dcatoolkit 0.3.0__tar.gz → 0.4.0__tar.gz

{dcatoolkit-0.3.0/src/dcatoolkit.egg-info → dcatoolkit-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcatoolkit
-Version: 0.3.0
+Version: 0.4.0
 Summary: Collection of useful modules and representations for managing DCA output data.
 Author-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
 Maintainer-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
@@ -35,13 +35,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: biotite>=1.0.1
+Requires-Dist: biotite>=1.7
 Requires-Dist: numpy>=1.26.0
 Requires-Dist: pandas>=2.1.0
 Requires-Dist: scipy>=1.11.0
@@ -69,7 +67,7 @@ pip install dcatoolkit
 pip install "dcatoolkit[plot]"  
 ```
 
-Requires Python 3.10+.
+Requires Python 3.12+.
 Upgrading from 0.2.x? See the [changelog](https://github.com/RaheelSyedAhmed/dcatoolkit/blob/main/CHANGELOG.md).
 
 ## Major Sections

{dcatoolkit-0.3.0 → dcatoolkit-0.4.0}/README.md

@@ -10,7 +10,7 @@ pip install dcatoolkit
 pip install "dcatoolkit[plot]"  
 ```
 
-Requires Python 3.10+.
+Requires Python 3.12+.
 Upgrading from 0.2.x? See the [changelog](https://github.com/RaheelSyedAhmed/dcatoolkit/blob/main/CHANGELOG.md).
 
 ## Major Sections

{dcatoolkit-0.3.0 → dcatoolkit-0.4.0}/pyproject.toml

@@ -4,14 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dcatoolkit"
-version = "0.3.0"
+version = "0.4.0"
 description = "Collection of useful modules and representations for managing DCA output data."
 keywords = ["dca", "toolkit", "DI", "coevolution"]
 
 readme = "README.md"
 license = {file = "LICENSE"}
 
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 
 authors = [
   {name = "Raheel Syed Ahmed", email = "raheelsyedahmed@gmail.com"}
@@ -21,7 +21,7 @@ maintainers = [
 ]
 
 dependencies = [
-  "biotite>=1.0.1",
+  "biotite>=1.7",
   "numpy>=1.26.0",
   "pandas>=2.1.0",
   "scipy>=1.11.0",
@@ -33,8 +33,6 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Bio-Informatics",
   "License :: OSI Approved :: MIT License",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
 ]
 

{dcatoolkit-0.3.0 → dcatoolkit-0.4.0}/src/dcatoolkit/representation/structure.py

@@ -1,3 +1,4 @@
+import io
 from typing import Literal, Union, overload
 
 import biotite.database.rcsb as rcsb
@@ -56,13 +57,18 @@ class StructureInformation:
         Raises
         ------
         TypeError
-            If the fetched data was not found and None was returned instead.
+            If the fetched data was not found and None was returned instead, or if RCSB returned binary data (``io.BytesIO``) instead of text.
         ValueError
             If `struc_format` is not ``"mmcif"`` or ``"pdb"``.
+        biotite.database.RequestError
+            If `pdb_id` is not a valid PDB ID (raised by `biotite.database.rcsb.fetch()`).
         """
         fetched_data = rcsb.fetch(pdb_id, struc_format)
         if fetched_data is None:
-            raise TypeError("RCSB fetch failed. Try fetch again.")
+            raise TypeError("RCSB fetch failed. Confirm RCSB's fetch API is available and, with stable internet connection, try fetch again.")
+        elif isinstance(fetched_data, io.BytesIO):
+            # rcsb.fetch returns binary formats (e.g. "bcif", or gzip=True) as BytesIO; the file readers below need text (StringIO).
+            raise TypeError(f"RCSB returned binary data for struc_format {struc_format!r}; only the text formats 'mmcif' and 'pdb' are supported.")
         elif struc_format == "mmcif":
             pdbx_file = pdbx.CIFFile.read(fetched_data)
             return MMCIFInformation(pdbx.get_structure(pdbx_file=pdbx_file, model=model_num, use_author_fields=False), pdbx_file, model_num)
@@ -255,7 +261,7 @@ class MMCIFInformation(StructureInformation):
                     unique_entry = atom_data[atom_data[:,2] == unique_chain][0]
                     self.chain_auth_dict[unique_entry[2]] = unique_entry[4]
                     self.auth_chain_dict[unique_entry[4]] = unique_entry[2]
-                self.atom_site_df = pd.DataFrame(np.column_stack([atom_site_category[category].as_array() for category in atom_site_category]), columns=atom_site_category.keys())
+                self.atom_site_df = pd.DataFrame(np.column_stack([atom_site_category[category].as_array() for category in atom_site_category]), columns=list(atom_site_category))
                 type_conversion_dict = {'label_seq_id': 'int64', 'auth_seq_id': 'int64', 'id': 'int64', 'Cartn_x': 'float', 'Cartn_y': 'float','Cartn_z': 'float', 'B_iso_or_equiv': 'float'}
                 self.atom_df = self.atom_site_df[self.atom_site_df['group_PDB'] == 'ATOM'].astype(type_conversion_dict)
 

{dcatoolkit-0.3.0 → dcatoolkit-0.4.0/src/dcatoolkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcatoolkit
-Version: 0.3.0
+Version: 0.4.0
 Summary: Collection of useful modules and representations for managing DCA output data.
 Author-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
 Maintainer-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
@@ -35,13 +35,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: biotite>=1.0.1
+Requires-Dist: biotite>=1.7
 Requires-Dist: numpy>=1.26.0
 Requires-Dist: pandas>=2.1.0
 Requires-Dist: scipy>=1.11.0
@@ -69,7 +67,7 @@ pip install dcatoolkit
 pip install "dcatoolkit[plot]"  
 ```
 
-Requires Python 3.10+.
+Requires Python 3.12+.
 Upgrading from 0.2.x? See the [changelog](https://github.com/RaheelSyedAhmed/dcatoolkit/blob/main/CHANGELOG.md).
 
 ## Major Sections

{dcatoolkit-0.3.0 → dcatoolkit-0.4.0}/src/dcatoolkit.egg-info/requires.txt

@@ -1,4 +1,4 @@
-biotite>=1.0.1
+biotite>=1.7
 numpy>=1.26.0
 pandas>=2.1.0
 scipy>=1.11.0