Thank you John; prompt and thorough as always.
I think smilb may be perfect for what I need. I simply want to derivitize a
core scaffold with R groups. Its for generation of compounds for hypothesis
testing. (I don't believe SMARTS can be used for this). I will also take
a look at your code and see if i can use it - it may be a a bit more tricky
but more maleable in the end.
zach cp
On Mon, Jan 8, 2018 at 4:12 PM, John Mayfield <john.wilkinson...@gmail.com>
wrote:
> RGroupQuery
> <http://cdk.github.io/cdk/2.1/docs/api/index.html?org/openscience/cdk/isomorphism/matchers/RGroupQuery.html>
> .getAllConfigurations
> <http://cdk.github.io/cdk/2.1/docs/api/org/openscience/cdk/isomorphism/matchers/RGroupQuery.html#getAllConfigurations-->
> ()
>
> Full Example: https://gist.github.com/johnmay/
> 84d49e537c31457d738c21ed6dec26ae. *Important:* note I define the correct
> valence ahead of time so I don't need to re-type the atom every time :-).
>
> IAtomContainer root = smipar.parseSmiles("CC1=CC=
>> NC2=C1C=CC(=C2)C1=CC([R1])=C([R2])C([R3])=C1");
>
> Map<IAtom, Map<Integer,IBond>> rootAttach = new HashMap<>();
>> Map<Integer,RGroupList> rgrpMap = new HashMap<>();
>> defineRgroup(root, rootAttach, rgrpMap, "R1",
>> newRGroupList("[H].[CH2]CO.[CH2]Cl",
>> 1));
>> defineRgroup(root, rootAttach, rgrpMap, "R2",
>> newRGroupList("[H].[CH2]CN.[CH2]F",
>> 2));
>> defineRgroup(root, rootAttach, rgrpMap, "R3",
>> newRGroupList("[H].[CH2]CCl.[CH2]F", 3));
>>
>> RGroupQuery query = new RGroupQuery(bldr);
>> query.setRootStructure(root);
>> query.setRootAttachmentPoints(rootAttach);
>> query.setRGroupDefinitions(rgrpMap);
>>
>> SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Isomeric);
>> for (IAtomContainer mol : query.getAllConfigurations()) {
>> System.out.println(smigen.create(mol));
>> }
>
>
> Mark Rijnbeek wrote these classes for OrChem matching, they're a little
> bit clunky as the API is very specific to RGRP CTfiles. For example the API
> only allows 'set' and not 'add'. Efficiency could be improved,
> getAllConfigurations() could be lazy (using an iterator). I've been meaning
> to update the API to be easier and handle attachment points the way
> CXSMILES does.
>
> SMILES concatenation is super quick (e.g. SmiLib:
> http://melolab.org/smilib/) and useful but limited.
>
> I would also ask why you need it? Is it for matching? If so then
> enumeration is the wrong way to do Markush matching, SMARTS get's you most
> of the way where with recursion $(...) but you need to avoid matches back
> on already mapped parts - CACTVS provides $$(...) syntax to do this. Also
> the way recursion is handled in the CDK is also sub-optimial but have been
> working on rewriting the SMARTS stack over Xmas.
>
> John
>
>
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
