Hi Zach,
I have some R (as in, the program R) code to expand R groups using a SMILES
basis that generates SMILES that I can then manipulate with rcdk, Open Babel
etc. Some of these “generic SMILES” that I use as input are compatible with the
CDK Depict, some are an ugly workaround and I haven’t got around to fixing that
since John and I had some discussions. I can do up to 4-way Rs and have a
tabulated system behind it, still a whole lot of manual work and it’s not ideal
– but a start. If you have some examples you want to throw my way please do,
I’d be happy to explore it and see if it works for you and eventually help work
towards a better solution within the CDK. It’s wrapped in a R package, which is
not yet online (mainly for time reasons).
Things started getting messy with unsaturations and R for n=0 cases – but we
used this code to do this and some other examples:
https://comptox.epa.gov/dashboard/dsstoxdb/results?abbreviation=EAWAGSURF&exact=1&mass=0&search=DTXSID3020041&single_component=0
(also exploring different ways to do this):
https://www.slideshare.net/AntonyWilliams/
markush-enumeration-to-manage-mesh-and-manipulate-substances-of-unknown-or-variable-composition
Happy to discuss further.
Thanks,
Emma
From: Zach Charlop-Powers [mailto:zach.charlop.pow...@gmail.com]
Sent: Monday, 8 January 2018 5:54 PM
To: cdk-user@lists.sourceforge.net
Subject: [Cdk-user] Combinatorially Expand R groups
Hi CDK-Users,
I am wondering if anyone has a suggestion on the best way to combinatorially
expand R groups.
Lets say that I have three R groups and three possibilities for each group.
What would be the best way to generate all 27 of the compounds? I can imagine
it would be possible to use string replacement in SMILES but that seems a bit
brittle. Is there a way to do PseudoAtom substitution with CDK itself? I'm
asking here before poking around the API in the hopes that this is an easy
problem that is already solved.
Thanks,
zach cp
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