diff --git a/modules/mol/alg/src/nonstandard.cc b/modules/mol/alg/src/nonstandard.cc
index ef878cbc80ea3d64d472a71d8f8234f11c2d2ceb..f675cc9746f15b0adbee11eaac817c72036f437c 100644
--- a/modules/mol/alg/src/nonstandard.cc
+++ b/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;
}
diff --git a/modules/mol/alg/tests/test_nonstandard.py b/modules/mol/alg/tests/test_nonstandard.py
index cbe8257a70576b5eb225ca3ba29293f95e362075..c7f49215eb79b559c1c43cd71659569de5e447fb 100644
--- a/modules/mol/alg/tests/test_nonstandard.py
+++ b/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())
diff --git a/modules/mol/alg/tests/testfiles/cbeta_fail.pdb b/modules/mol/alg/tests/testfiles/cbeta_fail.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..3c856297e848d7621a9d20414b336f2feec59c93
--- /dev/null
+++ b/modules/mol/alg/tests/testfiles/cbeta_fail.pdb
@@ -0,0 +1,13 @@
+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