biotite 1.0.1__cp311-cp311-macosx_10_9_x86_64.whl → 1.2.0__cp311-cp311-macosx_10_9_x86_64.whl

biotite/application/application.py

@@ -157,7 +157,7 @@ class Application(metaclass=abc.ABCMeta):
             if timeout is not None and time.time() - self._start_time > timeout:
                 self.cancel()
                 raise TimeoutError(
-                    f"The application expired its timeout " f"({timeout:.1f} s)"
+                    f"The application expired its timeout ({timeout:.1f} s)"
                 )
             else:
                 time.sleep(self.wait_interval())
@@ -214,7 +214,7 @@ class Application(metaclass=abc.ABCMeta):
         Returns
         -------
         finished : bool
-            True of the application has finished, false otherwise
+            True of the application has finished, false otherwise.
         """
         pass
 
@@ -230,7 +230,7 @@ class Application(metaclass=abc.ABCMeta):
         -------
         interval : float
             Time (in seconds) between calls of :func:`is_finished()` in
-            :func:`join()`
+            :func:`join()`.
         """
         pass
 

biotite/application/autodock/app.py

@@ -153,7 +153,7 @@ class VinaApp(LocalApp):
 
         Parameters
         ----------
-        number : float
+        energy_range : float
             The energy range (kcal/mol).
         """
         self._energy_range = energy_range

biotite/application/blast/webapp.py

@@ -46,7 +46,7 @@ class BlastWebApp(WebApp):
     obey_rules : bool, optional
         If true, the application raises an :class:`RuleViolationError`,
         if the server is contacted too often, based on the NCBI BLAST
-        usage rules. (Default: True)
+        usage rules.
     mail : str, optional
         If a mail address is provided, it will be appended in the
         HTTP request. This allows the NCBI to contact you in case

biotite/application/clustalo/app.py

@@ -172,7 +172,7 @@ class ClustalOmegaApp(MSAApp):
         """
         if self._mbed:
             raise ValueError(
-                "Getting the distance matrix requires " "'full_matrix_calculation()'"
+                "Getting the distance matrix requires 'full_matrix_calculation()'"
             )
         return self._dist_matrix
 

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,
@@ -175,7 +178,7 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         Returns
         -------
         process : Popen
-            The `Popen` instance
+            The `Popen` instance.
         """
         return self._process
 
@@ -276,7 +279,7 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         if exit_code != 0:
             err_msg = self.get_stderr().replace("\n", " ")
             raise SubprocessError(
-                f"'{self._bin_path}' returned with exit code {exit_code}: " f"{err_msg}"
+                f"'{self._bin_path}' returned with exit code {exit_code}: {err_msg}"
             )
 
     def clean_up(self):
@@ -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/msaapp.py

@@ -68,7 +68,7 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         # Check matrix symmetry
         if matrix is not None and not matrix.is_symmetric():
             raise ValueError(
-                "A symmetric matrix is required for " "multiple sequence alignments"
+                "A symmetric matrix is required for multiple sequence alignments"
             )
 
         # Check whether the program supports the alignment for the given
@@ -274,12 +274,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports nucleotide sequences for
         alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -290,12 +290,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports nucleotide sequences for
         alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -306,12 +306,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports custom substitution matrices
         for protein sequence alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -322,12 +322,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports custom substitution matrices
         for nucleotide sequence alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -342,7 +342,7 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Parameters
         ----------
         sequences : iterable object of Sequence
-            The sequences to be aligned
+            The sequences to be aligned.
         bin_path : str, optional
             Path of the MSA software binary. By default, the default
             path will be used.

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
 
@@ -31,9 +29,9 @@ class MuscleApp(MSAApp):
     matrix : SubstitutionMatrix, optional
         A custom substitution matrix.
 
-    See also
+    See Also
     --------
-    Muscle5App
+    Muscle5App : Interface to MUSCLE version ``>=5``.
 
     Examples
     --------
@@ -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}")
 
@@ -199,7 +197,7 @@ class MuscleApp(MSAApp):
         Parameters
         ----------
         sequences : iterable object of Sequence
-            The sequences to be aligned
+            The sequences to be aligned.
         bin_path : str, optional
             Path of the MSA software binary. By default, the default path
             will be used.
@@ -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):
@@ -22,9 +22,9 @@ class Muscle5App(MSAApp):
     bin_path : str, optional
         Path of the MUSCLE binary.
 
-    See also
+    See Also
     --------
-    MuscleApp
+    MuscleApp : Interface to MUSCLE version ``<5``.
 
