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

biotite/application/dssp/app.py

@@ -6,10 +6,11 @@ __name__ = "biotite.application.dssp"
 __author__ = "Patrick Kunzmann"
 __all__ = ["DsspApp"]
 
+from subprocess import SubprocessError
 from tempfile import NamedTemporaryFile
 import numpy as np
 from biotite.application.application import AppState, requires_state
-from biotite.application.localapp import LocalApp, cleanup_tempfile
+from biotite.application.localapp import LocalApp, cleanup_tempfile, get_version
 from biotite.structure.io.pdbx.cif import CIFFile
 from biotite.structure.io.pdbx.convert import set_structure
 
@@ -72,7 +73,13 @@ class DsspApp(LocalApp):
             self._array.set_annotation(
                 "occupancy", np.ones(self._array.array_length(), dtype=float)
             )
-
+        try:
+            # The parameters have changed in version 4
+            self._new_cli = get_version(bin_path)[0] >= 4
+        except SubprocessError:
+            # In older versions, the no version is returned with `--version`
+            # -> a SubprocessError is raised
+            self._new_cli = False
         self._in_file = NamedTemporaryFile("w", suffix=".cif", delete=False)
         self._out_file = NamedTemporaryFile("r", suffix=".dssp", delete=False)
 
@@ -81,7 +88,10 @@ class DsspApp(LocalApp):
         set_structure(in_file, self._array)
         in_file.write(self._in_file)
         self._in_file.flush()
-        self.set_arguments(["-i", self._in_file.name, "-o", self._out_file.name])
+        if self._new_cli:
+            self.set_arguments([self._in_file.name, self._out_file.name])
+        else:
+            self.set_arguments(["-i", self._in_file.name, "-o", self._out_file.name])
         super().run()
 
     def evaluate(self):

biotite/application/localapp.py

@@ -8,7 +8,10 @@ __all__ = ["LocalApp"]
 
 import abc
 import copy
+import re
+import subprocess
 from os import chdir, getcwd, remove
+from pathlib import Path
 from subprocess import PIPE, Popen, SubprocessError, TimeoutExpired
 from biotite.application.application import (
     Application,
@@ -306,3 +309,34 @@ def cleanup_tempfile(temp_file):
     except FileNotFoundError:
         # File was already deleted, e.g. due to `TemporaryFile(delete=True)`
         pass
+
+
+def get_version(bin_path, version_option="--version"):
+    """
+    Get the version of a locally installed application.
+
+    Parameters
+    ----------
+    bin_path : str or Path
+        Path of the application.
+    version_option : str, optional
+        The command line option to get the version.
+
+    Returns
+    -------
+    major, minor : int
+        The major and minor version number.
+    """
+    output = subprocess.run(
+        [bin_path, version_option], capture_output=True, text=True
+    ).stdout
+    # Find matches for version string containing major and minor version
+    match = re.search(r"\d+\.\d+", output)
+    if match is None:
+        raise subprocess.SubprocessError(
+            f"Could not determine '{Path(bin_path).name}' version "
+            f"from the string '{output}'"
+        )
+    version_string = match.group(0)
+    splitted = version_string.split(".")
+    return int(splitted[0]), int(splitted[1])

biotite/application/muscle/app3.py

@@ -7,13 +7,11 @@ __author__ = "Patrick Kunzmann"
 __all__ = ["MuscleApp"]
 
 import numbers
-import re
-import subprocess
 import warnings
 from collections.abc import Sequence
 from tempfile import NamedTemporaryFile
 from biotite.application.application import AppState, VersionError, requires_state
-from biotite.application.localapp import cleanup_tempfile
+from biotite.application.localapp import cleanup_tempfile, get_version
 from biotite.application.msaapp import MSAApp
 from biotite.sequence.phylo.tree import Tree
 
@@ -54,7 +52,7 @@ class MuscleApp(MSAApp):
     """
 
     def __init__(self, sequences, bin_path="muscle", matrix=None):
-        major_version = get_version(bin_path)[0]
+        major_version = get_version(bin_path, "-version")[0]
         if major_version != 3:
             raise VersionError(f"Muscle 3 is required, got version {major_version}")
 
