Hi John, all,
I am playing with SMIRKS but it's pretty new to me.
Transform neutralAcid = Smirks.compile("[O-:1]>>[O:1]");
IAtomContainer cdkStruct = parser.parseSmiles("CC(=O)[O-]");
Iterable<IAtomContainer> iterable = neutralAcid.apply(cdkStruct,
Transform.Mode.Exclusive);
for (IAtomContainer neutral : iterable) {
String neutralSmiles = generator.createSMILES(neutral);
System.out.println(neutralSmiles);
}
(I hope I did not make any copy/paste typos)
Why am I not getting this as output: CC(=O)O ?
(Actually, let's assume I can get that working, let's say we have multiple
carboxylic acids and amine groups, how would one enumerate all possible
charge states? Is that possible with just SMIRKS?)
Egon
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Maastricht University
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