From 918f255ac0cfc5af1b3280ade692ebcbe29723c4 Mon Sep 17 00:00:00 2001
From: juergen <juergen@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 29 Mar 2010 12:06:48 +0000
Subject: [PATCH] rule-based and heuristic build are now relying on the same
implementation for backbone torsion angles -removed isp torsion completely
-fixed omega torsion implementation +added check for res.IsPetideLinking()
before adding backbone torsions
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1896 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/conop/src/builder.cc | 43 ++++++++++
modules/conop/src/builder.hh | 3 +
modules/conop/src/heuristic_builder.cc | 17 +---
modules/conop/src/heuristic_connect_table.hh | 85 ++++++++++----------
modules/conop/src/rule_based_builder.cc | 33 +-------
modules/mol/base/pymod/export_residue.cc | 1 -
modules/mol/base/src/impl/residue_impl.cc | 35 ++------
modules/mol/base/src/impl/residue_impl.hh | 11 +--
modules/mol/base/src/residue_base.cc | 6 --
modules/mol/base/src/residue_base.hh | 6 --
10 files changed, 103 insertions(+), 137 deletions(-)
diff --git a/modules/conop/src/builder.cc b/modules/conop/src/builder.cc
index 538bb8f52..f82eede9b 100644
--- a/modules/conop/src/builder.cc
+++ b/modules/conop/src/builder.cc
@@ -159,6 +159,49 @@ bool Builder::AreResiduesConsecutive(const mol::ResidueHandle& r1,
r2.GetNumber().GetInsCode()==r1.GetNumber().NextInsertionCode().GetInsCode();
}
+void Builder::AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res)
+{
+
+ mol::ResidueHandle prev=res.GetPrev();
+ mol::ResidueHandle next=res.GetNext();
+ mol::XCSEditor e=res.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
+ //psi
+ if (next.IsValid() && next.IsPeptideLinking()){
+ mol::AtomHandle ca_this=res.FindAtom("CA");
+ mol::AtomHandle n_this=res.FindAtom("N");
+ mol::AtomHandle c_this=res.FindAtom("C");
+ mol::AtomHandle n_next=next.FindAtom("N");
+ if ((ca_this && n_this && c_this && n_next && BondExists(c_this, n_next))
+ && !res.GetPsiTorsion()) {
+ e.AddTorsion("PSI", n_this, ca_this, c_this, n_next);
+ }
+ };
+ //phi
+ if (prev.IsValid() && prev.IsPeptideLinking()) {
+ mol::AtomHandle c_prev=prev.FindAtom("C");
+ mol::AtomHandle n_this=res.FindAtom("N");
+ mol::AtomHandle ca_this=res.FindAtom("CA");
+ mol::AtomHandle c_this=res.FindAtom("C");
+ if ((c_prev && n_this && ca_this && c_this && BondExists(c_prev, n_this))
+ && !res.GetPhiTorsion()) {
+ e.AddTorsion("PHI", c_prev, n_this, ca_this, c_this);
+ }
+ }
+ //omega
+ if (prev.IsValid() && prev.IsPeptideLinking()) {
+ mol::AtomHandle ca_prev=prev.FindAtom("CA");
+ mol::AtomHandle c_prev=prev.FindAtom("C");
+ mol::AtomHandle n=res.FindAtom("N");
+ mol::AtomHandle ca=res.FindAtom("CA");
+ if ((ca_prev && c_prev && n && ca && BondExists(c_prev, n))
+ && !res.GetOmegaTorsion()) {
+ e.AddTorsion("OMEGA",ca_prev , c_prev, n, ca);
+ }
+ }
+}
+
+
+
void Builder::DistanceBasedConnect(const mol::AtomHandle& atom)
{
mol::EntityHandle ent=atom.GetEntity();
diff --git a/modules/conop/src/builder.hh b/modules/conop/src/builder.hh
index 47a9f29c0..b47e432ac 100644
--- a/modules/conop/src/builder.hh
+++ b/modules/conop/src/builder.hh
@@ -99,6 +99,9 @@ public:
/// \brief assign named torsions to single residue
virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue);
+ /// \brief assign Backbone torsions to single residue
+ void AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res);
+
/// \brief Check if peptide bond is formed between the two atoms.
