SCHWED-954: Fixed ring-punch fixing when neighboring residues are punched.

modelling/pymod/_closegaps.py

@@ -427,7 +427,9 @@ def MergeGapsByDistance(mhandle, distance):
             # get the distance between the gaps
             dist = next_gap.before.GetNumber().GetNum() \
                    - current_gap.after.GetNumber().GetNum()
-            if dist < 0:
+            # NOTE: -1 can currently only happen when fixing ring punches
+            #       in _pipeline.BuildSidechains
+            if dist < -1:
                 ost.LogInfo("Non-sequential gaps found. Ignoring.")
                 continue
             if dist <= distance:

modelling/pymod/_pipeline.py

@@ -58,6 +58,8 @@ def BuildSidechains(mhandle, merge_distance=4, scorer=None, fragment_db=None,
         # backup old gaps
         old_gaps = [g.Copy() for g in mhandle.gaps]
         # new gaps for mhandle
+        # NOTE: we currently do not delete the punched residues here
+        #       BUT they could be deleted when merging gaps below...
         mhandle.gaps = StructuralGapList()
         for res in ring_punches:
             mygap = StructuralGap(res.prev, res.next, res.one_letter_code)

modelling/tests/CMakeLists.txt

@@ -33,6 +33,7 @@ set(MODELLING_TEST_DATA
   data/gly.pdb
   data/hetero-punched.pdb
   data/ins.fasta
+  data/neighbor-punched.pdb
   data/sep.fasta
   data/sep.pdb
   data/seq.fasta

modelling/tests/test_pipeline.py

@@ -249,6 +249,17 @@ class PipelineTests(unittest.TestCase):
                                   torsion_sampler=self.torsion_sampler)
         rings = modelling.GetRings(mhandle.model)
         self.assertFalse(modelling.HasRingPunches(rings, mhandle.model))
+        # ring punches in neighboring entries
+        mhandle = self.getMockModel(io.LoadPDB('data/neighbor-punched.pdb'))
+        rings = modelling.GetRings(mhandle.model)
+        ring_punches = modelling.GetRingPunches(rings, mhandle.model)
+        self.assertEqual(len(ring_punches), 2)
+        self.assertTrue(ring_punches[0].next == ring_punches[1])
+        modelling.BuildSidechains(mhandle, fragment_db=self.frag_db,
+                                  structure_db=self.structure_db,
+                                  torsion_sampler=self.torsion_sampler)
+        rings = modelling.GetRings(mhandle.model)
+        self.assertFalse(modelling.HasRingPunches(rings, mhandle.model))
 
     def testMinimizeModelEnergy(self):
         '''Check energy minimization.'''