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CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
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Errors with BasicGroupCountDescriptor #23

Closed egonw closed 10 years ago

egonw commented 10 years ago

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 commented 10 years ago

Can you include the SD file

egonw commented 10 years ago

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 commented 10 years ago

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

egonw commented 10 years ago

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