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:

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").


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

  2. 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)?