From 21862098dbd2177c4f56be974f34f3469f5437e8 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 12 Apr 2018 13:37:06 +0200
Subject: [PATCH] Fixed loading from mmCIF file, secondary structure stays
unchanged
---
CHANGELOG.txt | 6 ++++++
modules/io/src/mol/mmcif_reader.cc | 21 ++-------------------
2 files changed, 8 insertions(+), 19 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 45ebdf60c..4eb6a634d 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,9 @@
+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'.
+
Changes in Release 1.7.1
--------------------------------------------------------------------------------
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 27a7c9bc8..905e28442 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -1543,17 +1543,7 @@ void MMCifReader::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 && // unit test
- (*(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 (MMCifHSVector::const_iterator i=strand_list_.begin(),
@@ -1565,14 +1555,7 @@ void MMCifReader::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 && // unit test
- (*(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);
}
}
--
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