biotite 0.39.0__tar.gz → 0.40.0__tar.gz

{biotite-0.39.0/src/biotite.egg-info → biotite-0.40.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biotite
-Version: 0.39.0
+Version: 0.40.0
 Summary: A comprehensive library for computational molecular biology
 Author: The Biotite contributors
 License: BSD 3-Clause License
@@ -52,7 +52,7 @@ Requires-Python: >=3.7
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 Requires-Dist: requests>=2.12
-Requires-Dist: numpy>=1.14.5
+Requires-Dist: numpy<=2.0,>=1.14.5
 Requires-Dist: msgpack>=0.5.6
 Requires-Dist: networkx>=2.0
 Provides-Extra: test

{biotite-0.39.0 → biotite-0.40.0}/pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
 # this should be manually updated as the minimum python version increases
 dependencies = [
   "requests >= 2.12",
-  "numpy >= 1.14.5",
+  "numpy >= 1.14.5, <= 2.0",
   "msgpack >= 0.5.6",
   "networkx >= 2.0",
 ]

{biotite-0.39.0 → biotite-0.40.0}/setup.py

@@ -84,7 +84,7 @@ setup(
         # Codon tables
         "biotite.sequence"          : ["codon_tables.txt"],
         # Structure data (masses, bonds, etc.)
-        "biotite.structure.info"    : ["*.json", "*.msgpack"]
+        "biotite.structure.info"    : ["atom_masses.json", "ccd/*"]
     },
 )
 

{biotite-0.39.0 → biotite-0.40.0}/src/biotite/__init__.py

@@ -9,11 +9,11 @@ it does provide utilities and base classes used by a lot of *Biotite*'s
 modules.
 """
 
-__version__ = "0.39.0"
+__version__ = "0.40.0"
 __name__ = "biotite"
 __author__ = "Patrick Kunzmann"
 
 from .file import *
 from .temp import *
-from .copyable import * 
-from .visualize import * 
+from .copyable import *
+from .visualize import *

{biotite-0.39.0 → biotite-0.40.0}/src/biotite/application/dssp/app.py

@@ -9,7 +9,7 @@ __all__ = ["DsspApp"]
 from tempfile import NamedTemporaryFile
 from ..localapp import LocalApp, cleanup_tempfile
 from ..application import AppState, requires_state
-from ...structure.io.pdbx.file import PDBxFile
+from ...structure.io.pdbx.cif import CIFFile
 from ...structure.io.pdbx.convert import set_structure
 import numpy as np
 
@@ -18,13 +18,13 @@ class DsspApp(LocalApp):
     r"""
     Annotate the secondary structure of a protein structure using the
     *DSSP* software.
-    
+
     Internally this creates a :class:`Popen` instance, which handles
     the execution.
-    
+
     DSSP differentiates between 8 different types of secondary
     structure elements:
-    
+
        - C: loop, coil or irregular
        - H: :math:`{\alpha}`-helix
        - B: :math:`{\beta}`-bridge
@@ -32,15 +32,15 @@ class DsspApp(LocalApp):
        - G: 3 :sub:`10`-helix
        - I: :math:`{\pi}`-helix
        - T: hydrogen bonded turn
-       - S: bend 
-    
+       - S: bend
+
     Parameters
     ----------
     atom_array : AtomArray
         The atom array to be annotated.
     bin_path : str, optional
         Path of the *DDSP* binary.
-    
+
     Examples
     --------
 
@@ -51,7 +51,7 @@ class DsspApp(LocalApp):
     ['C' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'T' 'T' 'G' 'G' 'G' 'G' 'T' 'C' 'C' 'C'
      'C' 'C']
     """
-    
+
     def __init__(self, atom_array, bin_path="mkdssp"):
         super().__init__(bin_path)
 
@@ -77,15 +77,15 @@ class DsspApp(LocalApp):
         self._out_file = NamedTemporaryFile("r", suffix=".dssp", delete=False)
 
     def run(self):
-        in_file = PDBxFile()
-        set_structure(in_file, self._array, data_block="DSSP_INPUT")
+        in_file = CIFFile()
+        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]
         )
         super().run()
-    
+
     def evaluate(self):
         super().evaluate()
         lines = self._out_file.read().split("\n")
@@ -106,17 +106,17 @@ class DsspApp(LocalApp):
         for i, line in enumerate(lines):
             self._sse[i] = line[16]
         self._sse[self._sse == " "] = "C"
-    
+
     def clean_up(self):
         super().clean_up()
         cleanup_tempfile(self._in_file)
         cleanup_tempfile(self._out_file)
-    
+
     @requires_state(AppState.JOINED)
     def get_sse(self):
         """
         Get the resulting secondary structure assignment.
-        
+
         Returns
         -------
         sse : ndarray, dtype="U1"
@@ -124,22 +124,22 @@ class DsspApp(LocalApp):
             corresponding to the residues in the input atom array.
         """
         return self._sse
-    
+
     @staticmethod
     def annotate_sse(atom_array, bin_path="mkdssp"):
         """
         Perform a secondary structure assignment to an atom array.
-        
+
         This is a convenience function, that wraps the :class:`DsspApp`
         execution.
-        
+
         Parameters
         ----------
         atom_array : AtomArray
             The atom array to be annotated.
         bin_path : str, optional
             Path of the DDSP binary.
-        
+
         Returns
         -------
         sse : ndarray, dtype="U1"

