Merge pull request #82 from rasbt/allow-ent

allow .ent & .ent.gz file extensions

Author: rasbt

biopandas/__init__.py

@@ -24,5 +24,5 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = '0.2.8'
+__version__ = '0.2.9dev'
 __author__ = "Sebastian Raschka <[email protected]>"

biopandas/pdb/pandas_pdb.py

@@ -263,14 +263,16 @@ def _init_get_dict():
     def _read_pdb(path):
         """Read PDB file from local drive."""
         r_mode = 'r'
-        if path.endswith('.pdb'):
+        if path.endswith(('.pdb', '.ent')):
             openf = open
-        elif path.endswith('pdb.gz'):
+        elif path.endswith(('pdb.gz', '.ent.gz')):
             r_mode = 'rb'
             openf = gzip.open
         else:
+            allowed_formats = ", ".join(('.pdb', '.pdb.gz', '.ent', '.ent.gz'))
             raise ValueError(
-                'Wrong file format; allowed file formats are .pdb and .pdb.gz.'
+                ('Wrong file format; allowed file formats are %s'
+                  % allowed_formats)
             )
 
         with openf(path, r_mode) as f:

biopandas/pdb/tests/test_read_pdb.py

@@ -61,8 +61,8 @@ def test__read_pdb_raises():
     """Test private _read_pdb:
     Test if ValueError is raised for wrong file formats."""
 
-    expect = ('Wrong file format; allowed file formats'
-              ' are .pdb and .pdb.gz.')
+    expect = ('Wrong file format; allowed file formats are '
+              '.pdb, .pdb.gz, .ent, .ent.gz')
 
     def run_code_1():
         PandasPdb()._read_pdb("protein.mol2")

docs/CHANGELOG.md

@@ -4,6 +4,25 @@ The CHANGELOG for the current development version is available at
 [https://github.com/rasbt/biopandas/blob/main/docs/sources/CHANGELOG.md](https://github.com/rasbt/biopandas/blob/main/docs/sources/CHANGELOG.md).
 
 
+### 0.2.9 (TBD)
+
+##### Downloads
+
+- -
+- -
+
+##### New Features
+
+- -
+
+##### Changes
+
+- Now also allow `.ent` and `.ent.gz` file endings for PDB files.  (via PR [82](https://github.com/rasbt/biopandas/pull/82/files)
+
+##### Bug Fixes
+
+- -
+
 ### 0.2.8 (03-30-2021)
 
 ##### Downloads