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
************************************************
Syed Asad Rahman PhD, PG, B.Engg
Research Scientist
EMBL-EBI
WTGC,
Hinxton CB10 1SD
Cambridge, UK
Homepage: www.ebi.ac.uk /~asad
LinkedIn: http://www.linkedin.com/in/asadrahman
Blog: http://chembioinfo.wordpress.com/
PubList: http://www.citeulike.org/user/sar/publications
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