@@ -227,14 +225,3 @@ class MuscleApp(MSAApp):
         app.start()
         app.join()
         return app.get_alignment()
-
-
-def get_version(bin_path="muscle"):
-    output = subprocess.run([bin_path, "-version"], capture_output=True, text=True)
-    # Find matches for version string containing major and minor version
-    match = re.search(r"\d+\.\d+", output.stdout)
-    if match is None:
-        raise subprocess.SubprocessError("Could not determine Muscle version")
-    version_string = match.group(0)
-    splitted = version_string.split(".")
-    return int(splitted[0]), int(splitted[1])

biotite/application/muscle/app5.py

@@ -7,8 +7,8 @@ __author__ = "Patrick Kunzmann"
 __all__ = ["Muscle5App"]
 
 from biotite.application.application import AppState, VersionError, requires_state
+from biotite.application.localapp import get_version
 from biotite.application.msaapp import MSAApp
-from biotite.application.muscle.app3 import get_version
 
 
 class Muscle5App(MSAApp):
@@ -49,7 +49,7 @@ class Muscle5App(MSAApp):
     """
 
     def __init__(self, sequences, bin_path="muscle"):
-        major_version = get_version(bin_path)[0]
+        major_version = get_version(bin_path, "-version")[0]
         if major_version < 5:
             raise VersionError(
                 f"At least Muscle 5 is required, got version {major_version}"

biotite/application/util.py

@@ -50,7 +50,7 @@ def map_matrix(matrix):
     # All trailing symbols are filled with zeros
     old_length = len(matrix.get_alphabet1())
     new_length = len(ProteinSequence.alphabet)
-    new_score_matrix = np.zeros((new_length, new_length))
+    new_score_matrix = np.zeros((new_length, new_length), dtype=np.int32)
     new_score_matrix[:old_length, :old_length] = matrix.score_matrix()
     return SubstitutionMatrix(
         ProteinSequence.alphabet, ProteinSequence.alphabet, new_score_matrix

biotite/application/viennarna/rnaplot.py

@@ -99,8 +99,12 @@ class RNAplotApp(LocalApp):
         self._in_file.write(self._dot_bracket)
         self._in_file.flush()
         self.set_arguments(
-            ["-i", self._in_file.name, "-o", "xrna", "-t", self._layout_type]
-        )
+            [
+                "-i", self._in_file.name,
+                "--output-format", "xrna",
+                "-t", self._layout_type,
+            ]
+        )  # fmt: skip
         super().run()
 
     def evaluate(self):

biotite/database/rcsb/query.py

@@ -146,9 +146,9 @@ class BasicQuery(SingleQuery):
     Examples
     --------
 
-    >>> query = BasicQuery("tc5b")
+    >>> query = BasicQuery("Miniprotein Construct")
     >>> print(sorted(search(query)))
-    ['1L2Y', '8ANG', '8ANH', '8ANI', '8ANM', '8QWW']
+    ['1L2Y']
     """
 
     def __init__(self, term):
@@ -346,9 +346,9 @@ class SequenceQuery(SingleQuery):
     --------
 
     >>> sequence = "NLYIQWLKDGGPSSGRPPPS"
-    >>> query = SequenceQuery(sequence, scope="protein", min_identity=0.8)
+    >>> query = SequenceQuery(sequence, scope="protein", min_identity=0.95)
     >>> print(sorted(search(query)))
-    ['1L2Y', '1RIJ', '2JOF', '2LDJ', '2LL5', '2MJ9', '3UC7', '3UC8']
+    ['1L2Y', '2LDJ', '9G22', '9G2N', '9G2O', '9G31', '9G32', '9GDL', '9GDN', '9GDT', '9GDU', '9GE1']
     """
 
     def __init__(self, sequence, scope, min_identity=0.0, max_expect_value=10000000.0):
@@ -441,7 +441,7 @@ class StructureQuery(SingleQuery):
 
