot be used.
+        file_name : str or Path
+            The path of the file to be read.
+            Any other file-like object cannot be used.
         """
         traj_type = self.traj_type()
         param = self.prepare_write_values(self._coord, self._box, self._time)
-        with traj_type(file_name, "w") as f:
+        with traj_type(str(file_name), "w") as f:
             f.write(**param)
 
     @classmethod
@@ -378,9 +378,9 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
 
         Parameters
         ----------
-        file_name : str
-            The path of the file to be written to.
-            A file-like-object cannot be used.
+        file_name : str or Path
+            The path of the file to be read.
+            Any other file-like object cannot be used.
         coord : generator or array-like of ndarray, shape=(n,3), dtype=float
             The atom coordinates for each frame.
         box : generator or array-like of ndarray, shape=(3,3), dtype=float, optional
@@ -398,7 +398,7 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
             time = itertools.repeat(None)
 
         traj_type = cls.traj_type()
-        with traj_type(file_name, "w") as f:
+        with traj_type(str(file_name), "w") as f:
             for c, b, t in zip(coord, box, time):
                 if c.ndim != 2:
                     raise IndexError(

biotite/version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.0.0'
-__version_tuple__ = version_tuple = (1, 0, 0)
+__version__ = version = '1.0.1'
+__version_tuple__ = version_tuple = (1, 0, 1)

{biotite-1.0.0.dist-info → biotite-1.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biotite
-Version: 1.0.0
+Version: 1.0.1
 Summary: A comprehensive library for computational molecular biology
 Project-URL: homepage, https://www.biotite-python.org
 Project-URL: repository, https://github.com/biotite-dev/biotite
@@ -56,6 +56,7 @@ Requires-Dist: numpy>=1.25
 Requires-Dist: requests>=2.12
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-codspeed; extra == 'test'
 Description-Content-Type: text/x-rst
 
 .. image:: https://img.shields.io/pypi/v/biotite.svg

{biotite-1.0.0.dist-info → biotite-1.0.1.dist-info}/RECORD

@@ -1,8 +1,4 @@
-biotite-1.0.0.dist-info/RECORD,,
-biotite-1.0.0.dist-info/WHEEL,sha256=0oG4CjoGfYHRJPy3gHncDJdYpmnqlf1ZuriAgA0fRmw,106
-biotite-1.0.0.dist-info/METADATA,sha256=C6tIVbg8HfB-DgcNYsM7sb56iNpH-n4EulEWtL_-2fQ,7111
-biotite-1.0.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
-biotite/version.py,sha256=DGJ4pj32xs3_DRJhSzQwCiRNnAQrMgo09USYpyMZsKc,411
+biotite/version.py,sha256=IIj5MPQqf7H30zvHF3gsfSLSw1SsdlKYR9SngW-9GC8,411
 biotite/copyable.py,sha256=C7ycTQxqanxT0SmXhzy5OLp7NpZdNWHyokozdoVDGNA,1897
 biotite/__init__.py,sha256=rL8ZyaCUjOrECEvRxyHj8MOMp4FHMJ8n6KKgrYf5OAQ,545
 biotite/visualize.py,sha256=EYUBKgeNrkPI53f7L4T893NMmLWgBp07aO2XFcdpYTU,10012
@@ -65,7 +61,7 @@ biotite/sequence/__init__.py,sha256=fSWhobaPGRMJI6-8UYFpjguxVtP4O4cAHmiRxNAGzYI,
 biotite/sequence/seqtypes.py,sha256=zdj3fFkb_EDB0T4rqQuq-ErtX6TcFiP8kZ0tWINibnI,19346
 biotite/sequence/codon.py,sha256=6SBjwz4c6IZiAFZL03qjcrjT84zczltc14haOOAkm6Q,16392
 biotite/sequence/search.py,sha256=dF-OtPocZ5XAIgS4GCMt2YOKz0Oxb9b8FvPmVUY8j-k,3089
-biotite/sequence/codec.cpython-312-darwin.so,sha256=cdGbxYio-bCY-yPHKKqa22sj7pEFosV_2lNd4M-3njs,282056
+biotite/sequence/codec.cpython-312-darwin.so,sha256=MCuoSegNP7mrlLQGZHH0Y7fbOWxLAEhC1EhL5vAgD1M,282056
 biotite/sequence/alphabet.py,sha256=OiUxnsbTaxuDjAiB96sVHYTOqG3XvwF5ceJ3tvViqh4,17190
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 biotite/sequence/graphics/color_schemes/clustalx_dna.json,sha256=xkNRgGj_ersYNx8eSDAnI1HQalGiAWHw97tO_pmfyNE,249
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@@ -268,19 +264,19 @@ biotite/structure/hbond.py,sha256=4y2FXeAXl7g2EDnwb1uDXFieGpZPQhnnkdATBechvW8,15
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@@ -297,7 +293,7 @@ biotite/structure/io/mol/__init__.py,sha256=WvcNPDdf9W1zPyJ0tjTvGNxA83ht18uRQA8B
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@@ -320,3 +316,7 @@ biotite/structure/info/ccd/nucleotides.txt,sha256=Q7Zjz45BAO6c2QDAgvYdKtWAqmjQxy
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