{biotite-0.39.0 → biotite-0.40.0}/src/biotite/database/rcsb/download.py

@@ -16,24 +16,25 @@ from ..error import RequestError
 
 _standard_url = "https://files.rcsb.org/download/"
 _mmtf_url = "https://mmtf.rcsb.org/v1.0/full/"
+_bcif_url = "https://models.rcsb.org/"
 _fasta_url = "https://www.rcsb.org/fasta/entry/"
 
-_binary_formats = ["mmtf"]
+_binary_formats = ["mmtf", "bcif"]
 
 
 def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
     """
     Download structure files (or sequence files) from the RCSB PDB in
     various formats.
-    
+
     This function requires an internet connection.
-    
+
     Parameters
     ----------
     pdb_ids : str or iterable object of str
         A single PDB ID or a list of PDB IDs of the structure(s)
         to be downloaded.
-    format : {'pdb', 'pdbx', 'cif', 'mmcif', 'mmtf', 'fasta'}
+    format : {'pdb', 'pdbx', 'cif', 'mmcif', 'bcif', 'mmtf', 'fasta'}
         The format of the files to be downloaded.
         ``'pdbx'``, ``'cif'`` and ``'mmcif'`` are synonyms for
         the same format.
@@ -48,7 +49,7 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
         the file is empty.
     verbose: bool, optional
         If set to true, the function will output the download progress.
-    
+
     Returns
     -------
     files : str or StringIO or BytesIO or list of (str or StringIO or BytesIO)
@@ -58,7 +59,7 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
         object) was given, a list of strings is returned.
         If no `target_path` was given, the file contents are stored in
         either :class:`StringIO` or :class:`BytesIO` objects.
-    
+
     Warnings
     --------
     Even if you give valid input to this function, in rare cases the
@@ -66,10 +67,10 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
     In these cases the request should be retried.
     When the issue occurs repeatedly, the error is probably in your
     input.
-    
+
     Examples
     --------
-    
+
     >>> import os.path
     >>> file = fetch("1l2y", "cif", path_to_directory)
     >>> print(os.path.basename(file))
@@ -88,21 +89,21 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
     # Create the target folder, if not existing
     if target_path is not None and not os.path.isdir(target_path):
         os.makedirs(target_path)
-    
+
     files = []
     for i, id in enumerate(pdb_ids):
         # Verbose output
         if verbose:
             print(f"Fetching file {i+1:d} / {len(pdb_ids):d} ({id})...",
                   end="\r")
-        
+
         # Fetch file from database
         if target_path is not None:
             file = join(target_path, id + "." + format)
         else:
             # 'file = None' -> store content in a file-like object
             file = None
-        
+
         if file is None \
            or not isfile(file) \
            or getsize(file) == 0 \
@@ -115,6 +116,10 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
                     r = requests.get(_standard_url + id + ".cif")
                     content = r.text
                     _assert_valid_file(content, id)
+                elif format in ["bcif"]:
+                    r = requests.get(_bcif_url + id + ".bcif")
+                    content = r.content
+                    _assert_valid_file(r.text, id)
                 elif format == "mmtf":
                     r = requests.get(_mmtf_url + id)
                     content = r.content
@@ -125,7 +130,7 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
                     _assert_valid_file(content, id)
                 else:
                     raise ValueError(f"Format '{format}' is not supported")
-                
+
                 if file is None:
                     if format in _binary_formats:
                         file = io.BytesIO(content)
@@ -135,7 +140,7 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
                     mode = "wb+" if format in _binary_formats else "w+"
                     with open(file, mode) as f:
                         f.write(content)
-        
+
         files.append(file)
     if verbose:
         print("\nDone")
@@ -153,7 +158,7 @@ def _assert_valid_file(response_text, pdb_id):
     """
     # Structure file and FASTA file retrieval
     # have different error messages
-    if any(err_msg in response_text for err_msg in [
+    if len(response_text) == 0 or any(err_msg in response_text for err_msg in [
         "404 Not Found",
         "<title>RCSB Protein Data Bank Error Page</title>",
         "No fasta files were found.",