biotite 0.41.2__cp312-cp312-macosx_11_0_arm64.whl → 1.0.0__cp312-cp312-macosx_11_0_arm64.whl

biotite/application/viennarna/rnaalifold.py

@@ -9,12 +9,12 @@ __all__ = ["RNAalifoldApp"]
 import copy
 from tempfile import NamedTemporaryFile
 import numpy as np
-from ..application import AppState, requires_state
-from ..localapp import LocalApp, cleanup_tempfile
-from ...sequence.io.fasta import FastaFile, set_alignment
-from ...structure.dotbracket import base_pairs_from_dot_bracket
-from ...structure.bonds import BondList
-from .util import build_constraint_string
+from biotite.application.application import AppState, requires_state
+from biotite.application.localapp import LocalApp, cleanup_tempfile
+from biotite.application.viennarna.util import build_constraint_string
+from biotite.sequence.io.fasta import FastaFile, set_alignment
+from biotite.structure.bonds import BondList
+from biotite.structure.dotbracket import base_pairs_from_dot_bracket
 
 
 class RNAalifoldApp(LocalApp):
@@ -45,9 +45,7 @@ class RNAalifoldApp(LocalApp):
         self._temperature = str(temperature)
         self._constraints = None
         self._enforce = None
-        self._in_file = NamedTemporaryFile(
-            "w", suffix=".fa", delete=False
-        )
+        self._in_file = NamedTemporaryFile("w", suffix=".fa", delete=False)
         self._constraints_file = NamedTemporaryFile(
             "w+", suffix=".constraints", delete=False
         )
@@ -57,15 +55,17 @@ class RNAalifoldApp(LocalApp):
         # -> Extremely high value for characters per line
         fasta_file = FastaFile(chars_per_line=np.iinfo(np.int32).max)
         set_alignment(
-            fasta_file, self._alignment,
-            seq_names=[str(i) for i in range(len(self._alignment.sequences))]
+            fasta_file,
+            self._alignment,
+            seq_names=[str(i) for i in range(len(self._alignment.sequences))],
         )
         fasta_file.write(self._in_file)
         self._in_file.flush()
 
         options = [
             "--noPS",
-            "-T", self._temperature,
+            "-T",
+            self._temperature,
         ]
         if self._enforce is True:
             options.append("--enforceConstraint")
@@ -78,7 +78,7 @@ class RNAalifoldApp(LocalApp):
 
         self.set_arguments(options + [self._in_file.name])
         super().run()
-    
+
     def clean_up(self):
         super().clean_up()
         cleanup_tempfile(self._in_file)
@@ -97,7 +97,7 @@ class RNAalifoldApp(LocalApp):
         self._free_energy = float(energy_contributions[0])
         self._covariance_energy = float(energy_contributions[1])
         self._dotbracket = dotbracket
-    
+
     @requires_state(AppState.CREATED)
     def set_temperature(self, temperature):
         """
@@ -110,10 +110,17 @@ class RNAalifoldApp(LocalApp):
             The temperature.
         """
         self._temperature = str(temperature)
-    
+
     @requires_state(AppState.CREATED)
-    def set_constraints(self, pairs=None, paired=None, unpaired=None,
-                        downstream=None, upstream=None, enforce=False):
+    def set_constraints(
+        self,
+        pairs=None,
+        paired=None,
+        unpaired=None,
+        downstream=None,
+        upstream=None,
+        enforce=False,
+    ):
         """
         Add constraints of known paired or unpaired bases to the folding
         algorithm.
@@ -138,15 +145,14 @@ class RNAalifoldApp(LocalApp):
             the respective base pairs must form.
             By default (false), a constraint does only forbid formation
             of a pair that would conflict with this constraint.
-        
+
         Warnings
         --------
         If a constraint is given for a gap position in the consensus sequence,
         the software may find no base pairs at all.
         """
         self._constraints = build_constraint_string(
-            len(self._alignment),
-            pairs, paired, unpaired, downstream, upstream
+            len(self._alignment), pairs, paired, unpaired, downstream, upstream
         )
         self._enforce = enforce
 
