diff --git a/loop/src/all_atom_positions.cc b/loop/src/all_atom_positions.cc
index 42925e2b5921397231e1f2bbbaf6b95a2b31d3ce..2dad21d0e0c802bd81cc771af31c4de0127a6db5 100644
--- a/loop/src/all_atom_positions.cc
+++ b/loop/src/all_atom_positions.cc
@@ -7,10 +7,24 @@
namespace promod3 { namespace loop {
+namespace {
+
// default chem. type and class for amino acids
const ost::mol::ChemClass aa_chem_class(ost::mol::ChemClass::L_PEPTIDE_LINKING);
const ost::mol::ChemType aa_chem_type(ost::mol::ChemType::AMINOACIDS);
+// set residue props
+void SetResidueProps(ost::mol::ResidueHandle& res, char olc) {
+ res.SetOneLetterCode(olc);
+ res.SetChemClass(aa_chem_class);
+ res.SetChemType(aa_chem_type);
+ res.SetIsProtein(true);
+}
+
+} // anon ns
+
+///////////////////////////////////////////////////////////////////////////////
+
AllAtomPositions::AllAtomPositions(const String& sequence)
: aa_lookup_(AminoAcidLookup::GetInstance()) {
Initialize(sequence);
@@ -245,9 +259,7 @@ ost::mol::EntityHandle AllAtomPositions::ToEntity() const {
}
}
// set residue data
- res.SetOneLetterCode(aa_lookup_.GetOLC(GetAA(res_idx)));
- res.SetChemClass(aa_chem_class);
- res.SetChemType(aa_chem_type);
+ SetResidueProps(res, aa_lookup_.GetOLC(GetAA(res_idx)));
}
// set connections
ost::conop::HeuristicProcessor heu_proc;
@@ -285,9 +297,7 @@ void AllAtomPositions::InsertInto(uint res_idx, ost::mol::ChainHandle& chain,
// rename if needed
edi.RenameResidue(res, rname);
}
- res.SetOneLetterCode(aa_lookup_.GetOLC(aa));
- res.SetChemClass(aa_chem_class);
- res.SetChemType(aa_chem_type);
+ SetResidueProps(res, aa_lookup_.GetOLC(aa));
// set new atom positions
bool backbone_added = false;
diff --git a/loop/src/backbone.cc b/loop/src/backbone.cc
index 0a04aa1260134c0c718f9b05387d298886f9b754..edb4dd63c7dbbf09997f30d0395166e21a9104ad 100644
--- a/loop/src/backbone.cc
+++ b/loop/src/backbone.cc
@@ -6,10 +6,22 @@
namespace promod3 { namespace loop {
+namespace {
+
// default chem. type and class for amino acids
const ost::mol::ChemClass aa_chem_class(ost::mol::ChemClass::L_PEPTIDE_LINKING);
const ost::mol::ChemType aa_chem_type(ost::mol::ChemType::AMINOACIDS);
+// set residue props
+void SetResidueProps(ost::mol::ResidueHandle& res, char olc) {
+ res.SetOneLetterCode(olc);
+ res.SetChemClass(aa_chem_class);
+ res.SetChemType(aa_chem_type);
+ res.SetIsProtein(true);
+}
+
+} // anon ns
+
///////////////////////////////////////////////////////////////////////////////
// Backbone public
Backbone::Backbone(const geom::Vec3& n, const geom::Vec3& ca,
@@ -131,7 +143,8 @@ BackboneList::BackboneList(const String& sequence,
}
}
-ost::mol::EntityHandle BackboneList::ToEntity() const{
+ost::mol::EntityHandle BackboneList::ToEntity() const {
+ // make entity
ost::mol::EntityHandle ent = ost::mol::CreateEntity();
ost::mol::XCSEditor edi = ent.EditXCS(ost::mol::BUFFERED_EDIT);
ost::mol::ChainHandle chain = edi.InsertChain("A");
@@ -152,14 +165,14 @@ ost::mol::EntityHandle BackboneList::ToEntity() const{
cb = edi.InsertAtom(res, "CB", GetCB(i), "C");
