From b63bd5f1ab8fb0d20c4c4baab63d92a7fedd92e9 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 18 May 2020 14:54:25 +0200
Subject: [PATCH] Added new ChemClass observed in HSQ
---
modules/io/src/mol/chemdict_parser.cc | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index cf97f5e23..9ff88e2f0 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -175,6 +175,9 @@ std::map<String, mol::ChemType> ChemdictParser::xtm_=std::map<String, mol::ChemT
void ChemdictParser::InitTypeMap()
{
+ // This list is manually kept up to date to include all types appearing in PDB
+ // See doc for how to create a compound library from scratch to test this
+ // https://openstructure.org/docs/conop/compoundlib/#creating-a-compound-library
if (!tm_.empty())
return;
tm_["L-PEPTIDE COOH CARBOXY TERMINUS"]=mol::ChemClass(mol::ChemClass::L_PEPTIDE_LINKING);
@@ -184,6 +187,7 @@ void ChemdictParser::InitTypeMap()
tm_["D-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::D_PEPTIDE_LINKING);
tm_["D-BETA-PEPTIDE, C-GAMMA LINKING"]=mol::ChemClass(mol::ChemClass::D_PEPTIDE_LINKING);
tm_["D-GAMMA-PEPTIDE, C-DELTA LINKING"]=mol::ChemClass(mol::ChemClass::D_PEPTIDE_LINKING);
+ tm_["L-SACCHARIDE, ALPHA LINKING"]=mol::ChemClass(mol::ChemClass::L_SACCHARIDE);
tm_["L-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::L_SACCHARIDE);
tm_["D-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::D_SACCHARIDE);
tm_["L-SACCHARIDE"]=mol::ChemClass(mol::ChemClass::L_SACCHARIDE);
--
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