From 87fbc665323042277e027bc30223d2d2406b9c26 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 25 Jan 2024 18:02:19 +0100
Subject: [PATCH] poly/ non-poly/ branched entity handling like RCSB in mmCIF
writer
---
modules/io/src/mol/mmcif_writer.cc | 23 ++++++++++++++---------
1 file changed, 14 insertions(+), 9 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 921a13ed0..eb9614718 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -200,7 +200,7 @@ namespace {
// - polymer
// - water
- // this function is overly simplistic and won't identify macrolid
+ // this function is overly simplistic and won't identify macrolide
std::set<char> chem_classes;
for(auto res: res_list) {
@@ -213,22 +213,27 @@ namespace {
return "water";
}
- // DISCUSS THIS OVER A BEER...
- // Entities must have at least 3 residues to be considered polymers
- // for now, we just set entities with 1 or 2 residues as non-polymer
- if(res_list.size() == 1 || res_list.size() == 2) {
- 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) {
+ // Single saccharides are non-poly (handled in next conditional), from 2
+ // accharides covalently bound onwards, its called a 'branched' molecular
+ // entity. Check 3AXH & 1A4G from RCSB for examples.
+ if(branched_set.size() == 3 && res_list.size() > 1) {
return "branched";
}
+ // Entities must have at least 3 residues to be considered polymers
+ // For now, we just set entities with 1 or 2 residues as non-polymer
+ // For examples from RCSB, check 1E8K (dipeptide), 4K9A (dinucleotide), BUT
+ // watch out for oligosaccharides like 3AXH, 2 sugars are already of type
+ // `branched` and single sugars are non-polymer (1A4G)
+ if(res_list.size() == 1 || res_list.size() == 2) {
+ return "non-polymer";
+ }
+
return "polymer";
}
--
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