Merge branch 'hotfix-1.0.1'

CMakeLists.txt

@@ -15,7 +15,7 @@ include(PROMOD3)
 
 set(PROMOD3_VERSION_MAJOR 1)
 set(PROMOD3_VERSION_MINOR 0)
-set(PROMOD3_VERSION_PATCH 0)
+set(PROMOD3_VERSION_PATCH 1)
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
 

modelling/pymod/_pipeline.py

@@ -13,7 +13,7 @@ from _ring_punches import *
 import ost
 from ost import mol
 from ost.mol import mm
-import os
+import os, math
 
 def BuildSidechains(mhandle, merge_distance=4, scorer=None, fragment_db=None,
                     structure_db=None, torsion_sampler=None):
@@ -140,6 +140,11 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
         settings.platform = mm.Platform.Reference
         sim = mm.Simulation(mhandle.model, settings)
         ost.LogWarning("Switched to slower reference platform of OpenMM!")
+    # check for certain failure -> we get NaN if atoms are on top each other
+    if math.isnan(sim.GetEnergy()):
+        ost.LogError("OpenMM could not minimize energy as atoms are on top of "
+                     "each other!")
+        return
     # settings to check for stereochemical problems
     clashing_distances = mol.alg.DefaultClashingDistances()
     bond_stereo_chemical_param = mol.alg.DefaultBondStereoChemicalParams()

modelling/src/model.cc

@@ -46,8 +46,25 @@ bool CheckBackboneAtoms(ResidueView res)
   return true;
 }
 
+void CleanupAtomConflicts(ResidueView& res) {
+  // remove atoms which are on top of any other atoms in the tpl entity
+  EntityView tpl = res.GetEntity();
+  AtomViewList atom_views = res.GetAtomList();
+  for (uint i = 0; i < atom_views.size(); ++i) {
+    AtomViewList on_top_atoms = tpl.FindWithin(atom_views[i].GetPos(), 0.0);
+    if (on_top_atoms.size() > 1) {
+      res.RemoveAtom(atom_views[i]);
+      // report
+      std::stringstream ss;
+      ss << "residue " << res.GetQualifiedName() << " has conflicting atom "
+         << atom_views[i].GetName() << " - skipping atom.";
+      LOG_WARNING(ss.str());
+    }
+  }
 }
 
+} // anon ns
+
 int CountEnclosedGaps(ModellingHandle& mhandle, const StructuralGap& gap,
                       bool insertions_only)
 {
@@ -541,6 +558,8 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
         src_res.GetOneLetterCode() << "'";
       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)){