From a157470bbd72c077e162c7ff03b77a763ee024a5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 27 Jul 2022 18:09:40 +0200
Subject: [PATCH] Force SDF writer to write elements with capital first char
and rest lower case
---
modules/io/src/mol/sdf_writer.cc | 14 +++++++++++++-
1 file changed, 13 insertions(+), 1 deletion(-)
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index 8089d7ac1..be5d7245c 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -49,11 +49,23 @@ namespace {
ostr_ << format("%10.4f") % atom.GetPos()[0]
<< format("%10.4f") % atom.GetPos()[1]
<< format("%10.4f ") % atom.GetPos()[2]
- << format("%-3s") % atom.GetElement()
+ << format("%-3s") % SDFAtomWriter::FormatEle(atom.GetElement())
<< " 0 0 0 0 0 0"
<< std::endl;
return true;
}
+
+ static String FormatEle(const String& ele) {
+ // OpenStructure has no strict requirements on lower or upper case
+ // for elements. However, some sdf readers (read: rdkit) want the first
+ // character to upper case, the rest in lower case.
+ String return_ele = ele;
+ if(!return_ele.empty()) return_ele[0] = toupper(return_ele[0]);
+ for(size_t i = 1; i < return_ele.size(); ++i) {
+ return_ele[i] = tolower(return_ele[i]);
+ }
+ return return_ele;
+ }
private:
std::ostream& ostr_;
std::map<long, int>& atom_indices_;
--
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