From 53a6eb5840edcee41ceb02395f20319c28774af3 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 1 Jun 2023 18:49:59 +0200
Subject: [PATCH] fix: permit trailing blank space in atoms block
---
modules/io/src/mol/sdf_reader.cc | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index ec84d1a01..9c832e6ae 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -188,9 +188,15 @@ void SDFReader::ParseAndAddAtom(const String& line, int line_num,
LOG_TRACE( "line: [" << line << "]" );
if(line.length()<48 || line.length()>69) {
- String msg="Bad atom line %d: Not correct number of characters on the"
- " line: %i (should be between 48 and 69)";
- throw IOException(str(format(msg) % line_num % line.length()));
+ // Handle the case where we have trailing space characters
+ if (line.length()>69 && boost::trim_copy(line.substr(69)) == "") {
+ LOG_DEBUG( "Ignoring trailing space" );
+ }
+ else {
+ String msg="Bad atom line %d: Not correct number of characters on the"
+ " line: %i (should be between 48 and 69)";
+ throw IOException(str(format(msg) % line_num % line.length()));
+ }
}
int anum = line_num-4; // start at 1 on fifth line since first four lines are header
String s_posx=line.substr(0,10);
@@ -255,7 +261,7 @@ void SDFReader::ParseAndAddBond(const String& line, int line_num,
if(line.length()<9 || line.length()>21) {
// Handle the case where we have trailing space characters
if (line.length()>21 && boost::trim_copy(line.substr(21)) == "") {
- LOG_ERROR( "Ignoring trailing space" );
+ LOG_DEBUG( "Ignoring trailing space" );
}
else {
String msg="Bad bond line %d: Not correct number of characters on the"
--
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