[Cdk-devel] Smiles parser leaves massNumber null

[bbd <bb...@pe...>]

Sorry if this is a duplicate.  I tried to post it yesterday, but have not seen it returned from the list.

I think I may have run across a problem with the SmilesParser. 

If I use the following code to parse a smiles string, atoms in the resulting molecule have massNumber==null. This causes an NullPointerException in AbstractRenderer2D if I try to render the molecule. The problem seems to happen given any 

try {
	SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
	mol = sp.parseSmiles("c");
	StructureDiagramGenerator sdg = new StructureDiagramGenerator();
	sdg.setMolecule((Molecule) mol.clone());
	sdg.generateCoordinates();
	mol = sdg.getMolecule();
	has2DCoordinates = true;
} 
catch (CDKException e) {
	ERROR.error("ERROR parsing molfile. "+e.getMessage(),e);
}
catch (Exception e)
{
	ERROR.error("Error generating 2D coordinates for LocalProviderERL '"+erl+"'.
"+e.getMessage(),e);
}

The problem seems to happen with any smiles string.

I have been working with the latest trunk as of 5/22/2008

Am I doing something wrong, or is this a bug?

Thanks
Rich

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