rajarshi
commented
6 years ago The download issue is caused by the fact that your original URL needs Javscript to work. Thus it works in your browser but won't work from the command line using wget or curl. Instead you need to use PUG - https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6442441/SDF.
Using this URL works with load.molecules. Also the descriptors now compute properly with the latest Github version of rcdk
load.molecules(molfiles="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6442441&disopt=SaveSDF")
Error in as.character.default(X[[1L]], ...) : no method for coercing this S4 class to a vector
Same Error for the local file of this chemical.
however in version 3.2.3.2 This error will be https://www.biostars.org/p/100384/ (in my comments)
for CID: 6442441, http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6442441&disopt=SaveSDF
descriptors: "org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor"; "org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor"
! /usr/bin/Rscript
require(rcdk) drug.mols <- load.molecules(molfiles="./CID_6442441.sdf") drug.descs <- eval.desc(drug.mols, "org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor", verbose=T)
drug.descs <- eval.desc(drug.mols, "org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor", verbose=T)
Error in .jcall(b, "Lorg/openscience/cdk/qsar/DescriptorValue;", "calculate", : java.lang.NullPointerException
Thank you. the rcdk is will helpful to me.