Fix auth_residues=False for MMCIFParser (biopython#4277)

* fix warnings.warn calls * add name to NEWS.rst * tests for label res and chain in MMCIFParser
peterjc · Apr 5, 2023 · ca64586 · ca64586
1 parent a5b93f6
commit ca64586
Show file tree

Hide file tree

Showing 3 changed files with 19 additions and 6 deletions.
diff --git a/Bio/PDB/MMCIFParser.py b/Bio/PDB/MMCIFParser.py
@@ -215,8 +215,7 @@ def _build_structure(self, structure_id):
             except ValueError:
                 serial = atom_serial_list[i]
                 warnings.warn(
-                    "PDBConstructionWarning: "
-                    "Some atom serial numbers are not numerical",
+                    "PDBConstructionWarning: Some atom serial numbers are not numerical",
                     PDBConstructionWarning,
                 )
 
@@ -239,8 +238,7 @@ def _build_structure(self, structure_id):
                 except (KeyError, IndexError):
                     msg = f"Non-existing residue ID in chain '{chainid}'"
                 warnings.warn(
-                    "PDBConstructionWarning: ",
-                    msg,
+                    "PDBConstructionWarning: " + msg,
                     PDBConstructionWarning,
                 )
                 continue
@@ -530,8 +528,7 @@ def _build_structure(self, structure_id, filehandle):
                 except (KeyError, IndexError):
                     msg = f"Non-existing residue ID in chain '{chainid}'"
                 warnings.warn(
-                    "PDBConstructionWarning: ",
-                    msg,
+                    "PDBConstructionWarning: " + msg,
                     PDBConstructionWarning,
                 )
                 continue

diff --git a/NEWS.rst b/NEWS.rst
@@ -27,6 +27,7 @@ possible, especially the following contributors:
 - Cam McMenamie
 - Ricardas Ralys
 - Vladislav Kuznetsov
+- Joe Greener
 
 12 February 2023: Biopython 1.81
 ===============================================

diff --git a/Tests/test_PDB_MMCIFParser.py b/Tests/test_PDB_MMCIFParser.py
@@ -54,6 +54,21 @@ def test_parsers(self):
         self.assertEqual(len(structure), 1)
         self.assertEqual(len(f_structure), 1)
 
+        parser_lab_res = MMCIFParser(auth_residues=False, QUIET=True)
+        fast_parser_lab_res = FastMMCIFParser(auth_residues=False, QUIET=True)
+        parser_lab_chain = MMCIFParser(auth_chains=False, QUIET=True)
+        fast_parser_lab_chain = FastMMCIFParser(auth_chains=False, QUIET=True)
+
+        structure_lr = parser_lab_res.get_structure("example", "PDB/1A8O.cif")
+        f_structure_lr = fast_parser_lab_res.get_structure("example", "PDB/1A8O.cif")
+        structure_lc = parser_lab_chain.get_structure("example", "PDB/1A8O.cif")
+        f_structure_lc = fast_parser_lab_chain.get_structure("example", "PDB/1A8O.cif")
+
+        self.assertEqual(len(list(structure_lr.get_atoms())), 556)
+        self.assertEqual(len(list(f_structure_lr.get_atoms())), 556)
+        self.assertEqual(len(list(structure_lc.get_atoms())), 644)
+        self.assertEqual(len(list(f_structure_lc.get_atoms())), 644)
+
         for ppbuild in [PPBuilder(), CaPPBuilder()]:
             # ==========================================================
             # Check that serial_num (model column) is stored properly