///
/// This method is called by ConnectResidueWithNext() after making sure that
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index c154c0c11..00e7f251b 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -359,18 +359,6 @@ 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;
}
@@ -404,10 +392,13 @@ void HeuristicBuilder::AssignTorsions(const mol::ChainHandle& chain)
if (chain.GetResidueCount()==0)
return;
std::vector<mol::ResidueHandle> rlist = chain.GetResidueList();
- mol::AtomHandleList atom_list = rlist[0].GetAtomList();
for(unsigned int ri=0;ri<rlist.size();++ri) {
mol::ResidueHandle res=rlist[ri];
this->AssignTorsionsToResidue(res);
+ if (!res.IsPeptideLinking()) {
+ return;
+ }
+ Builder::AssignBackBoneTorsionsToResidue(res);
}
}
diff --git a/modules/conop/src/heuristic_connect_table.hh b/modules/conop/src/heuristic_connect_table.hh
index 8f22ebcd3..6251d1070 100644
--- a/modules/conop/src/heuristic_connect_table.hh
+++ b/modules/conop/src/heuristic_connect_table.hh
@@ -34,7 +34,7 @@ struct CONN_DEF_ENTRY {
struct CONN_TORSION_TMP {
int n1,n2,n3,n4;
String name;
- }tor_list[12];
+ }tor_list[8];
int tor_count;
int flag_list[128];
int flag_count;
@@ -44,159 +44,158 @@ 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"},{2,3,-3,-4,"OMEGA"},
- },4,
+ {
+ },0,
{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"},{2,3,-3,-4,"OMEGA"},
- {1,2,5,6,"CHI1"}
- },5,
+ {{1,2,5,6,"CHI1"}
+ },1,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"}
- },7,
+ },3,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
- },4,
+ {
+ },0,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,8,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"},{6,7,8,9,"CHI4"}
- },8,
+ },4,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"}
- },7,
+ },3,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"},{5,6,7,8,"CHI3"}
- },7,
+ },3,
{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"},{2,3,-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"}
- },9,
+ {
+ {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"}
+ },5,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"}
- },5,
+ },1,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"}
- },5,
+ },1,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"}
- },5,
+ },1,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{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"},{2,3,-3,-4,"OMEGA"},
+ {
{1,2,5,6,"CHI1"},{2,5,6,7,"CHI2"}
- },6,
+ },2,
{0},1
},
/* NUCLEIC ACIDS */
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index a4ddb247e..0f12cbc63 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -203,34 +203,6 @@ void RuleBasedBuilder::ConnectResidueToNext(const mol::ResidueHandle& rh,
}
}
-void RuleBasedBuilder::AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res)
-{
-
- mol::ResidueHandle prev=res.GetPrev();
- mol::ResidueHandle next=res.GetNext();
- mol::XCSEditor e=res.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
- if (next.IsValid() && next.IsPeptideLinking()){
- mol::AtomHandle ca_this=res.FindAtom("CA");
- mol::AtomHandle n_this=res.FindAtom("N");
- mol::AtomHandle c_this=res.FindAtom("C");
- mol::AtomHandle n_next=next.FindAtom("N");
- if ((ca_this && n_this && c_this && n_next && BondExists(c_this, n_next))
- && !res.GetPsiTorsion()) {
- e.AddTorsion("PSI", n_this, ca_this, c_this, n_next);
- }
- };
- if (prev.IsValid() && prev.IsPeptideLinking()) {
- mol::AtomHandle c_prev=prev.FindAtom("C");
- mol::AtomHandle n_this=res.FindAtom("N");
- mol::AtomHandle ca_this=res.FindAtom("CA");
- mol::AtomHandle c_this=res.FindAtom("C");
- if ((c_prev && n_this && ca_this && c_this && BondExists(c_prev, n_this))
- && !res.GetPhiTorsion()) {
- e.AddTorsion("PHI", c_prev, n_this, ca_this, c_this);
- }
- }
-}
-
void RuleBasedBuilder::AssignTorsions(const mol::ChainHandle& chain) {
if (chain.GetResidueCount()==0)
@@ -247,15 +219,14 @@ void RuleBasedBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& residue
/// The only components having named torsions are the standard set of amino
/// acids, plus some of compounds derived from them such as selenium
/// methionine. Things are simplified a lot by only storing the torsions
- /// of the side chains in the database. PHI and PSI torsions are checked
- /// without a lookup in the database.
