diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index a2d59e4452c7d20cec149f1f3b787b7d289ca9e2..c154c0c1119aa386a40ddc5d9693e6b9c54d3f18 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -25,6 +25,7 @@
#include "heuristic_connect_table.hh"
#include <ost/mol/residue_handle.hh>
+
namespace ost { namespace conop {
namespace detail {
@@ -172,8 +173,11 @@ HeuristicBuilder::HeuristicBuilder():
tor_nam[cid]="-";
} else if (tor_id[cid]==-3) {
tor_nam[cid]="+";
+ } else if (tor_id[cid]==-4) {
+ tor_nam[cid]=":";
}
}
+
entry.AddTors(tor_nam[0],tor_nam[1],tor_nam[2],tor_nam[3],tor_nam2);
}
@@ -345,7 +349,7 @@ void HeuristicBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& res)
flag=true;
}
}
- } else if (tel[ti].a[ahi]=="-") {
+ } else if (cur_name=="-") {
mol::ResidueHandle prev=res.GetPrev();
if (Builder::AreResiduesConsecutive(prev, res)) {
centry2=LookupResEntry(prev.GetKey());
@@ -355,6 +359,18 @@ void HeuristicBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& res)
flag=true;
}
}
+ } else if (cur_name==":") {
+ mol::ResidueHandle next=res.GetNext();
+ if (Builder::AreResiduesConsecutive(res,next)) {
+ centry2=LookupResEntry(next.GetKey());
+ if (centry2.second) {
+ //force CA since only N can be accessed by using centry2.first.GetNext();
+ //TODO refactor using hardcoded torsions from heuristic and place in base class.
+ cur_name="CA";
+ search_in=next;
+ flag=true;
+ }
+ }
} else {
flag=true;
}
diff --git a/modules/conop/src/heuristic_connect_table.hh b/modules/conop/src/heuristic_connect_table.hh
index 22093c24b7587fb931cfd0907199124dff2f5773..8f22ebcd365fb0668f280a6ce8ee682bcdb36fd1 100644
--- a/modules/conop/src/heuristic_connect_table.hh
+++ b/modules/conop/src/heuristic_connect_table.hh
@@ -44,159 +44,159 @@ CONN_DEF_ENTRY def_entry_table[]={
{"Alanine","ALA",'A', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","OXT"},6,
{{-2,1}, {1,2}, {2,3}, {3,4}, {2,5}, {3,-3}, {6, 3}},7,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
- },3,
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
+ },4,
{0, 0, 0, 0, 0, 0},6
},
{"Cystein","CYS",'C', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","SG","OXT"},7,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{3,-3},{8, 3}},8,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"}
- },4,
+ },5,
{0, 0, 0, 0, 0, 0, 0},7
},
{"Aspartate","ASP",'D', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","OD1","OD2","OXT"},9,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{6,8},{3,-3},{9, 3}},10,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0, 0, 0, 0, 0, 0, 0, 0, 0},9
},
{"Glutamate","GLU",'E', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD","OE1","OE2","OXT"},10,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{7,8},{7,9},{3,-3},{10, 3}},11,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"}
- },6,
+ },7,
{0},1
},
{"Phenylalanine","PHE",'F', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD1","CD2","CE1","CE2","CZ","OXT"},12,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{6,8},{7,9},{8,10},{9,11},{10,11},{3,-3},{12, 3}},14,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0},1
},
{"Glycin","GLY",'G', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","OXT"},5,
{{-2,1},{1,2},{2,3},{3,4},{3,-3},{5, 3}},6,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
- },3,
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
+ },4,
{0},1
},
{"Histidine","HIS",'H', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","ND1","CD2","CE1","NE2","OXT"},11,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{6,8},{7,9},{8,10},{9,10},{3,-3},{11, 3}},13,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0},1
},
{"Isoleucine","ILE",'I', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG1","CG2","CD1","OXT"},9,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{5,7},{6,8},{3,-3},{9, 3}},10,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,8,"CHI2"}
- },5,
+ },6,
{0},1
},
{"Lysin","LYS",'K', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD","CE","NZ","OXT"},10,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{7,8},{8,9},{3,-3},{10, 3}},11,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"},{6,7,8,9,"CHI4"}
- },7,
+ },8,
{0},1
},
{"Leucin","LEU",'L', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD1","CD2","OXT"},9,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{6,8},{3,-3},{9, 3}},10,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0},1
},
{"Methionine","MET",'M', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","SD","CE","OXT"},9,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{7,8},{3,-3},{10, 3}},10,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"}
- },6,