     >>> query = StructureQuery("1L2Y", chain="A")
     >>> print(sorted(search(query)))
-    ['1L2Y', '1RIJ', '2JOF', '2LDJ', '2M7D', '7MQS']
+    ['1L2Y', '1RIJ', '2JOF', '2LDJ', '2M7D', '7MQS', '9DPF']
     """
 
     def __init__(self, pdb_id, chain=None, assembly=None, strict=True):
@@ -868,7 +868,7 @@ def search(
     ...     query, return_type="polymer_entity", return_groups=True,
     ...     group_by=UniprotGrouping(sort_by="rcsb_accession_info.initial_release_date"),
     ... ))
-     {'P24297': ['5NW3_1'], 'P27707': ['4JLJ_1'], 'P80176': ['5D8V_1'], 'O29777': ['7R0H_1'], 'P01542': ['1EJG_1', '3NIR_1']}
+    {'P24297': ['5NW3_1'], 'P27707': ['4JLJ_1'], 'P80176': ['5D8V_1'], 'O29777': ['7R0H_1'], 'P01542': ['3NIR_1', '1EJG_1']}
     """
     query_dict = _initialize_query_dict(query, return_type, group_by, content_types)
 

biotite/database/uniprot/check.py

@@ -10,7 +10,7 @@ from biotite.database.error import RequestError
 
 
 # Taken from https://www.uniprot.org/help/api_retrieve_entries
-def assert_valid_response(response_status_code):
+def assert_valid_response(response):
     """
     Checks whether the response is valid.
 
@@ -19,17 +19,22 @@ def assert_valid_response(response_status_code):
     response_status_code: int
         Status code of request.get.
     """
-    if response_status_code == 400:
-        raise RequestError("Bad request. There is a problem with your input.")
-    elif response_status_code == 404:
-        raise RequestError("Not found. The resource you requested doesn't exist.")
-    elif response_status_code == 410:
-        raise RequestError("Gone. The resource you requested was removed.")
-    elif response_status_code == 500:
-        raise RequestError(
-            "Internal server error. Most likely a temporary problem, but if the problem persists please contact UniProt team."
-        )
-    elif response_status_code == 503:
-        raise RequestError(
-            "Service not available. The server is being updated, try again later."
-        )
+    if len(response.content) == 0:
+        raise RequestError("No content returned")
+    match response.status_code:
+        case 400:
+            raise RequestError("Bad request. There is a problem with your input.")
+        case 404:
+            raise RequestError("Not found. The resource you requested doesn't exist.")
+        case 410:
+            raise RequestError("Gone. The resource you requested was removed.")
+        case 500:
+            raise RequestError(
+                "Internal server error. "
+                "Most likely a temporary problem, "
+                "but if the problem persists please contact UniProt team."
+            )
+        case 503:
+            raise RequestError(
+                "Service not available. The server is being updated, try again later."
+            )

biotite/database/uniprot/download.py

@@ -111,7 +111,7 @@ def fetch(ids, format, target_path=None, overwrite=False, verbose=False):
             if format in ["fasta", "gff", "txt", "xml", "rdf", "tab"]:
                 r = requests.get(_fetch_url + db_name + "/" + id + "." + format)
                 content = r.text
-                assert_valid_response(r.status_code)
+                assert_valid_response(r)
             else:
                 raise ValueError(f"Format '{format}' is not supported")
             if file is None:

biotite/database/uniprot/query.py

@@ -289,5 +289,5 @@ def search(query, number=500):
     params = {"query": str(query), "format": "list", "size": str(number)}
     r = requests.get(_base_url, params=params)
     content = r.text
-    assert_valid_response(r.status_code)
+    assert_valid_response(r)
     return content.split("\n")[:-1]

biotite/sequence/align/alignment.py

@@ -9,7 +9,6 @@ import numbers
 import textwrap
 from collections.abc import Sequence
 import numpy as np
-from biotite.sequence.alphabet import LetterAlphabet
 
