Tuesday 9 February 2010

Looking for Open Source Chemical Descriptors

Just asked a question about this point on the Blue Obelisk Exchange.

With RCDK is very easy to get a good number of descriptors with few rows of code:


library(rcdk)
dn <- get.desc.names(dc[1])
mol <- parse.smiles("c1ccccc1")
descNames <- unique(unlist(sapply(get.desc.categories(), get.desc.names)))
descs <- eval.desc(mol, descNames)


Nice!, 288 descriptors (but 65 of them are "NA").
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2 comments:

  1. Egon Willighagen5 March 2010 at 15:04

    Matteo, I guess a lot of them are caused by the fact that the molecules do not have 3D coordinates.

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  2. Matteo Floris5 March 2010 at 15:13

    thanks for the suggestion, Egon!
    I will check if all of the 65 "NA" require 3D coords...
    A question: does the CDK generates 3D conformers with simple force fields (such as OpenBabel does)?

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