@@ -160,19 +166,19 @@ class RNAalifoldApp(LocalApp):
         -------
         free_energy : float
             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_covariance_energy
         """
         return self._free_energy
-    
+
     @requires_state(AppState.JOINED)
     def get_covariance_energy(self):
         """
@@ -183,19 +189,19 @@ class RNAalifoldApp(LocalApp):
         -------
         covariance_energy : float
             The energy of the 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_free_energy
         """
         return self._covariance_energy
-    
+
     @requires_state(AppState.JOINED)
     def get_consensus_sequence_string(self):
         """
@@ -265,7 +271,7 @@ class RNAalifoldApp(LocalApp):
             pair_list = pair_list[trace != -1]
             # Convert back to array of base pairs,
             # remove unused BondType column
-            base_pairs = pair_list.as_array()[:,:2]
+            base_pairs = pair_list.as_array()[:, :2]
         return base_pairs
 
     @staticmethod
@@ -300,5 +306,5 @@ class RNAalifoldApp(LocalApp):
         return (
             app.get_dot_bracket(),
             app.get_free_energy(),
-            app.get_covariance_energy()
+            app.get_covariance_energy(),
         )

biotite/application/viennarna/rnafold.py

@@ -6,14 +6,13 @@ __name__ = "biotite.application.viennarna"
 __author__ = "Tom David Müller, Patrick Kunzmann"
 __all__ = ["RNAfoldApp"]
 
-import warnings
 from tempfile import NamedTemporaryFile
 import numpy as np
-from ..application import AppState, requires_state
-from ..localapp import LocalApp, cleanup_tempfile
-from ...sequence.io.fasta import FastaFile, set_sequence
-from ...structure.dotbracket import base_pairs_from_dot_bracket
-from .util import build_constraint_string
+from biotite.application.application import AppState, requires_state
+from biotite.application.localapp import LocalApp, cleanup_tempfile
+from biotite.application.viennarna.util import build_constraint_string
+from biotite.sequence.io.fasta import FastaFile, set_sequence
+from biotite.structure.dotbracket import base_pairs_from_dot_bracket
 
 
 class RNAfoldApp(LocalApp):
@@ -51,9 +50,7 @@ class RNAfoldApp(LocalApp):
         self._temperature = str(temperature)
         self._constraints = None
         self._enforce = None
-        self._in_file = NamedTemporaryFile(
-            "w", suffix=".fa", delete=False
-        )
+        self._in_file = NamedTemporaryFile("w", suffix=".fa", delete=False)
         super().__init__(bin_path)
 
     def run(self):
@@ -65,10 +62,11 @@ class RNAfoldApp(LocalApp):
             fasta_file.lines.append(self._constraints)
         fasta_file.write(self._in_file)
         self._in_file.flush()
-        
+
         options = [
             "--noPS",
-            "-T", self._temperature,
+            "-T",
+            self._temperature,
         ]
         if self._enforce is True:
             options.append("--enforceConstraint")
@@ -87,11 +85,11 @@ class RNAfoldApp(LocalApp):
 
         self._free_energy = free_energy
         self._dotbracket = dotbracket
-    
+
     def clean_up(self):
         super().clean_up()
         cleanup_tempfile(self._in_file)
-    
+
     @requires_state(AppState.CREATED)
     def set_temperature(self, temperature):
         """
@@ -104,10 +102,17 @@ class RNAfoldApp(LocalApp):
             The temperature.
         """
         self._temperature = str(temperature)
-    
+
     @requires_state(AppState.CREATED)
-    def set_constraints(self, pairs=None, paired=None, unpaired=None,
-                        downstream=None, upstream=None, enforce=False):
+    def set_constraints(
+        self,
+        pairs=None,
+        paired=None,
+        unpaired=None,
+        downstream=None,
+        upstream=None,
+        enforce=False,
+    ):
         """
         Add constraints of known paired or unpaired bases to the folding
         algorithm.
@@ -134,11 +139,10 @@ class RNAfoldApp(LocalApp):
             of a pair that would conflict with this constraint.
         """
         self._constraints = build_constraint_string(
-            len(self._sequence),
-            pairs, paired, unpaired, downstream, upstream
+            len(self._sequence), pairs, paired, unpaired, downstream, upstream
         )
         self._enforce = enforce
-    
+
     @requires_state(AppState.JOINED)
     def get_free_energy(self):
         """
@@ -162,25 +166,6 @@ class RNAfoldApp(LocalApp):
         """
         return self._free_energy
 