+ },7,
{0},1
},
{"Asparagine","ASN",'N', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","OD1","ND2","OXT"},9,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{6,8},{3,-3},{9, 3}},10,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0},1
},
{"Proline","PRO",'P', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD","OXT"},8,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{3,-3},{1,7},{8, 3}},10,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0},1
},
{"Glutamine","GLN",'Q', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD","OE1","NE2","OXT"},10,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{7,8},{7,9},{3,-3},{10, 3}},11,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"}
- },6,
+ },7,
{0},1
},
{"Arginine","ARG",'R', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD","NE","CZ","NH1","NH2","OXT"},12,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{7,8},{8,9},{9,10},{9,11},{3,-3},{12, 3}},13,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"},{6,7,8,9,"CHI4"},{7,8,9,10,"CHI5"}
- },8,
+ },9,
{0},1
},
{"Serine","SER",'S', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","OG","OXT"},7,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{3,-3},{7, 3}},8,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"}
- },4,
+ },5,
{0},1
},
{"Threonine","THR",'T', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","OG1","CG2","OXT"},8,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{5,7},{3,-3},{8, 3}},9,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"}
- },4,
+ },5,
{0},1
},
{"Valine","VAL",'V', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG1","CG2","OXT"},8,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{5,7},{3,-3},{8, 3}},9,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"}
- },4,
+ },5,
{0},1
},
{"Tryptophan","TRP",'W', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD1","CD2","NE1","CE2","CE3","CZ2","CZ3","CH2","OXT"},15,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{6,8},{7,9},{8,10},{9,10},{8,11},{10,12},{11,13},{12,14},{13,14},{3,-3},{15, 3}},18,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0},1
},
{"Tyrosin","TYR",'Y', mol::ChemClass(mol::ChemClass::LPeptideLinking),
{"N","CA","C","O","CB","CG","CD1","CD2","CE1","CE2","CZ","OH","OXT"},13,
{{-2,1},{1,2},{2,3},{3,4},{2,5},{5,6},{6,7},{6,8},{7,9},{8,10},{9,11},{10,11},{11,12},{3,-3},{13, 3}},15,
- {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},
+ {{-2,1,2,3,"PHI"},{1,2,3,-3,"PSI"},{-3,3,2,1,"ISP"},{2,3,-3,-4,"OMEGA"},
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },5,
+ },6,
{0},1
},
/* NUCLEIC ACIDS */
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 77e15ad61d8a64af1dab5dc97451d9a528e42e4f..42498a4e1df504730a66b7e64e0676e380b0b60a 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -85,6 +85,8 @@ void export_Residue()
.def("SetSecStructure", &ResidueBase::SetSecStructure)
.def("GetPhiTorsion", &ResidueBase::GetPhiTorsion)
.def("GetPsiTorsion", &ResidueBase::GetPsiTorsion)
+ .def("GetIspTorsion", &ResidueBase::GetIspTorsion)
+ .def("GetOmegaTorsion", &ResidueBase::GetOmegaTorsion)
.def("IsValid", &ResidueBase::IsValid)
.def(self_ns::str(self))
.def("GetOneLetterCode", &ResidueBase::GetOneLetterCode)
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index ccdbe30e5c603478ccd577ebaceeef0e1c6fd439..2fd41b0bad9d05a4c0b70085560f7759e25bb877 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -306,6 +306,32 @@ TorsionImplP ResidueImpl::FindTorsion(const String& torsion_name) const {
return TorsionImplP();
}
+
+TorsionImplP ResidueImpl::GetOmegaTorsion() const {
+ ChainImplPtr chain=this->GetChain();
+ ResidueImplPtr self=const_cast<ResidueImpl*>(this)->shared_from_this();
+ ResidueImplPtr next=chain->GetNext(self);
+ if (!next || !InSequence(self, next))
+ return TorsionImplP();
+
+ AtomImplPtr calpha=this->FindAtom("CA");
+ AtomImplPtr c=this->FindAtom("C");
+ AtomImplPtr nne=next->FindAtom("N");
+ AtomImplPtr calphane=next->FindAtom("CA");
+ TorsionImplList::const_iterator i=torsion_list_.begin();
+
+ for (;i!=torsion_list_.end(); ++i) {
+ TorsionImplP t=*i;
+ if (t->Matches(calpha, c, nne, calphane))
+ return t;
+ }
+
+ LOGN_DUMP("Can't find torsion Omega for " <<
+ this->GetKey() << this->GetNumber());
+ return TorsionImplP();
+}
+
+
TorsionImplP ResidueImpl::GetPhiTorsion() const {
ChainImplPtr chain=this->GetChain();
ResidueImplPtr self=const_cast<ResidueImpl*>(this)->shared_from_this();
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index 47a833b56652ecf35201e117efc224cf7c4e10f8..21b3bcc9cc093558ed4d433fabb265d6117615bc 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -103,11 +103,17 @@ public:
/// TorsionImplP will be returned.
