On Apr 23, 2009, at 3:13 PM, Loren Lenzen wrote:
>
> 3) I would like to eventually use the SMARTSQueryTool to perform
> the the same search as above. Do any of the answers to the above
> questions change?
>
I don't use Taverna, but if you were to use the SMARTSQueryTool, it
would go something like this:
String[] smarts = {"c", ....};
IAtomContainer[] mols = ....
SMARTSQueryTool sqt = new SMARTSQueryTool("C");
for (IAtomContainer ac : mols) {
for (String s : smarts) {
sqt.setSmarts(s);
if (sqt.matchs(ac)) {
// save ac with s
}
}
}
In general, if you're matching multiple SMARTS against multiple target
mols, it is more efficient to have the SMARTS matching as the inner
loop, to avoid repeated pre-processing of the same molecule by the
parser.
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