Merge pull request #183 from Autodesk/missing-terminal-parsing

Fix bug in chain detection

moldesign/_tests/test_pdb_processing.py

@@ -122,6 +122,14 @@ def test_numeric_residue_name_1PYN(request, mol):
     assert len(contents) == 1
     assert list(contents.keys())[0] == '941'
 
+
+def test_missing_atoms_3b5x():
+    mol = mdt.read(get_data_path('3b5x.cif.bz2'))
+    assert mol.num_chains == 2
+    assert mol.num_atoms == 1144
+    assert mol.num_residues == 1144
+
+
 MISSINGRES_2JAJ = [('A', 'GLY', -4), ('A', 'PRO', -3), ('A', 'LEU', -2), ('A', 'GLY', -1),
                    ('A', 'MET', 0), ('A', 'ALA', 1), ('A', 'GLY', 2), ('A', 'LEU', 3),
                    ('A', 'GLY', 4), ('A', 'HIS', 5), ('A', 'PRO', 6), ('A', 'ALA', 7),

moldesign/molecules/residue.py

@@ -247,11 +247,10 @@ def _is_ending_residue(self):
         except KeyError:
             # If we're here, the residue is missing some atoms. We'll fall back to checking the
             # next residues in line
-            if self.index == len(self.molecule.residues):
+            if self.index == len(self.molecule.residues) - 1:
                 return True
             else:
-                print('WARNING: %s is missing expected atoms. Attempting to infer chain end' % \
-                    self)
+                print('WARNING: %s is missing expected atoms. Attempting to infer chain end' % self)
                 nextres = self.molecule.residues[self.index + 1]
                 return not self._same_polymer(nextres)