From c8c57dd922ac1e455523368cb9f2f93f700c41d1 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 21 Sep 2010 14:32:14 +0000
Subject: [PATCH] fix BZDNG-156
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2722 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/mol/pdb_reader.cc | 8 +++++---
modules/mol/base/src/impl/chain_impl.cc | 22 +++++++++++++++++-----
2 files changed, 22 insertions(+), 8 deletions(-)
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 5a628c2cc..938fc23f7 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -250,7 +250,8 @@ void PDBReader::AssignSecStructure(mol::EntityHandle ent)
// two secondary structure segments to insert one residue of coil
// conformation.
mol::ResNum start=i->start, end=i->end;
- if (helix_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1) {
+ if (helix_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1 &&
+ (*(i+1)).end.GetNum()>end.GetNum()) {
end=mol::ResNum((*(i+1)).start.GetNum()-2);
}
chain.AssignSecondaryStructure(alpha, start, end);
@@ -266,7 +267,8 @@ void PDBReader::AssignSecStructure(mol::EntityHandle ent)
mol::SecStructure extended(mol::SecStructure::EXTENDED);
mol::ResNum start=i->start, end=i->end;
// see comment for helix assignment
- if (strand_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1) {
+ if (strand_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1 &&
+ (*(i+1)).end.GetNum()>end.GetNum()) {
end=mol::ResNum((*(i+1)).start.GetNum()-2);
}
chain.AssignSecondaryStructure(extended, start, end);
@@ -612,7 +614,7 @@ void PDBReader::ParseStrandEntry(const StringRef& line)
throw IOException(str(format("invalid strand entry on line %d")%line_num_));
}
LOG_DEBUG("making strand entry: " << start_num.second << ", " << line[26]
- << " " << end_num.second << " " << line[37]);
+ << " " << end_num.second << " " << line[37] << " chain=" << line[21]);
HSEntry hse = {to_res_num(start_num.second, line[26]),
to_res_num(end_num.second, line[37]),
line.substr(21,1).str()};
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 1a2e0e137..c6b3192d3 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -341,11 +341,23 @@ void ChainImpl::AssignSecondaryStructure(SecStructure ss,
const ResNum& start,
const ResNum& end)
{
- int i=this->GetIndex(start);
- int j=this->GetIndex(end);
- if (i>=0 && j>=0 && i<=j && j<static_cast<int>(residue_list_.size())) {
- std::for_each(residue_list_.begin()+i, residue_list_.begin()+j+1,
- bind(&ResidueImpl::SetSecStructure, _1, ss));
+ int start_index=this->GetIndex(start);
+ int i=start_index;
+ bool found_end=false;
+ if (i>=0) {
+ while (i<static_cast<int>(residue_list_.size())) {
+ if (residue_list_[i]->GetNumber()==end) {
+ found_end=true;
+ break;
+ }
+ ++i;
+ }
+ }
+ if (!found_end) {
+ return;
+ }
+ for (int end=i, i=start_index; i<=end; ++i) {
+ residue_list_[i]->SetSecStructure(ss);
}
}
--
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