edi.Connect(ca, cb);
}
- res.SetOneLetterCode(GetOLC(i));
- res.SetChemClass(aa_chem_class);
- res.SetChemType(aa_chem_type);
+ SetResidueProps(res, GetOLC(i));
if (last.IsValid()) {
edi.Connect(last.FindAtom("C"), n);
}
last = res;
}
+ // set torsions
+ ost::conop::AssignBackboneTorsions(chain);
return ent;
}
@@ -286,9 +299,7 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
before = edi.AppendResidue(chain,
ost::conop::OneLetterCodeToResidueName(GetOLC(0)),
n_num);
- before.SetOneLetterCode(GetOLC(0));
- before.SetChemClass(aa_chem_class);
- before.SetChemType(aa_chem_type);
+ SetResidueProps(before, GetOLC(0));
ost::mol::AtomHandle n = edi.InsertAtom(before, "N", GetN(0), "N");
ost::mol::AtomHandle ca = edi.InsertAtom(before, "CA", GetCA(0), "C");
ost::mol::AtomHandle c = edi.InsertAtom(before, "C", GetC(0), "C");
@@ -358,9 +369,7 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
} else { // !after.IsValid()
after = edi.AppendResidue(chain, ost::conop::OneLetterCodeToResidueName(GetOLC(last_idx)), c_num);
- after.SetOneLetterCode(GetOLC(last_idx));
- after.SetChemClass(aa_chem_class);
- after.SetChemType(aa_chem_type);
+ SetResidueProps(after, GetOLC(last_idx));
ost::mol::AtomHandle n = edi.InsertAtom(after, "N", GetN(last_idx), "N");
ost::mol::AtomHandle ca = edi.InsertAtom(after, "CA", GetCA(last_idx), "C");
ost::mol::AtomHandle c = edi.InsertAtom(after, "C", GetC(last_idx), "C");
@@ -399,9 +408,7 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
String rname = ost::conop::OneLetterCodeToResidueName(GetOLC(i));
ost::mol::ResidueHandle res = edi.AppendResidue(chain, rname,
last.GetNumber() + 1);
- res.SetOneLetterCode(GetOLC(i));
- res.SetChemClass(aa_chem_class);
- res.SetChemType(aa_chem_type);
+ SetResidueProps(res, GetOLC(i));
ost::mol::AtomHandle n = edi.InsertAtom(res, "N", GetN(i), "N");
ost::mol::AtomHandle ca = edi.InsertAtom(res, "CA", GetCA(i), "C");
ost::mol::AtomHandle c = edi.InsertAtom(res, "C", GetC(i), "C");
diff --git a/loop/tests/test_all_atom_positions.cc b/loop/tests/test_all_atom_positions.cc
index a37fe16cd956b62324d1a60d2b5fecb14343e07a..bdecca598bd2d86da16db22ec0d2c440f6c818a8 100644
--- a/loop/tests/test_all_atom_positions.cc
+++ b/loop/tests/test_all_atom_positions.cc
@@ -74,6 +74,29 @@ void CompareResidues(const ost::mol::ResidueHandle& new_res,
}
}
+void CheckEntity(const ost::mol::EntityHandle& ent) {
+ // look at all residues
+ ost::mol::ResidueHandleList res_list = ent.GetResidueList();
+ for (uint res_idx = 0; res_idx < res_list.size(); ++res_idx) {
+ // get residues
+ const ost::mol::ResidueHandle& r = res_list[res_idx];
+ const ost::mol::ResidueHandle r_next = r.GetNext();
+ const ost::mol::ResidueHandle r_prev = r.GetPrev();
+ // check types
+ BOOST_CHECK(r.IsPeptideLinking());
+ BOOST_CHECK(r.IsProtein());
+ // peptide links checked in CompareResidues
+ // check torsions
+ if (r_prev.IsValid() && ost::mol::InSequence(r_prev, r)) {
+ BOOST_CHECK(r.GetPhiTorsion().IsValid());
+ BOOST_CHECK(r.GetOmegaTorsion().IsValid());
