From 704311bb153fc811260d99b988830d5c33e885f2 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Thu, 12 Jul 2012 08:09:28 +0200
Subject: [PATCH] properly connect DNA/RNA
---
modules/conop/src/heuristic_builder.cc | 22 +++++++++++++++-----
modules/conop/src/heuristic_builder.hh | 2 ++
modules/conop/src/heuristic_connect_table.hh | 10 ++++-----
3 files changed, 24 insertions(+), 10 deletions(-)
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 458370078..07922d6a2 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -187,6 +187,7 @@ HeuristicBuilder::HeuristicBuilder():
emap_[def_entry.abbrev]=entry;
}
}
+ default_nucleotide_=LookupResEntry("G").first;
LOG_DEBUG("done importing internal tables");
}
@@ -321,6 +322,10 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
res0_ret.first=builder->DefaultPeptide();
res0_ret.second=true;
}
+ if (res0.FindAtom("C3'") && res0.FindAtom("P")) {
+ res0_ret.first=builder->DefaultNucleotide();
+ res0_ret.second=true;
+ }
}
if(!res1_ret.second) {
@@ -329,6 +334,10 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
res1_ret.first=builder->DefaultPeptide();
res1_ret.second=true;
}
+ if (res1.FindAtom("C3'") && res1.FindAtom("P")) {
+ res1_ret.first=builder->DefaultNucleotide();
+ res1_ret.second=true;
+ }
}
if(res0_ret.second && res1_ret.second) {
@@ -348,16 +357,19 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
if(flag) {
if (builder->DoesPeptideBondExist(res0_atom, res1_atom)) {
editor.Connect(res0_atom,res1_atom);
- res0.SetIsProtein(true);
- res1.SetIsProtein(true);
+ if (res0_ret.first.GetChemClass().IsPeptideLinking()) {
+ res0.SetIsProtein(true);
+ res1.SetIsProtein(true);
+ }
}
} else {
if (builder->DoesPeptideBondExist(res1_atom, res0_atom)) {
editor.Connect(res1_atom, res0_atom);
- res0.SetIsProtein(true);
- res1.SetIsProtein(true);
+ if (res0_ret.first.GetChemClass().IsPeptideLinking()) {
+ res0.SetIsProtein(true);
+ res1.SetIsProtein(true);
+ }
}
-
}
}
} else {
diff --git a/modules/conop/src/heuristic_builder.hh b/modules/conop/src/heuristic_builder.hh
index bc3930bca..09a991345 100644
--- a/modules/conop/src/heuristic_builder.hh
+++ b/modules/conop/src/heuristic_builder.hh
@@ -110,6 +110,7 @@ public:
virtual void FillAtomProps(mol::AtomHandle atom);
const detail::ConnResEntry& DefaultPeptide() const {return default_peptide_;}
+ const detail::ConnResEntry& DefaultNucleotide() const {return default_nucleotide_;}
protected:
void ConnectivityFromAtomNames(const mol::ResidueHandle& res,
detail::ConnResEntry& centry,
@@ -117,6 +118,7 @@ protected:
private:
detail::ConnResEntryMap emap_;
detail::ConnResEntry default_peptide_;
+ detail::ConnResEntry default_nucleotide_;
};
diff --git a/modules/conop/src/heuristic_connect_table.hh b/modules/conop/src/heuristic_connect_table.hh
index aa5c0b651..15e0f1a25 100644
--- a/modules/conop/src/heuristic_connect_table.hh
+++ b/modules/conop/src/heuristic_connect_table.hh
@@ -267,31 +267,31 @@ CONN_DEF_ENTRY def_entry_table[]={
{{0,0,0,0,""}},1,
{0},1
},
- {"Adenosin","A",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
+ {"Adenosin","DA",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
{"P","O5'","C5'","C4'","O4'","C3'","O3'","C2'","C1'","O1P","O2P","N9","C8","N7","C5","C6","N6","N1","C2","N3","C4","O2'"},12,
{{-2,1},{1,2},{2,3},{3,4},{4,5},{4,6},{6,7},{6,8},{8,9},{5,9},{1,10},{1,11},{8,22},{9,12},{7,-3}},15,
{{0,0,0,0,""}},1,
{0},1
},
- {"Cytosin","C",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
+ {"Cytosin","DC",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
{"P","O5'","C5'","C4'","O4'","C3'","O3'","C2'","C1'","O1P","O2P","O2'"},12,
{{-2,1},{1,2},{2,3},{3,4},{4,5},{4,6},{6,7},{6,8},{8,9},{5,9},{1,10},{1,11},{8,12},{7,-3}},14,
{{0,0,0,0,""}},1,
{0},1
},
- {"Guanidin","G",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
+ {"Guanidin","DG",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
{"P","O5'","C5'","C4'","O4'","C3'","O3'","C2'","C1'","O1P","O2P","O2'"},12,
{{-2,1},{1,2},{2,3},{3,4},{4,5},{4,6},{6,7},{6,8},{8,9},{5,9},{7,-3},{1,10},{1,11},{8,12}},14,
{{0,0,0,0,""}},1,
{0},1
},
- {"Thymidin","T",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
+ {"Thymidin","DT",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
{"P","O5'","C5'","C4'","O4'","C3'","O3'","C2'","C1'","O1P","O2P","O2'"},12,
{{-2,1},{1,2},{2,3},{3,4},{4,5},{4,6},{6,7},{6,8},{8,9},{5,9},{7,-3},{1,10},{8,12},{1,11}},15,
{{0,0,0,0,""}},1,
{0},1
},
- {"Uracil","U",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
+ {"Uracil","DU",'?', mol::ChemClass(mol::ChemClass::DNA_LINKING),
{"P","O5'","C5'","C4'","O4'","C3'","O3'","C2'","C1'","O1P","O2P","O2'"},12,
{{-2,1},{1,2},{2,3},{3,4},{4,5},{4,6},{6,7},{6,8},{8,9},{5,9},{7,-3},{1,10},{1,11},{8,12}},14,
{{0,0,0,0,""}},1,
--
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