     Notes
     -----
@@ -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}"
@@ -147,7 +147,7 @@ class Muscle5App(MSAApp):
         Parameters
         ----------
         sequences : iterable object of Sequence
-            The sequences to be aligned
+            The sequences to be aligned.
         bin_path : str, optional
             Path of the MSA software binary. By default, the default path
             will be used.

biotite/application/sra/app.py

@@ -45,11 +45,6 @@ class _DumpApp(Application, metaclass=abc.ABCMeta):
     prefetch_path, fasterq_dump_path : str, optional
         Path to the ``prefetch_path`` and ``fasterq-dump`` binary,
         respectively.
-    offset : int or {'Sanger', 'Solexa', 'Illumina-1.3', 'Illumina-1.5', 'Illumina-1.8'}, optional
-        This value is subtracted from the FASTQ ASCII code to obtain the
-        quality score.
-        Can either be directly the value, or a string that indicates
-        the score format.
     """
 
     def __init__(

biotite/application/util.py

@@ -17,6 +17,16 @@ def map_sequence(sequence):
     Map a sequence with an arbitrary alphabet into a
     :class:`ProteinSequence`, in order to support arbitrary sequence
     types in software that can handle protein sequences.
+
+    Parameters
+    ----------
+    sequence : Sequence
+        The sequence to be mapped.
+
+    Returns
+    -------
+    mapped_sequence : ProteinSequence
+        The mapped sequence.
     """
     if len(sequence.alphabet) > len(ProteinSequence.alphabet):
         # Cannot map into a protein sequence if the alphabet
@@ -40,17 +50,27 @@ def map_matrix(matrix):
     class:`SubstitutionMatrix` for protein sequences, in order to support
     arbitrary sequence types in software that can handle protein
     sequences.
+
+    Parameters
+    ----------
+    matrix : SubstitutionMatrix
+        The substitution matrix to be mapped.
+
+    Returns
+    -------
+    mapped_matrix : SubstitutionMatrix
+        The mapped substitution matrix.
     """
     if matrix is None:
         raise TypeError(
-            "A substitution matrix must be provided for custom " "sequence types"
+            "A substitution matrix must be provided for custom sequence types"
         )
     # Create a protein substitution matrix with the values taken
     # from the original 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/rnaalifold.py

@@ -167,15 +167,15 @@ class RNAalifoldApp(LocalApp):
         free_energy : float
             The free energy.
 
+        See Also
+        --------
+        get_covariance_energy : Get the energy of the artificial covariance term.
+
         Notes
         -----
         The total energy of the secondary structure regarding the
         minimization objective is the sum of the free energy and the
         covariance term.
-
-        See also
-        --------
-        get_covariance_energy
         """
         return self._free_energy
 
@@ -190,15 +190,15 @@ class RNAalifoldApp(LocalApp):
         covariance_energy : float
             The energy of the covariance term.
 
+        See Also
+        --------
+        get_free_energy : Get the free energy.
+
         Notes
         -----
         The total energy of the secondary structure regarding the
         minimization objective is the sum of the free energy and the
         covariance term.
-
-        See also
-        --------
-        get_free_energy
         """
         return self._covariance_energy
 

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):
@@ -120,7 +124,7 @@ class RNAplotApp(LocalApp):
 
         Parameters
         ----------
-        type : RNAplotApp.Layout
+        layout_type : RNAplotApp.Layout
             The layout type.
         """
         self._layout_type = str(layout_type)
@@ -181,6 +185,8 @@ class RNAplotApp(LocalApp):
         length : int, optional (default: None)
             The number of bases in the strand. This parameter is
             required if ``base_pairs`` is given.
+        layout_type : Layout
+            The desired layout of the plot.
         bin_path : str, optional
             Path of the *RNAplot* binary.
 

biotite/application/viennarna/util.py

@@ -39,7 +39,7 @@ def build_constraint_string(
     Returns
     -------
     constraints : str
-        The constraint string
+        The constraint string.
     """
     constraints = np.full(sequence_length, ".", dtype="U1")
 

biotite/application/webapp.py

@@ -29,7 +29,7 @@ class WebApp(Application, metaclass=abc.ABCMeta):
         URL of the web app.
     obey_rules : bool, optional
         If true, the application raises an :class:`RuleViolationError`, if
-        the server rules are violated. (Default: True)
+        the server rules are violated.
     """
 
     def __init__(self, app_url, obey_rules=True):

biotite/database/afdb/__init__.py

@@ -0,0 +1,12 @@
+# 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.
+
+"""
+A subpackage for downloading predicted protein structures from the AlphaFold DB.
+"""
+
+__name__ = "biotite.database.afdb"
+__author__ = "Alex Carlin"
+
+from .download import *