+ }
+ if (r_next.IsValid() && ost::mol::InSequence(r, r_next)) {
+ BOOST_CHECK(r.GetPsiTorsion().IsValid());
+ }
+ }
+}
+
}
BOOST_AUTO_TEST_CASE(test_aap_setup) {
@@ -410,6 +433,7 @@ BOOST_AUTO_TEST_CASE(test_aap_to_ost) {
for (uint res_idx = 0; res_idx < res_list.size(); ++res_idx) {
CompareResidues(new_res_list[res_idx], res_list[res_idx]);
}
+ CheckEntity(new_prot);
}
BOOST_AUTO_TEST_CASE(test_aap_into_ost) {
@@ -469,6 +493,7 @@ BOOST_AUTO_TEST_CASE(test_aap_into_ost) {
BOOST_CHECK_EQUAL(new_res.GetNumber(), res_list[res_idx].GetNumber());
CompareResidues(new_res, res_list[res_idx]);
}
+ CheckEntity(new_prot);
// check overwrite of residue with killed sidechain atom
geom::Vec3 new_pos = atoms.GetPos(2, BB_C_INDEX) + geom::Vec3(1,1,1);
diff --git a/loop/tests/test_backbone.cc b/loop/tests/test_backbone.cc
index e10dff36e70c62fa4e1d4dc91cf2d35cf2b762f4..4b82781ca072c3ebd504f4a502a59e13a30a4958 100644
--- a/loop/tests/test_backbone.cc
+++ b/loop/tests/test_backbone.cc
@@ -83,6 +83,65 @@ bool CheckBackbonePlausibility(const BackboneList& bb_list, bool skip_last){
return true;
}
+
+void CheckEntity(const ost::mol::EntityHandle& ent) {
+ // look at all residues
+ ost::mol::ResidueHandleList res_list = ent.GetResidueList();
+ for (uint res_idx = 0; res_idx < res_list.size(); ++res_idx) {
+ // get residues
+ const ost::mol::ResidueHandle& r = res_list[res_idx];
+ const ost::mol::ResidueHandle r_next = r.GetNext();
+ const ost::mol::ResidueHandle r_prev = r.GetPrev();
+ // check types
+ BOOST_CHECK(r.IsPeptideLinking());
+ BOOST_CHECK(r.IsProtein());
+ // check links
+ if (r_next.IsValid() && r_next.GetNumber() - 1 == r.GetNumber()) {
+ BOOST_CHECK(ost::mol::InSequence(r, r_next));
+ }
+ // check torsions
+ if (r_prev.IsValid() && ost::mol::InSequence(r_prev, r)) {
+ BOOST_CHECK(r.GetPhiTorsion().IsValid());
+ BOOST_CHECK(r.GetOmegaTorsion().IsValid());
+ }
+ if (r_next.IsValid() && ost::mol::InSequence(r, r_next)) {
+ BOOST_CHECK(r.GetPsiTorsion().IsValid());
+ }
+ }
+}
+
+void CheckEntityBB(const ost::mol::EntityHandle& ent,
+ const BackboneList& bb_list) {
+ // look at all backbone atoms
+ ost::mol::ResidueHandleList res_list = ent.GetResidueList();
+ for (uint res_idx = 0; res_idx < res_list.size(); ++res_idx) {
+ // get atoms
+ const ost::mol::ResidueHandle& r = res_list[res_idx];
+ ost::mol::AtomHandle n = r.FindAtom("N");
+ ost::mol::AtomHandle ca = r.FindAtom("CA");
+ ost::mol::AtomHandle c = r.FindAtom("C");
+ ost::mol::AtomHandle o = r.FindAtom("O");
+ ost::mol::AtomHandle cb = r.FindAtom("CB");
+ // check validity
+ BOOST_CHECK(n.IsValid());
+ BOOST_CHECK(ca.IsValid());
+ BOOST_CHECK(c.IsValid());
+ BOOST_CHECK(o.IsValid());
+ // compare pos
+ BOOST_CHECK_EQUAL(n.GetPos(), bb_list.GetN(res_idx));
+ BOOST_CHECK_EQUAL(ca.GetPos(), bb_list.GetCA(res_idx));
+ BOOST_CHECK_EQUAL(c.GetPos(), bb_list.GetC(res_idx));
+ BOOST_CHECK_EQUAL(o.GetPos(), bb_list.GetO(res_idx));
+ // check CB
+ if (bb_list.GetAA(res_idx) == ost::conop::GLY) {
+ BOOST_CHECK(!cb.IsValid());
