From 1645c2c9185d77c046043d2458d1dfca875d233d Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Mon, 4 Sep 2023 15:39:59 +0200
Subject: [PATCH] fix: allow short count lines
The RCSB ModelServer SDF files contain counts line with only 33
characters. Although invalid, they can be read by RDKit (which only
requires 6 characters). This commit emmulates the behavior of RDKit.
---
modules/io/src/mol/sdf_reader.cc | 18 ++++++++++++++----
modules/io/tests/test_io_sdf.cc | 12 ++++++++++++
.../io/tests/testfiles/sdf/1atg_C_ACT.sdf.gz | Bin 0 -> 427 bytes
3 files changed, 26 insertions(+), 4 deletions(-)
create mode 100644 modules/io/tests/testfiles/sdf/1atg_C_ACT.sdf.gz
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 381f5cbe9..660a9dcb5 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -182,12 +182,22 @@ void SDFReader::ParseHeader(const String& line, int line_num,
break;
case 4: // counts line
{
- if (line.length() < 39) {
- String msg="Bad counts line %d: Not correct number of characters on "
- "the line: %i (should be at least 39)";
+ String version_str;
+ if (line.length() < 6) {
+ String msg="Bad counts line %d: too short (%i characters, "
+ "should be at least 6 or 39)";
throw IOException(str(format(msg) % line_num % line.length()));
}
- String version_str=line.substr(34, 5);
+ else if (line.length() < 39) {
+ String msg="Bad counts line %d: too short (%i characters, "
+ "should be at least 39). "
+ "Proceeding assuming V2000 format.";
+ LOG_WARNING(str(format(msg) % line_num % line.length()));
+ version_str="V2000";
+ }
+ else {
+ version_str=line.substr(34, 5);
+ }
if (version_str == "V2000" || version_str == "V3000") {
version_=version_str;
}
diff --git a/modules/io/tests/test_io_sdf.cc b/modules/io/tests/test_io_sdf.cc
index df84041b0..68009e9c9 100644
--- a/modules/io/tests/test_io_sdf.cc
+++ b/modules/io/tests/test_io_sdf.cc
@@ -252,5 +252,17 @@ BOOST_AUTO_TEST_CASE(empty_dataheader_error_sdf)
BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/empty_dataheader.sdf"), IOException);
}
+BOOST_AUTO_TEST_CASE(rcsb_modelserver_sdf)
+{
+ // Check that we can read invalid SDF files from the RCSB model server.
+ // These files have too short
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ sdfh.Import(eh,"testfiles/sdf/1atg_C_ACT.sdf.gz");
+
+ // check success
+ BOOST_CHECK_EQUAL(eh.GetChainCount(), 1);
+}
+
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/testfiles/sdf/1atg_C_ACT.sdf.gz b/modules/io/tests/testfiles/sdf/1atg_C_ACT.sdf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..436ae0021cac71c13e18238d165b9ebde27cb208
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--
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