On Aug 7, 2008, at 9:50 PM, "" <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> wrote:
> public class Test {
>
> public static void main(String[] args) throws CDKException {
> SmilesParser sp = new SmilesParser();
> AtomContainer atomContainer = (AtomContainer) sp
>
> .parseSmiles("NC5NCNC1C5(NCN1C2OC(C(O)C2(O))C(OP(O)(=O)OP(O)(=O)
> OP(O)(O)=O)c3c
> cc4c(O)cccc4(c3))");
This SMILES does not seem to be correct - Daylight depict does not
parse it
> QueryAtomContainer query = SMARTSParser.parse("C1CCCCC1");//or
> these
> SMILES:("c1ccc2ccccc2(c1)");//("c1ccccc1");
All these are valid SMARTS so I'm not sure what's going on here. Are
you using trunk?
> boolean queryMatch = UniversalIsomorphismTester.isSubgraph(
> atomContainer, query);
> if (queryMatch)
> System.out.println("successful");
> else
> System.out.println("failed");
> }
>
> }
I would suggest not to use this approach, but rather use the
SMARTSQueryTool - a usage example is provided in the Javadocs
> and the following is Egon's answer of my question, but i still
> don't know what to
> do:
> That's because a SMILES is not always a valid SMARTS... they
> basically are
> two different languages.
Actually I think it's the other way round: every SMILES can be a
SMARTS, but not all SMARTS are valid SMILES
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Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
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