+ } else {
+ BOOST_CHECK(cb.IsValid());
+ BOOST_CHECK_EQUAL(cb.GetPos(), bb_list.GetCB(res_idx));
+ }
+ }
+}
+
}
BOOST_AUTO_TEST_CASE(test_initialization){
@@ -278,7 +337,7 @@ BOOST_AUTO_TEST_CASE(test_replace_fragment) {
BOOST_AUTO_TEST_CASE(test_superpose) {
- // get dummy backbone and fragment
+ // get dummy backbones
String seq = "HELLYEAHEYECATCHER";
BackboneList bb_list(seq);
BackboneList bb_list2(seq);
@@ -296,4 +355,30 @@ BOOST_AUTO_TEST_CASE(test_superpose) {
BOOST_CHECK(bb_list.CARMSD(bb_list, true) < 1e-4);
}
+BOOST_AUTO_TEST_CASE(test_bb_to_ost) {
+
+ // get dummy backbone and fragment
+ String seq = "HELLYEAHEYECATCHER";
+ BackboneList bb_list(seq);
+ BackboneList frag = bb_list.Extract(4, 9);
+
+ // extract OST entity
+ ost::mol::EntityHandle ent = bb_list.ToEntity();
+ CheckEntity(ent);
+ CheckEntityBB(ent, bb_list);
+
+ // insert fragment in position of 4th residue (fragment pos.)
+ ost::mol::ResidueHandleList res_list = ent.GetResidueList();
+ ost::mol::ResidueHandle res = res_list[4];
+ ost::mol::ChainHandle chain = res.GetChain();
+ frag.InsertInto(chain, res.GetNumber());
+ CheckEntity(ent);
+ CheckEntityBB(ent, bb_list);
+
+ // trigger exceptions
+ ost::mol::ChainHandle invalid_chain;
+ BOOST_CHECK_THROW(frag.InsertInto(invalid_chain, res.GetNumber()),
+ promod3::Error);
+}
+
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index 747513b72c839a16ffc1873ad9422932ea98aba7..4504b7ea1c18b08e6dbcd982f3a53a8e65b29921 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -1033,6 +1033,7 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
}
String name=conop::OneLetterCodeToResidueName(col[0]);
ResidueHandle dst_res=edi.AppendResidue(chain, name, ResNum(res_num));
+ dst_res.SetIsProtein(true);
bool form_peptide_bond=false;
if (last_num+1!=res_num) {
// that's an insertion
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index 95cc8af15c240f72cf39c252556fb9ad759b74cf..b43d05a308e0530df362d3b3e4e2018b31cba31f 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -186,8 +186,25 @@ class PipelineTests(unittest.TestCase):
return mhandle
def checkFinalModel(self, mhandle, exp_gaps=0, num_chains=0):
- '''Check if model has exp_gaps and that CheckFinalModel reports it.'''
- # setup
+ '''Check if:
+ - model has exp_gaps and that CheckFinalModel reports it
+ - model residues are properly set (peptide_linking, protein, torsion)
+ '''
+ # check residue properties
+ for r in mhandle.model.residues:
+ # check types
+ self.assertTrue(r.peptide_linking)
+ self.assertTrue(r.is_protein)
+ # check links
+ if r.next.IsValid() and (r.next.number - r.number) == 1:
+ self.assertTrue(mol.InSequence(r, r.next))
+ # check torsions
+ if r.prev.IsValid() and mol.InSequence(r.prev, r):
+ self.assertTrue(r.phi_torsion.IsValid())
+ self.assertTrue(r.omega_torsion.IsValid())
+ if r.next.IsValid() and mol.InSequence(r, r.next):
+ self.assertTrue(r.psi_torsion.IsValid())
+ # setup gap check
self.assertEqual(len(mhandle.gaps), exp_gaps)
log = _FetchLog()
ost.PushLogSink(log)