-    @requires_state(AppState.JOINED)
-    def get_mfe(self):
-        """
-        Get the free energy (kcal/mol) of the suggested
-        secondary structure.
-
-        DEPRECATED: Use :meth:`get_free_energy()` instead.
-
-        Returns
-        -------
-        mfe : float
-            The minimum free energy.
-        """
-        warnings.warn(
-            "'get_mfe()' is deprecated, use 'get_free_energy()' instead",
-            DeprecationWarning
-        )
-        return self.get_free_energy()
-
     @requires_state(AppState.JOINED)
     def get_dot_bracket(self):
         """
@@ -243,7 +228,7 @@ class RNAfoldApp(LocalApp):
     @staticmethod
     def compute_secondary_structure(sequence, bin_path="RNAfold"):
         """
-        Compute the minimum free energy secondary structure of a 
+        Compute the minimum free energy secondary structure of a
         ribonucleic acid sequence using *ViennaRNA's* *RNAfold* software.
 
         This is a convenience function, that wraps the

biotite/application/viennarna/rnaplot.py

@@ -6,13 +6,14 @@ __name__ = "biotite.application.viennarna"
 __author__ = "Tom David Müller"
 __all__ = ["RNAplotApp"]
 
-import numpy as np
-from tempfile import NamedTemporaryFile
-from os import remove
 from enum import IntEnum
-from ..localapp import LocalApp, cleanup_tempfile
-from ..application import AppState, requires_state
-from ...structure.dotbracket import dot_bracket as dot_bracket_
+from os import remove
+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.structure.dotbracket import dot_bracket as dot_bracket_
+
 
 class RNAplotApp(LocalApp):
     """
@@ -60,21 +61,28 @@ class RNAplotApp(LocalApp):
         This enum type represents the layout type of the plot according
         to the official *RNAplot* orientation.
         """
-        RADIAL = 0,
-        NAVIEW = 1,
-        CIRCULAR = 2,
-        RNATURTLE = 3,
+
+        RADIAL = (0,)
+        NAVIEW = (1,)
+        CIRCULAR = (2,)
+        RNATURTLE = (3,)
         RNAPUZZLER = 4
 
-    def __init__(self, dot_bracket=None, base_pairs=None, length=None,
-                 layout_type=Layout.NAVIEW, bin_path="RNAplot"):
+    def __init__(
+        self,
+        dot_bracket=None,
+        base_pairs=None,
+        length=None,
+        layout_type=Layout.NAVIEW,
+        bin_path="RNAplot",
+    ):
         super().__init__(bin_path)
 
         if dot_bracket is not None:
             self._dot_bracket = dot_bracket
         elif (base_pairs is not None) and (length is not None):
             self._dot_bracket = dot_bracket_(
-                base_pairs, length, max_pseudoknot_order = 0
+                base_pairs, length, max_pseudoknot_order=0
             )[0]
         else:
             raise ValueError(
@@ -84,10 +92,10 @@ class RNAplotApp(LocalApp):
 
         # Get the value of the enum type
         self._layout_type = str(int(layout_type))
-        self._in_file  = NamedTemporaryFile("w", suffix=".fold",  delete=False)
+        self._in_file = NamedTemporaryFile("w", suffix=".fold", delete=False)
 
     def run(self):
-        self._in_file.write("N"*len(self._dot_bracket) + "\n")
+        self._in_file.write("N" * len(self._dot_bracket) + "\n")
         self._in_file.write(self._dot_bracket)
         self._in_file.flush()
         self.set_arguments(
@@ -146,8 +154,11 @@ class RNAplotApp(LocalApp):
 
     @staticmethod
     def compute_coordinates(
-        dot_bracket=None, base_pairs=None, length=None,
-        layout_type=Layout.NAVIEW, bin_path="RNAplot"
+        dot_bracket=None,
+        base_pairs=None,
+        length=None,
+        layout_type=Layout.NAVIEW,
+        bin_path="RNAplot",
     ):
         """
         Get coordinates for a 2D representation of any unknotted RNA
@@ -179,9 +190,13 @@ class RNAplotApp(LocalApp):
             The 2D coordinates. Each row represents the *x* and *y*
             coordinates for a total sequence length of *n*.
         """
-        app = RNAplotApp(dot_bracket=dot_bracket, base_pairs=base_pairs,
-                         length=length, layout_type=layout_type,
-                         bin_path=bin_path)
+        app = RNAplotApp(
+            dot_bracket=dot_bracket,
+            base_pairs=base_pairs,
+            length=length,
+            layout_type=layout_type,
+            bin_path=bin_path,
+        )
         app.start()
         app.join()
-        return app.get_coordinates()
+        return app.get_coordinates()

