Since my longer answer was rejected by my mail server, Zach and I are continuing the discussion without the list for now ________________________________________ From: Zach Charlop-Powers [zach.charlop.pow...@gmail.com] Sent: 08 January 2018 20:10 To: Emma SCHYMANSKI Cc: cdk-user@lists.sourceforge.net; Williams, Antony Subject: Re: [Cdk-user] Combinatorially Expand R groups
Emma, I'm planning on using R as well..... If you've already got some code that could get me started I would happily kick the tires. The main thing I am concerned about for SMILES is unintentionally altering the structure of the compound but for simple R groups. Most of the time this shouldn't be mucah of an issue and you've already part of the way there if you've been generating and vetting compounds with your code. Thank You, zach cp On Mon, Jan 8, 2018 at 12:36 PM, Emma SCHYMANSKI <emma.schyman...@uni.lu<mailto:emma.schyman...@uni.lu>> wrote: 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<mailto:zach.charlop.pow...@gmail.com>] Sent: Monday, 8 January 2018 5:54 PM To: cdk-user@lists.sourceforge.net<mailto: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 ------------------------------------------------------------------------------ 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
