From faa3024a8485fc66cba44c96e4c252f1b7a856d0 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sun, 21 Jan 2024 21:18:01 +0100
Subject: [PATCH] mmcif writer: correctly guess _entity.type "branched"
If all residues in a chain are saccharides in some form, the
respective _entity.type should be "branched"
---
modules/io/src/mol/mmcif_writer.cc | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 4ad71c449..1b3bcf548 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -199,9 +199,7 @@ namespace {
// - polymer
// - water
- // this function is overly simplistic and won't identify macrolid or
- // branched => explicitely checks for water, everything else is either
- // non-polymer or polymer depending on number of residues
+ // this function is overly simplistic and won't identify macrolid
std::set<char> chem_classes;
for(auto res: res_list) {
@@ -221,6 +219,15 @@ namespace {
return "non-polymer";
}
+ std::set<char> branched_set;
+ branched_set.insert(ost::mol::ChemClass::L_SACCHARIDE);
+ branched_set.insert(ost::mol::ChemClass::D_SACCHARIDE);
+ branched_set.insert(ost::mol::ChemClass::SACCHARIDE);
+ branched_set.insert(chem_classes.begin(), chem_classes.end());
+ if(branched_set.size() == 3) {
+ return "branched";
+ }
+
return "polymer";
}
--
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