TorsionImplP GetPhiTorsion() const;
- /// \brief Get isp torsion between this and the next residue
+ /// \brief Get isp torsion between this and the prev residue
///
/// If no isp torsion has been assigned to this residue an invalid
/// TorsionImplP will be returned.
TorsionImplP GetIspTorsion() const;
+
+ /// \brief Get omega torsion between this and the prev residue
+ ///
+ /// If no isp torsion has been assigned to this residue an invalid
+ /// TorsionImplP will be returned.
+ TorsionImplP ResidueImpl::GetOmegaTorsion() const;
/// \brief Get psi torsion
///
/// If no psi torsion has been assigned to this residue an invalid
diff --git a/modules/mol/base/src/residue_base.cc b/modules/mol/base/src/residue_base.cc
index 802db679e4e280c89fca2c291e5d148bf68fbf98..dfd4b16fbc03a3dfb99fbcea8b64d3ffe776b78c 100644
--- a/modules/mol/base/src/residue_base.cc
+++ b/modules/mol/base/src/residue_base.cc
@@ -119,6 +119,18 @@ TorsionHandle ResidueBase::GetPsiTorsion() const
return impl_->GetPsiTorsion();
}
+TorsionHandle ResidueBase::GetIspTorsion() const
+{
+ this->CheckValidity();
+ return impl_->GetIspTorsion();
+}
+
+TorsionHandle ResidueBase::GetOmegaTorsion() const
+{
+ this->CheckValidity();
+ return impl_->GetOmegaTorsion();
+}
+
impl::ResidueImplPtr& ResidueBase::Impl()
{
return impl_;
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index 270cce51d4e5ad7b0ec0cef2b415768b3c51d96a..024812ab6afc908f96e139cd59cd6097bcca3c80 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -122,6 +122,17 @@ public:
/// will be returned.
TorsionHandle GetPsiTorsion() const;
+ /// \brief Get isp torsion
+ ///
+ /// If no isp torsion has been assigned to this residue an invalid TorsionHandle
+ /// will be returned.
+ TorsionHandle GetIspTorsion() const;
+
+ /// \brief Get omega torsion
+ ///
+ /// If no omega torsion has been assigned to this residue an invalid TorsionHandle
+ /// will be returned.
+ TorsionHandle GetOmegaTorsion() const;
char GetOneLetterCode() const;
void SetOneLetterCode(char olc);
diff --git a/modules/mol/base/src/residue_handle.hh b/modules/mol/base/src/residue_handle.hh
index d3c228585154c70712373ed1610f5ed9a5222770..0d85e6e7fd460be23d463f1c7210da729e74edee 100644
--- a/modules/mol/base/src/residue_handle.hh
+++ b/modules/mol/base/src/residue_handle.hh
@@ -127,7 +127,7 @@ public:
int GetBondCount() const;
/// \brief Find torsion by name
- /// \note For the PHI and PSI torsions of the backbone use the designated
+ /// \note For the PHI, ISP and PSI torsions of the backbone use the designated
/// GetPhiTorsion and GetPsiTorsion methods, respectively.
/// \param torsion_name
/// is the name of the torsion you are looking for. Torsions are named
@@ -137,7 +137,7 @@ public:
/// \sa ResidueBase::GetPhiTorsion, ResidueBase::GetPsiTorsion
TorsionHandle FindTorsion(const String& torsion_name) const;
- /// \brief Get list of all torsion of this residue
+ /// \brief Get list of all torsion angles of this residue
TorsionHandleList GetTorsionList() const;
/// \brief Get position of residue in chain.