 __all__ = [
     "Alignment",
@@ -111,7 +110,7 @@ class Alignment(object):
         for i in range(len(self.trace)):
             j = self.trace[i][seq_index]
             if j != -1:
-                seq_str += self.sequences[seq_index][j]
+                seq_str += str(self.sequences[seq_index][j])
             else:
                 seq_str += "-"
         return seq_str
@@ -133,7 +132,7 @@ class Alignment(object):
         # has an non-single letter alphabet
         all_single_letter = True
         for seq in self.sequences:
-            if not isinstance(seq.get_alphabet(), LetterAlphabet):
+            if not _is_single_letter(seq.alphabet):
                 all_single_letter = False
         if all_single_letter:
             # First dimension: sequence number,
@@ -665,3 +664,17 @@ def remove_terminal_gaps(alignment):
             "no overlap and the resulting alignment would be empty"
         )
     return alignment[start:stop]
+
+
+def _is_single_letter(alphabet):
+    """
+    More relaxed version of :func:`biotite.sequence.alphabet.is_letter_alphabet()`:
+    It is sufficient that only only the string representation of each symbol is only
+    a single character.
+    """
+    if alphabet.is_letter_alphabet():
+        return True
+    for symbol in alphabet:
+        if len(str(symbol)) != 1:
+            return False
+    return True

biotite/sequence/align/banded.pyx

@@ -214,9 +214,6 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
     else:
         is_swapped = False
     lower_diag, upper_diag = min(band), max(band)
-    band_width = upper_diag - lower_diag + 1
-    if band_width < 1:
-        raise ValueError("The width of the band is 0")
     if len(seq1) + upper_diag <= 0 or lower_diag >= len(seq2):
         raise ValueError(
             "Alignment band is out of range, the band allows no overlap "
@@ -226,6 +223,9 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
     # covers the search space of an unbanded alignment
     lower_diag = max(lower_diag, -len(seq1)+1)
     upper_diag = min(upper_diag,  len(seq2)-1)
+    band_width = upper_diag - lower_diag + 1
+    if band_width < 1:
+        raise ValueError("The width of the band is 0")
 
     # This implementation uses transposed tables in comparison
     # to the common visualization
@@ -249,12 +249,12 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
     ###############
     
     # A score value that signals that the respective direction in the
-    # dynamic programming matrix should not be used since, it would be
+    # dynamic programming matrix should not be used, since it would be
     # outside the band
     # It is the 'worst' score available, so the trace table will never
     # include such a direction
     neg_inf = np.iinfo(np.int32).min
-    # Correct the 'negative infinity' integer, by making it more positve
+    # Correct the 'negative infinity' integer, by making it more positive
     # This prevents an integer underflow when the gap penalty or
     # match score is added to this value
     neg_inf -= min(gap_penalty) if affine_penalty else gap_penalty

biotite/sequence/align/kmeralphabet.pyx

@@ -568,6 +568,23 @@ class KmerAlphabet(Alphabet):
         return int(len(self._base_alph) ** self._k)
 
 
+    def __iter__(self):
+        # Creating all symbols is expensive
+        # -> Use a generator instead
+        if isinstance(self._base_alph, LetterAlphabet):
+            return ("".join(self.decode(code)) for code in range(len(self)))
+        else:
+            return (list(self.decode(code)) for code in range(len(self)))
+
+
+    def __contains__(self, symbol):
+        try:
+            self.fuse(self._base_alph.encode_multiple(symbol))
+            return True
+        except AlphabetError:
+            return False
+
+
 def _to_array_form(model_string):
     """
     Convert the the common string representation of a *k-mer* spacing

biotite/sequence/align/kmertable.pyx

@@ -1384,8 +1384,7 @@ cdef class KmerTable:
 
 
     def __getstate__(self):
-        relevant_kmers = self.get_kmers()
-        return _pickle_c_arrays(self._ptr_array, relevant_kmers)
+        return _pickle_c_arrays(self._ptr_array)
 
 
     def __setstate__(self, state):
@@ -2836,12 +2835,7 @@ cdef class BucketKmerTable:
 
 
     def __getstate__(self):
-        cdef int64[:] relevant_buckets = np.where(
-            np.asarray(self._ptr_array) != 0
-        )[0]
-        return _pickle_c_arrays(self._ptr_array, relevant_buckets)
-
-
+        return _pickle_c_arrays(self._ptr_array)
 
     def __setstate__(self, state):
         _unpickle_c_arrays(self._ptr_array, state)
@@ -3097,27 +3091,44 @@ def _append_entries(ptr[:] trg_ptr_array, ptr[:] src_ptr_array):
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-def _pickle_c_arrays(ptr[:] ptr_array, int64[:] relevant_buckets):
+def _pickle_c_arrays(ptr[:] ptr_array):
     """
-    Pickle the `relevant_buckets` (i.e. the buckets that actualy point
-    to an array) of the `ptr_array` into a list of bytes.
+    Pickle the C arrays into a single concatenated :class:`ndarray`.
+    The lengths of each C-array on these concatenated array is saved as well.
     """
-    cdef int64 i
-    cdef int64 bucket
+    cdef int64 pointer_i, bucket_i, concat_i
     cdef int64 length
     cdef uint32* bucket_ptr
 
