Errors with BasicGroupCountDescriptor

[egonw]

Source: https://www.biostars.org/p/100384/

Reproducible with rcdk 3.2.3.2 with:

#! /usr/bin/Rscript
require(rcdk)
drug.mols <- load.molecules(molfiles="./CID_175540.sdf")
descNames <- unique(unlist(sapply(get.desc.categories(), get.desc.names)))
drug.descs <- eval.desc(drug.mols, descNames, verbose=T)

The error you get:

Processing  BasicGroupCountDescriptor 
Error in if (is.na(dval)) return(NA) : argument is of length zero
In addition: Warning message:
In is.na(dval) : is.na() applied to non-(list or vector) of type 'NULL'

[rajarshi]

Can you include the SD file

[egonw]

Sorry, forgot to include that; it was in the original. It's this one (but I think any SD file will do it...):

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=175540&disopt=SaveSDF

[rajarshi]

Fixed in github (3.2.7). Note you'll need to install rcdk and rcdklibs from github (haven't pushed to cran yet)

[egonw]

Can you please comment here too? https://www.biostars.org/p/100384/