SCHWED-3566: Report all stereo chemical problems correctly.

modelling/pymod/_pipeline.py

@@ -386,7 +386,9 @@ def CheckFinalModel(mhandle):
     ost.PopVerbosityLevel()
     # set bool props in model-residues
     atoms = [e.GetFirstAtom() for e in clash_info.GetClashList()]\
+          + [e.GetSecondAtom() for e in clash_info.GetClashList()]\
           + [e.GetFirstAtom() for e in stereo_info.GetBondViolationList()]\
+          + [e.GetSecondAtom() for e in stereo_info.GetBondViolationList()]\
           + [e.GetSecondAtom() for e in stereo_info.GetAngleViolationList()]
     for atomui in atoms:
         res = model_src.FindResidue(atomui.GetChainName(), atomui.GetResNum())