Hi all,
I'm trying to use CDK to parse a file of SMILES strings. Once in a
while, however, I get a weird error sent to standard out (and not an
exception). Here's a very short example demonstrating the error.
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.smiles.SmilesParser;
public class SandBox
{
public static void main(String[] args) throws CDKException
{
SmilesParser parser = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
String smilesString =
"C[C@@H](C(=O)n1cc...@h]1c(=O)O)[NH2][C@@H](CCc1ccccc1)C(=O)O";
IMolecule molecule = parser.parseSmiles(smilesString);
System.out.println(molecule);
}
}
Here's the output
Cannot percieve atom type for the 13th atom: N
Molecule(136998678, ... omitted for brevity ...)
As you can see, the molecule is still parsed. The smiles strings were
generated using openbabel, the molecules were taken from the DUD sets
SDF files.
Any ideas why this error occurs? Is the input still valid?
Thomas
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