biotite/application/viennarna/util.py

@@ -7,12 +7,17 @@ __author__ = "Patrick Kunzmann"
 __all__ = ["build_constraint_string"]
 
 import numpy as np
-from ...structure.pseudoknots import pseudoknots
+from biotite.structure.pseudoknots import pseudoknots
 
 
-def build_constraint_string(sequence_length,
-                            pairs=None, paired=None, unpaired=None,
-                            downstream=None, upstream=None):
+def build_constraint_string(
+    sequence_length,
+    pairs=None,
+    paired=None,
+    unpaired=None,
+    downstream=None,
+    upstream=None,
+):
     """
     Build a ViennaRNA constraint string.
 
@@ -30,7 +35,7 @@ def build_constraint_string(sequence_length,
         Positions of bases that are paired with any downstream base.
     upstream : ndarray, shape=(n,), dtype=int or dtype=bool, optional
         Positions of bases that are paired with any upstream base.
-    
+
     Returns
     -------
     constraints : str
@@ -45,21 +50,21 @@ def build_constraint_string(sequence_length,
             raise ValueError("Given pairs include pseudoknots")
         # Ensure the lower base comes first for each pair
         pairs = np.sort(pairs, axis=-1)
-        _set_constraints(constraints, pairs[:,0], "(")
-        _set_constraints(constraints, pairs[:,1], ")")
+        _set_constraints(constraints, pairs[:, 0], "(")
+        _set_constraints(constraints, pairs[:, 1], ")")
 
     _set_constraints(constraints, paired, "|")
     _set_constraints(constraints, unpaired, "x")
     _set_constraints(constraints, downstream, "<")
     _set_constraints(constraints, upstream, ">")
-    
+
     return "".join(constraints)
-    
+
 
 def _set_constraints(constraints, index, character):
     if index is None:
         return
-    
+
     # Search for conflicts with other constraints
     potential_conflict_indices = np.where(constraints[index] != ".")[0]
     if len(potential_conflict_indices) > 0:
@@ -68,5 +73,5 @@ def _set_constraints(constraints, index, character):
             f"Constraint '{character}' at position {conflict_i} "
             f"conflicts with existing constraint '{constraints[conflict_i]}'"
         )
-    
-    constraints[index] = character
+
+    constraints[index] = character

biotite/application/webapp.py

@@ -7,22 +7,22 @@ __author__ = "Patrick Kunzmann"
 __all__ = ["WebApp", "RuleViolationError"]
 
 import abc
-from .application import Application
+from biotite.application.application import Application
 
 
 class WebApp(Application, metaclass=abc.ABCMeta):
     """
     The base class for all web based applications.
-    
+
     It allows for getting and setting the URL of the app and raises
     an :class:`RuleViolationError` when a subclass calls
     :func:`violate_rule()`
     (e.g. when the server was contacted too often.)
-    
+
     Be careful, when calling func:`get_app_state()`. This may involve a
     server contact and therefore frequent calls may raise a
     :class:`RuleViolationError`.
-    
+
     Parameters
     ----------
     app_url : str
@@ -31,19 +31,19 @@ class WebApp(Application, metaclass=abc.ABCMeta):
         If true, the application raises an :class:`RuleViolationError`, if
         the server rules are violated. (Default: True)
     """
-    
+
     def __init__(self, app_url, obey_rules=True):
         super().__init__()
         self._obey_rules = obey_rules
         self._app_url = app_url
-    
+
     def violate_rule(self, msg=None):
         """
         Indicate that a server rule was violated, i.e. this raises a
         :class:`RuleViolationError` unless `obey_rules` is false.
-        
+
         PROTECTED: Do not call from outside.
-        
+
         Parameters
         ----------
         msg : str, optional
@@ -51,16 +51,14 @@ class WebApp(Application, metaclass=abc.ABCMeta):
         """
         if self._obey_rules:
             if msg is None:
-                raise RuleViolationError(
-                    "The user guidelines would be violated"
-                )
+                raise RuleViolationError("The user guidelines would be violated")
             else:
                 raise RuleViolationError(msg)
-    
+
     def app_url(self):
         """
         Get the URL of the web app.
-        
+
         Returns
         -------
         url : str
@@ -74,4 +72,5 @@ class RuleViolationError(Exception):
     Indicates that the user guidelines of the web application would be
     violated, if the program continued.
     """
-    pass
+
+    pass

