From 79a12145585663fd828ca50f6c6fc56262f91d1f Mon Sep 17 00:00:00 2001 From: Stefan Bienert <stefan.bienert@unibas.ch> Date: Thu, 12 Apr 2018 14:11:42 +0200 Subject: [PATCH] Fixed loading from PDB file, secondary structure stays unchanged --- CHANGELOG.txt | 4 ++-- modules/io/src/mol/pdb_reader.cc | 19 ++----------------- 2 files changed, 4 insertions(+), 19 deletions(-) diff --git a/CHANGELOG.txt b/CHANGELOG.txt index 4eb6a634d..249616245 100644 --- a/CHANGELOG.txt +++ b/CHANGELOG.txt @@ -1,8 +1,8 @@ Changes in Release <RELEASE NUMBER> -------------------------------------------------------------------------------- * Removed habit of changing secondary structure of entities when loading - from mmCIF files. Before, OST would turn secondary structure 'EEH' into - 'ECH' to make it look nicer in DNG. Now, 'EEH' stays 'EEH'. + from mmCIF PDB files. Before, OST would turn secondary structure 'EEH' + into 'ECH' to make it look nicer in DNG. Now, 'EEH' stays 'EEH'. Changes in Release 1.7.1 -------------------------------------------------------------------------------- diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc index a203234ec..ffa04e6ec 100644 --- a/modules/io/src/mol/pdb_reader.cc +++ b/modules/io/src/mol/pdb_reader.cc @@ -520,16 +520,7 @@ void PDBReader::AssignSecStructure(mol::EntityHandle ent) continue; } mol::SecStructure alpha(mol::SecStructure::ALPHA_HELIX); - // some PDB files contain helix/strand entries that are adjacent to each - // other. To avoid visual artifacts, we effectively shorten the first of the - // 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 && - (*(i+1)).end.GetNum()>end.GetNum()) { - end=mol::ResNum((*(i+1)).start.GetNum()-2); - } - chain.AssignSecondaryStructure(alpha, start, end); + chain.AssignSecondaryStructure(alpha, i->start, i->end); } for (HSList::const_iterator i=strand_list_.begin(), e=strand_list_.end(); @@ -540,13 +531,7 @@ void PDBReader::AssignSecStructure(mol::EntityHandle ent) continue; } 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 && - (*(i+1)).end.GetNum()>end.GetNum()) { - end=mol::ResNum((*(i+1)).start.GetNum()-2); - } - chain.AssignSecondaryStructure(extended, start, end); + chain.AssignSecondaryStructure(extended, i->start, i->end); } } -- GitLab