+ /// of the side chains in the database. PHI, PSI and OMEGA torsions are checked without a lookup in the database.
LookupCompound(residue);
if (!last_compound_)
return;
if (!last_compound_->IsPeptideLinking()) {
return;
}
- AssignBackBoneTorsionsToResidue(residue);
+ Builder::AssignBackBoneTorsionsToResidue(residue);
}
bool RuleBasedBuilder::IsResidueComplete(const mol::ResidueHandle& residue)
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 42498a4e1..615c6bc3d 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -85,7 +85,6 @@ 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))
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index 2fd41b0ba..b45dae810 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -246,29 +246,6 @@ const AtomImplList& ResidueImpl::GetAtomList() const
return atom_list_;
}
-TorsionImplP ResidueImpl::GetIspTorsion() 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 n=next->FindAtom("N");
- AtomImplPtr ca_po=next->FindAtom("CA");
- TorsionImplList::const_iterator i=torsion_list_.begin();
- for (;i!=torsion_list_.end(); ++i) {
- TorsionImplP t=*i;
- if (t->Matches(calpha, c, n, ca_po))
- return t;
- }
-
- LOGN_DUMP("Can't find torsion ISP for " <<
- this->GetKey() << this->GetNumber());
- return TorsionImplP();
-
-}
-
TorsionImplP ResidueImpl::GetPsiTorsion() const {
ChainImplPtr chain=this->GetChain();
ResidueImplPtr self=const_cast<ResidueImpl*>(this)->shared_from_this();
@@ -310,19 +287,19 @@ TorsionImplP ResidueImpl::FindTorsion(const String& torsion_name) const {
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))
+ ResidueImplPtr prev=chain->GetPrev(self);
+ if (!prev || !InSequence(prev, self))
return TorsionImplP();
+ AtomImplPtr calpha_prev=prev->FindAtom("CA");
+ AtomImplPtr c_prev=prev->FindAtom("C");
+ AtomImplPtr n=this->FindAtom("N");
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))
+ if (t->Matches(calpha_prev, c_prev, n, calpha))
return t;
}
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index ee47bdbb2..6a36a75bc 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -103,17 +103,12 @@ public:
/// TorsionImplP will be returned.
TorsionImplP GetPhiTorsion() const;
- /// \brief Get isp torsion between this and the prev residue
+ /// \brief Retrieve omega torsion between this and the previous 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
+ /// If no omega torsion has been assigned to this residue an invalid
/// TorsionImplP will be returned.
TorsionImplP 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 dfd4b16fb..e53801668 100644
--- a/modules/mol/base/src/residue_base.cc
+++ b/modules/mol/base/src/residue_base.cc
@@ -119,12 +119,6 @@ TorsionHandle ResidueBase::GetPsiTorsion() const
return impl_->GetPsiTorsion();
}
-TorsionHandle ResidueBase::GetIspTorsion() const
-{
- this->CheckValidity();
- return impl_->GetIspTorsion();
-}
-
TorsionHandle ResidueBase::GetOmegaTorsion() const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index 024812ab6..da5cd0525 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -122,12 +122,6 @@ 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
--
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