biotite/copyable.py

@@ -12,22 +12,22 @@ import abc
 class Copyable(metaclass=abc.ABCMeta):
     """
     Base class for all objects, that should be copyable.
-    
+
     The public method `copy()` first creates a fresh instance of the
     class of the instance, that is copied via the `__copy_create__()`
     method. All variables, that could not be set via the constructor,
     are then copied via `__copy_fill__()`, starting with the method in
     the uppermost base class and ending with the class of the instance
     to be copied.
-    
+
     This approach solves the problem of encapsulated variables in
     superclasses.
     """
-    
+
     def copy(self):
         """
         Create a deep copy of this object.
-        
+
         Returns
         -------
         copy
@@ -36,36 +36,36 @@ class Copyable(metaclass=abc.ABCMeta):
         clone = self.__copy_create__()
         self.__copy_fill__(clone)
         return clone
-    
+
     def __copy_create__(self):
         """
         Instantiate a new object of this class.
-        
+
         Only the constructor should be called in this method.
         All further attributes, that need to be copied are handled
         in `__copy_fill__()`
-        
+
         Do not call the `super()` method here.
-        
+
         This method must be overridden, if the constructor takes
         parameters.
-        
+
         Returns
         -------
         copy
             A freshly instantiated copy of *self*.
         """
         return type(self)()
-    
+
     def __copy_fill__(self, clone):
         """
         Copy all necessary attributes to the new object.
-        
+
         Always call the `super()` method as first statement.
-        
+
         Parameters
         ----------
         clone
             The freshly instantiated copy of *self*.
         """
-        pass
+        pass

biotite/database/__init__.py

@@ -20,4 +20,4 @@ download the associated files.
 __name__ = "biotite.database"
 __author__ = "Patrick Kunzmann"
 
-from .error import *
+from .error import *

biotite/database/entrez/__init__.py

@@ -11,5 +11,5 @@ __author__ = "Patrick Kunzmann"
 
 from .dbnames import *
 from .download import *
+from .key import *
 from .query import *
-from .key import *

biotite/database/entrez/check.py

@@ -7,8 +7,7 @@ __author__ = "Patrick Kunzmann, Maximilian Dombrowsky"
 __all__ = ["check_for_errors"]
 
 import json
-from ..error import RequestError
-
+from biotite.database.error import RequestError
 
 # Taken from https://github.com/kblin/ncbi-entrez-error-messages
 _error_messages = [
@@ -58,4 +57,4 @@ def check_for_errors(message):
     for error_msg in _error_messages:
         # Often whitespace is also replaced by '+' in error message
         if error_msg.replace(" ", "") in message_end:
-            raise RequestError(error_msg)
+            raise RequestError(error_msg)

biotite/database/entrez/dbnames.py

@@ -7,6 +7,7 @@ __author__ = "Patrick Kunzmann"
 __all__ = ["get_database_name"]
 
 
+# fmt: off
 _db_names = {
     "BioProject"        : "bioproject",
     "BioSample"         : "biosample",
@@ -45,26 +46,27 @@ _db_names = {
     "UniGene"           : "unigene",
     "UniSTS"            : "unists"
 }
+# fmt: on
 
 
 def get_database_name(database):
     """
     Map a common NCBI Entrez database name to an E-utility database
     name.
-    
+
     Parameters
     ----------
     database : str
         Entrez database name.
-    
+
     Returns
     -------
     name : str
         E-utility database name.
-    
+
     Examples
     --------
-    
+
     >>> print(get_database_name("Nucleotide"))
     nuccore
     """
@@ -86,4 +88,4 @@ def sanitize_database_name(db_name):
         # Is already E-utility database name
         return db_name
     else:
-        raise ValueError("Database '{db_name}' is not existing")
+        raise ValueError("Database '{db_name}' is not existing")