From b63721f2362427ed830056be8b01757090c64bd8 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 10 May 2023 09:23:10 +0200
Subject: [PATCH] Bugfix: SDFReader - only add new chain when first of its
atoms is parsed
Previously, a new chain got added at the first newline after $$$$.
So if an sdf file ends with a newline, you got an unwanted empty chain.
---
modules/io/src/mol/sdf_reader.cc | 24 +++++++++++++++++-------
modules/io/src/mol/sdf_reader.hh | 2 ++
2 files changed, 19 insertions(+), 7 deletions(-)
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 7f3a7f560..42e15e9b3 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -125,6 +125,8 @@ void SDFReader::NextMolecule()
atom_count_=0;
bond_count_=0;
line_num=0;
+ curr_residue_ = ost::mol::ResidueHandle();
+ curr_chain_ = ost::mol::ChainHandle();
}
void SDFReader::ParseAndAddHeader(const String& line, int line_num,
@@ -145,13 +147,10 @@ void SDFReader::ParseAndAddHeader(const String& line, int line_num,
String msg="Bad molecule name line %d: Line is empty";
throw IOException(str(format(msg) % line_num));
}
- curr_chain_=editor.InsertChain(s_chain);
- LOG_DEBUG("new chain " << s_chain);
-
- mol::ResidueKey rkey=boost::trim_copy(s_title);
- mol::ResNum rnum(++residue_count_);
- curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
- LOG_DEBUG("new residue " << rkey << "(" << rnum << ")");
+ // prepeare required variables to add new chain and residue
+ // once we parse the first atom
+ curr_chain_name_ = s_chain;
+ curr_res_key_ = boost::trim_copy(s_title);
break;
}
case 2: // user information line
@@ -228,6 +227,17 @@ void SDFReader::ParseAndAddAtom(const String& line, int line_num,
throw IOException(str(format(msg) % line_num % s_charge));
}
+ if(!curr_chain_.IsValid()) {
+ curr_chain_=editor.InsertChain(curr_chain_name_);
+ LOG_DEBUG("new chain " << curr_chain_name_);
+ }
+
+ if(!curr_residue_.IsValid()) {
+ mol::ResNum rnum(++residue_count_);
+ curr_residue_=editor.AppendResidue(curr_chain_, curr_res_key_, rnum);
+ LOG_DEBUG("new residue " << rkey << "(" << rnum << ")");
+ }
+
LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
mol::AtomHandle atom=editor.InsertAtom(curr_residue_, aname, apos, upper_ele);
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
index 04d05a2d6..f786f4e54 100644
--- a/modules/io/src/mol/sdf_reader.hh
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -53,6 +53,8 @@ private:
void ParseAndAddBond(const String& line, int line_num, mol::EntityHandle& ent,
mol::XCSEditor& editor);
+ String curr_chain_name_;
+ mol::ResidueKey curr_res_key_;
mol::ChainHandle curr_chain_;
mol::ResidueHandle curr_residue_;
int chain_count_;
--
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