Hi Lee, I cannot help you with the R issue but wanted to add that I recently ran a few tests to check if RandomGenerator coverers all of constitutional space, which it did in my few test cases. The overhead for a small set of atoms (like C10H16) was 200-fold, i. e. RG needs to visit 200 times the actual size of constitutional space to visit all constitutional isomers of that space. There is the added complexity that it seems to have problems (I don’t know why) with explicit hydrogens. I only use it in cases where the hydrogen distribution is known. If that is the case, my gut feeling is that the RandomGenerator is a good choice for your problem, rather than a deterministic generator like OMG, which might have a sampling bias if you only take the first 100k. Furthermore, OMG will take very long if you move to slightly larger molecules.
Will be interesting to learn about your progress here :) Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 29 Mar 02018, at 05:03, Lee Ferguson <[email protected]> wrote: > > Hello all, > > I’m trying to work out a good way to perform structure generation from > molecular formula for integration into an analytical pipeline in our lab. > Specifically, what I want to do is generate (up to) ~100,000 structures for > any given molecular formula and subsequently down-select from that set using > some structural similarity filtering. It looks like I could potentially bend > the RandomGenerator function within the structgen package to my structure > generation needs, but I was hoping to do this within R, and from what Zach > tells me, there is no wrapper for the structgen package in rCDK as of yet. > Zack suggested I could use rJava, which is a great idea, but he also pointed > out that I might consider posting here in case someone else had tried to do > something similar already and thus I might avoid reinventing the wheel. > > I’d appreciate any ideas or guidance you all might have. > > Best regards, > Lee > > -- > P. Lee Ferguson, Ph.D. > Associate Professor > Department of Civil & Environmental Engineering > Pratt School of Engineering & > Nicholas School of the Environment > Duke University > 121 Hudson Hall, Box 90287 > Durham, NC 27708-0287 > http://ferguson.cee.duke.edu > > Phone: 919-660-5460 > Fax: 919-660-5454 > > > > > ------------------------------------------------------------------------------ > 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
