Make CorrectForPH respect perceived chains.

src/phmodel.cpp

@@ -154,6 +154,8 @@ namespace OpenBabel
     if (mol.GetDimension() > 0 && !mol.AutomaticFormalCharge())
       return;
 
+    bool hasChainsPerceived = mol.HasChainsPerceived();
+
     mol.SetCorrectedForPH();
 
     obErrorLog.ThrowError(__FUNCTION__,
@@ -197,6 +199,10 @@ namespace OpenBabel
       }
     }
 
+    if (hasChainsPerceived)
+    {
+      mol.SetChainsPerceived();
+    }
   }
 
 

test/CMakeLists.txt

@@ -40,7 +40,7 @@ set(lssr_parts 1 2 3 4 5)
 set(isomorphism_parts 1 2 3 4 5 6 7 8 9)
 set(multicml_parts 1)
 set(periodic_parts 1 2 3 4)
-set(regressions_parts 1 2 221 222 223 224 225 226 227 228 229 240 241 242 1794 2111 2428 2646)
+set(regressions_parts 1 2 221 222 223 224 225 226 227 228 229 240 241 242 1794 2111 2428 2646 2677)
 set(rotor_parts 1 2 3 4)
 set(shuffle_parts 1 2 3 4 5)
 set(smiles_parts 1 2 3)

test/regressionstest.cpp

@@ -646,6 +646,21 @@ void test_github_issue_2646()
   OB_COMPARE(can, "c1ccccc1");
 }
 
+// https://github.com/openbabel/openbabel/issues/2677
+void test_github_issue_2677()
+{
+  // Make sure that CorrectForPH doesn't mess up residues in pdb
+  OBMolPtr mol = OBTestUtil::ReadFile("1DRF.pdb");
+  OB_ASSERT(mol->HasChainsPerceived());
+  OBAtom *atom_before = mol->GetAtom(1);
+  OBResidue *res_before = atom_before->GetResidue();
+  mol->AddNewHydrogens(PolarHydrogen, true);
+  OBAtom *atom_after = mol->GetAtom(1);
+  OBResidue *res_after = atom_after->GetResidue();
+  OB_REQUIRE(res_after != nullptr);
+  OB_COMPARE(res_after->GetIdx(), res_before->GetIdx());
+}
+
 void test_SegCopySubstructure()
 {
   // Invalid memory access (atom->GetIdx()) detected in valgrind and sometimes
@@ -754,6 +769,9 @@ int regressionstest(int argc, char *argv[])
   case 2646:
     test_github_issue_2646();
     break;
+  case 2677:
+    test_github_issue_2677();
+    break;
   // case N:
   //   YOUR_TEST_HERE();
   //   Remember to update CMakeLists.txt with the number of your test