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

@@ -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;
       }

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();