Hi Egon,
I also started playing with SMIRKS only a few days ago but I think you need to
specify the neutral charge and hydrogen saturation in the product explicitly. I
tried “[O-:1]>>[O;+0;H1:1]” and it produced the output you are looking for
(O=C(O)C).
> 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?
If you use the transform mode “Unique”, you will get as many structures
returned as there are matches to your SMIRKS in the molecule. So in each
returned structure, one carboxylic acid would be neutralised. But I guess this
is only the first step towards what you are looking for. I am actually faced
with a similar problem right now, i.e. enumerating all possible transformation
combinations for one molecule and multiple SMIRKS…
Hope this was of help.
Kind regards,
Jonas
From: Egon Willighagen <egon.willigha...@gmail.com>
Sent: Saturday, November 23, 2024 6:52 PM
To: CDK users list <cdk-user@lists.sourceforge.net>
Subject: [Cdk-user] SMIRKS in 2.10-SNAPSHOT
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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