-    cdef list pickled_arrays = [b""] * relevant_buckets.shape[0]
-
-    for i in range(relevant_buckets.shape[0]):
-        bucket = relevant_buckets[i]
-        bucket_ptr = <uint32*>ptr_array[bucket]
-        length = (<int64*>bucket_ptr)[0]
-        # Get directly the bytes coding for each C-array
-        pickled_arrays[i] \
-            = <bytes>(<char*>bucket_ptr)[:sizeof(uint32) * length]
+    # First pass: Count the total concatenated size
+    cdef int64 total_length = 0
+    for pointer_i in range(ptr_array.shape[0]):
+        bucket_ptr = <uint32*>ptr_array[pointer_i]
+        if bucket_ptr != NULL:
+            # The first element of the C-array is the length
+            # of the array
+            total_length += (<int64*>bucket_ptr)[0]
+
+    # Second pass: Copy the C-arrays into a single concatenated array
+    # and track the start position of each C-array
+    cdef uint32[:] concatenated_array = np.empty(total_length, dtype=np.uint32)
+    cdef int64[:] lengths = np.empty(ptr_array.shape[0], dtype=np.int64)
+    concat_i = 0
+    for pointer_i in range(ptr_array.shape[0]):
+        bucket_ptr = <uint32*>ptr_array[pointer_i]
+        if bucket_ptr != NULL:
+            length = (<int64*>bucket_ptr)[0]
+            lengths[pointer_i] = length
+            memcpy(
+                &concatenated_array[concat_i],
+                bucket_ptr,
+                length * sizeof(uint32),
+            )
+            concat_i += length
+        else:
+            lengths[pointer_i] = 0
 
-    return np.asarray(relevant_buckets), pickled_arrays
+    return np.asarray(concatenated_array), np.asarray(lengths)
 
 
 @cython.boundscheck(False)
@@ -3126,28 +3137,27 @@ def _unpickle_c_arrays(ptr[:] ptr_array, state):
     """
     Unpickle the pickled `state` into the given `ptr_array`.
     """
-    cdef int64 i
-    cdef int64 bucket
-    cdef int64 byte_length
+    cdef int64 pointer_i, concat_i
+    cdef int64 length
     cdef uint32* bucket_ptr
-    cdef bytes pickled_bytes
-
-    cdef int64[:] relevant_buckets = state[0]
-    cdef list pickled_pointers = state[1]
-
-    for i in range(relevant_buckets.shape[0]):
-        bucket = relevant_buckets[i]
-        if bucket < 0 or bucket >= ptr_array.shape[0]:
-            raise ValueError("Invalid bucket found while unpickling")
-        pickled_bytes = pickled_pointers[i]
-        byte_length = len(pickled_bytes)
-        if byte_length != 0:
-            bucket_ptr = <uint32*>malloc(byte_length)
+
+    cdef uint32[:] concatenated_array = state[0]
+    cdef int64[:] lengths = state[1]
+
+    concat_i = 0
+    for pointer_i in range(ptr_array.shape[0]):
+        length = lengths[pointer_i]
+        if length != 0:
+            bucket_ptr = <uint32*>malloc(length * sizeof(uint32))
             if not bucket_ptr:
                 raise MemoryError
-            # Convert bytes back into C-array
-            memcpy(bucket_ptr, <char*>pickled_bytes, byte_length)
-            ptr_array[bucket] = <ptr>bucket_ptr
+            memcpy(
+                bucket_ptr,
+                &concatenated_array[concat_i],
+                length * sizeof(uint32),
+            )
+            concat_i += length
+            ptr_array[pointer_i] = <ptr>bucket_ptr
 
 
 cdef inline void _deallocate_ptrs(ptr[:] ptrs):