From 596fb45ef7649fb11d933c86202317eb6e20db1b Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Mon, 22 Jul 2024 17:49:09 +0200
Subject: [PATCH] fix: fill header line
This commit adds the second header line. While this line can be
substituted for a blank line per specification, its absence triggers a
warning in RDKit about the missing 3D dimension tag.
---
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 e9fd0ded4..e270049f4 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -22,6 +22,7 @@
#include "sdf_writer.hh"
+#include <time.h>
#include <ost/boost_filesystem_helper.hh>
#include <ost/mol/atom_view.hh>
#include <ost/mol/residue_view.hh>
@@ -251,8 +252,19 @@ bool SDFWriter::VisitChain(const mol::ChainView& chain) {
}
// print header lines
+ // line 1: molecule name
ostr_ << cname << std::endl;
- ostr_ << std::endl;
+ // line 2: program name and time
+ // IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
+ std::time_t t = std::time(nullptr);
+ std::tm tm = *std::localtime(&t);
+ ostr_ << " " // User's first and last initials
+ << " OST" // program name
+ << std::put_time(&tm, "%m%d%y%H%M") // date/time
+ << "3D" // dimensional codes
+ << " " // scaling factors, energy, internal registry number
+ << std::endl;
+ // line 3: comment (blank)
ostr_ << std::endl;
// print counts line
ostr_ << format("%3d") % chain.GetAtomCount()
--
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