Improve PDB warning message to help with large structures (#4714)

* Improve warning message to help with debugging on very large structures. * Update test assertion.
biopython · Apr 29, 2024 · 2906ac6 · 2906ac6
1 parent 5f25209
commit 2906ac6
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/Bio/PDB/StructureBuilder.py b/Bio/PDB/StructureBuilder.py
@@ -169,8 +169,8 @@ def init_residue(self, resname: str, field: str, resseq: int, icode: str):
                         # if this exception is ignored, a residue will be missing
                         self.residue = None
                         raise PDBConstructionException(
-                            "Blank altlocs in duplicate residue %s ('%s', %i, '%s')"
-                            % (resname, field, resseq, icode)
+                            "Blank altlocs in duplicate residue %s ('%s', %i, '%s') of chain '%s'"
+                            % (resname, field, resseq, icode, self.chain.id)
                         )
                     self.chain.detach_child(res_id)
                     new_residue = Residue(res_id, resname, self.segid)

diff --git a/Tests/test_PDB_PDBParser.py b/Tests/test_PDB_PDBParser.py
@@ -61,7 +61,7 @@ def test_1_flawedpdb_permissive(self):
                     "Atom N defined twice in residue <Residue ARG het=  resseq=2 icode= > at line 22.",
                     "disordered atom found with blank altloc before line 34.",
                     "Residue (' ', 4, ' ') redefined at line 44.",
-                    "Blank altlocs in duplicate residue SER (' ', 4, ' ') at line 44.",
+                    "Blank altlocs in duplicate residue SER (' ', 4, ' ') of chain 'A' at line 44.",
                     "Residue (' ', 10, ' ') redefined at line 76.",
                     "Residue (' ', 14, ' ') redefined at line 107.",
                     "Residue (' ', 16, ' ') redefined at line 136.",