Hi, 

I got an error while processing a SMILES string (mentioned below)

smiles= "C1C(CC(=O)C(C1(CC(CC(CC(=O)S[R])=O)=O)O)C(CC(CC(CC(CC)=O)=O)=O)=O)=O"

My code:
SmilesParser sp = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
try {
           atomContainer = sp.parseSmiles(smiles);
       } catch (Exception e) {
           System.out.println("ERROR: Invalid SMILES " + smiles);
           e.printStackTrace();
       }

error message...

org.openscience.cdk.exception.InvalidSmilesException: Expected element symbol, found null!
at org.openscience.cdk.smiles.SmilesParser.assembleAtom(SmilesParser.java:701)
at org.openscience.cdk.smiles.SmilesParser.parseString(SmilesParser.java:423)
at org.openscience.cdk.smiles.SmilesParser.parseSmiles(SmilesParser.java:230)

I was wondering if this a valid error?

Best wishes,

Asad




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Syed Asad Rahman PhD, PG, B.Engg
Research Scientist

EMBL-EBI     
WTGC,  
Hinxton CB10 1SD                                           
Cambridge, UK   

Homepage: www.ebi.ac.uk /~asad   
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