SCHWED-949: skip olc-check for modified residues.

modelling/src/model.cc

@@ -1024,19 +1024,29 @@ void BuildRawChain(const seq::AlignmentHandle& aln,
       continue;
     }
     const char src_olc = src_res.GetOneLetterCode();
+    // sanity check that src_res matches aligned sequence
     if (src_olc != col[1]) {
       std::stringstream ss;
       ss << "Alignment-structure mismatch at pos " << i << " in chain " <<
         chain_name <<
         ", alignment is '" << col[1] << "' structure residue is '" <<
         src_olc << "'";
-      throw promod3::Error(ss.str());
+      // We often have non-standard AA residues changing OLC mapping over time.
+      // This can make it likely for this check to fail and hence we only
+      // check the 20 standard amino acids.
+      if (conop::ResidueToAminoAcid(src_res.GetHandle()) == conop::XXX) {
+        ss << ". Ok for modified residue " << src_res.GetName() << ".";
+        LOG_WARNING(ss.str())
+      } else {
+        ss << ". Not ok for standard amino acid " << src_res.GetName() << "!";
+        throw promod3::Error(ss.str());
+      }
     }
     // remove atoms with conflicting positions (i.e. on top of each other)
     CleanupAtomConflicts(src_res);
     // check for complete backbone, or in case of Calpha only model building,
     // if the src_res has a Calpha atom
-    if(!CheckBackboneAtoms(src_res)){
+    if (!CheckBackboneAtoms(src_res)) {
       LOG_INFO(src_res << " has incomplete backbone. skipping");
       gap_seq += trg_olc;
       continue;

modelling/tests/test_modelling.py

@@ -149,6 +149,28 @@ class ModellingTests(unittest.TestCase):
         self.assertTrue(residues[0].FindAtom("CB"))
         self.assertTrue(residues[0].FindAtom("OG"))
 
+    def testModifiedMismatch(self):
+        # test if we allow OLC mismatch for modified AA
+        tpl = io.LoadPDB('data/sep.pdb')
+        aln = seq.CreateAlignment(
+            seq.CreateSequence('trg', 'S'),
+            seq.CreateSequence('tpl', 'X'))
+        aln.AttachView(1, tpl.CreateFullView())
+        result = modelling.BuildRawModel(aln)
+        residues = result.model.residues
+        # same as before as OLC of SEP is 'S' (i.e. matches)
+        self.assertEqual(len(residues), 1)
+        self.assertEqual(len(residues[0].atoms), 6)
+        self.assertTrue(residues[0].FindAtom("N"))
+        self.assertTrue(residues[0].FindAtom("CA"))
+        self.assertTrue(residues[0].FindAtom("C"))
+        self.assertTrue(residues[0].FindAtom("O"))
+        self.assertTrue(residues[0].FindAtom("CB"))
+        self.assertTrue(residues[0].FindAtom("OG"))
+        # NOTE: relevant seq-vs-str mismatch tested in testOffset
+        # See OST's nonstandard.cc for additional tests of handling modified
+        # residues. Code duplication will be removed in SCHWED-3569.
+
     def testInsertCBeta(self):
         # test if the dst residues contain cbeta, unless they are glycines
         tpl = io.LoadPDB('data/cbeta.pdb')