SCHWED-4658: mol.alg.CopyResidue can deal with bad backbones now.

This is used in Molck's MapNonStandardResidues which used to fail if there
were missing (or unmappable) backbone atoms in modified residues.

modules/mol/alg/src/nonstandard.cc

@@ -21,6 +21,7 @@
   Author: Marco Biasini, Juergen Haas
  */
 
+#include <ost/message.hh>
 #include <ost/log.hh>
 #include <ost/dyn_cast.hh>
 #include <ost/conop/conop.hh>
@@ -58,8 +59,15 @@ bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res,
   }
   // insert Cbeta, unless dst residue is glycine.
   if (!has_cbeta && dst_res.GetName()!="GLY") {
-    geom::Vec3 cbeta_pos=mol::alg::CBetaPosition(dst_res);
-    edi.InsertAtom(dst_res, "CB", cbeta_pos, "C");
+    try {
+      geom::Vec3 cbeta_pos = mol::alg::CBetaPosition(dst_res);
+      edi.InsertAtom(dst_res, "CB", cbeta_pos, "C");
+    } catch (ost::Error& e) {
+      LOG_WARNING("Issue in CB reconstruction while copying residue "
+                  << src_res.GetQualifiedName() << " to "
+                  << dst_res.GetQualifiedName() << ": " << e.what()
+                  << ". Skipped reconstruction.");
+    }
   }
   return ret;
 }

modules/mol/alg/tests/test_nonstandard.py

@@ -57,11 +57,56 @@ class TestNonStandard(unittest.TestCase):
     self.assertTrue(residues[3].FindAtom("CB").IsValid())
 
 
+  def test_CBetaFail(self):
+    # make sure that we can handle cases where CB reconstruction fails
+
+    # NOTES:
+    # - SNN is (since June 2011) labeled as a modified ASN but has a weird
+    #   backbone structure without any overlap in atom names with ASN
+    #   -> we hence expect it to a) always fall back to CopyNonConserved
+    #      and b) fail to copy any atoms (and hence also fail to)
+    # - SNN also removes N of following residue which is expected to have an
+    #   incomplete backbone which would make it impossible to create a CB pos.
+    
+    # source of file: residues A.198 and A.199 from PDB ID 2YHW
+    tpl = io.LoadPDB('testfiles/cbeta_fail.pdb')
+    new_hdl = mol.CreateEntity();
+    ed = new_hdl.EditXCS()
+    c = ed.InsertChain('A')
+    ed.AppendResidue(c, 'GLY')
+    ed.AppendResidue(c, 'ALA')
+    ed.AppendResidue(c, 'ASN')
+    ed.AppendResidue(c, 'GLY')
+    ed.AppendResidue(c, 'ALA')
+    # SNN to GLY
+    err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
+    self.assertFalse(err)
+    self.assertEqual(new_hdl.residues[0].atom_count, 0)
+    # SNN to ALA
+    err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[1], ed)
+    self.assertFalse(err)
+    self.assertEqual(new_hdl.residues[1].atom_count, 0)
+    # SNN to ASN
+    err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[2], ed)
+    self.assertFalse(err)
+    self.assertEqual(new_hdl.residues[2].atom_count, 0)
+    # GLY to GLY
+    err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[3], ed)
+    self.assertTrue(err)
+    self.assertEqual(new_hdl.residues[3].atom_count, 3)
+    self.assertFalse(new_hdl.residues[3].FindAtom("CB").IsValid())
+    # GLY to ALA
+    err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[4], ed)
+    self.assertFalse(err)
+    self.assertEqual(new_hdl.residues[4].atom_count, 3)
+    self.assertFalse(new_hdl.residues[4].FindAtom("CB").IsValid())
+
+
   def test_CopyResidue(self):
-    tpl=io.LoadPDB('testfiles/cbeta.pdb')
-    new_hdl=mol.CreateEntity();
-    ed=new_hdl.EditXCS()
-    c=ed.InsertChain('A')
+    tpl = io.LoadPDB('testfiles/cbeta.pdb')
+    new_hdl = mol.CreateEntity();
+    ed = new_hdl.EditXCS()
+    c = ed.InsertChain('A')
     ed.AppendResidue(c, 'MET')
     ed.AppendResidue(c, 'GLY')
     ed.AppendResidue(c, 'GLY')
@@ -72,31 +117,31 @@ class TestNonStandard(unittest.TestCase):
     ed.AppendResidue(c, 'MET')
     
     # MET to MET
-    err =mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
+    err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
     self.assertTrue(err)
     #GLY to GLY
-    err =mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[1], ed)
+    err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[1], ed)
     self.assertTrue(err)
     # GLY to GLY
-    err =mol.alg.CopyResidue(tpl.residues[2], new_hdl.residues[2], ed)
+    err = mol.alg.CopyResidue(tpl.residues[2], new_hdl.residues[2], ed)
     self.assertTrue(err)
     #now we copy a HIS to a HIS
-    err =mol.alg.CopyResidue(tpl.residues[3], new_hdl.residues[3], ed)
+    err = mol.alg.CopyResidue(tpl.residues[3], new_hdl.residues[3], ed)
     self.assertTrue(err)
     # copy a GLY to a HIS
-    err, has_cbeta=mol.alg.CopyNonConserved(tpl.residues[1], new_hdl.residues[4], ed)
+    err, has_cbeta = mol.alg.CopyNonConserved(tpl.residues[1], new_hdl.residues[4], ed)
     self.assertFalse(has_cbeta)
-    # copy a MET to a GLY 
-    err =mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[5], ed)
+    # copy a MET to a GLY
+    err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[5], ed)
     self.assertFalse(err)
-    # copy a MET to a HIS 
-    err =mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[6], ed)
+    # copy a MET to a HIS
+    err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[6], ed)
     self.assertFalse(err)
     # copy a GLY to a MET with adding CB
-    err=mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[7], ed)
+    err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[7], ed)
     self.assertFalse(err)
       
-    residues=new_hdl.residues
+    residues = new_hdl.residues
     self.assertEqual(len(residues), 8)
     # MET to MET
     self.assertTrue(residues[0].FindAtom("CB").IsValid())

modules/mol/alg/tests/testfiles/cbeta_fail.pdb

+ATOM      1  N1  SNN A 198     -29.170  34.390  20.593  1.00 19.36           N  
+ATOM      2  C2  SNN A 198     -29.098  33.236  19.935  1.00 22.44           C  
+ATOM      3  C3  SNN A 198     -30.445  32.723  19.591  1.00 22.60           C  
+ATOM      4  N3  SNN A 198     -30.638  31.540  20.497  1.00 19.05           N  
+ATOM      5  C4  SNN A 198     -31.361  33.870  20.080  1.00 24.77           C  
+ATOM      6  C5  SNN A 198     -30.421  34.922  20.754  1.00 31.46           C  
+ATOM      7  O2  SNN A 198     -28.057  32.598  19.660  1.00 21.86           O  
+ATOM      8  O5  SNN A 198     -30.731  36.074  21.349  1.00 31.34           O  
+ATOM      9  CA  GLY A 199     -27.868  35.007  21.247  1.00 21.30           C  
+ATOM     10  C   GLY A 199     -27.140  35.813  20.142  1.00 19.04           C  
+ATOM     11  O   GLY A 199     -27.544  35.877  18.965  1.00 19.95           O  
+TER      12      GLY A 199                                                      
+END