Fix NoSuchAtomException issue in MDLV2000Reader #388
Merged
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In two lines of code, method 'readAtomContainer' of class
'MDLV2000Reader' uses variable 'molecule' instead of variable
'outputContainer'. If a loaded molfile contains a query bond, then
'molecule' and 'outputContainer' do not reference the same container.
This can cause an issue in next parts of the code because atoms are
searched in the empty container referenced by 'molecule'.
To reproduce the issue, you can use the following code:
import java.net.URL;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.silent.AtomContainer;
public class Test
{
public static void main(String[] args) throws Exception
{
URL url = new URL("http://www.ebi.ac.uk/chebi/saveStructure.do?"
+ "sdf=true&chebiId=48572");
new MDLV2000Reader(url.openStream()).read(new AtomContainer());
}
}