Fix negative residue IDs in PDB saving (resolves #29)

atomium/pdb.py

@@ -600,7 +600,7 @@ def atom_to_atom_line(a, lines):
     if a.het:
         id_, residue_name = a.het.id, a.het._name
         chain_id = a.chain.id if a.chain is not None else ""
-        residue_id = int("".join([c for c in id_ if c.isdigit()]))
+        residue_id = int("".join([c for c in id_ if c.isdigit() or c == "-"]))
         insert_code = id_[-1] if id_ and id_[-1].isalpha() else ""
     atom_name = a._name or ""
     atom_name = " " + atom_name if len(atom_name) < 4 else atom_name

tests/integration/test_file_saving.py

@@ -26,6 +26,11 @@ def check_file_saving(self, filename):
             self.assertEqual(chain1.sequence, chain2.sequence)
             self.assertEqual(chain1.id, chain2.id)
             self.assertEqual(chain1, chain2)
+            for res1, res2 in zip(sorted(chain1.residues(), key=lambda r: r.id),
+             sorted(chain2.residues(), key=lambda r: r.id)):
+                self.assertEqual(res1.id, res2.id)
+                self.assertEqual(res1.name, res2.name)
+                self.assertEqual(res1, res2)
         for lig1, lig2 in zip(sorted(f.model.ligands(), key=lambda c: c.id),
          sorted(f2.model.ligands(), key=lambda c: c.id)):
             self.assertEqual(lig1.name, lig2.name)