drugs descriptors that are not working for now (rcdk issue)

[MohammedFCIS]

• I opened a PR for that handle .jcall unexpected error CDK-R/cdkr#120
• The descriptors are:
  • CPSADescriptor (geometrical)
  • GravitationalIndexDescriptor (geometrical)
  • IPMolecularLearningDescriptor
  • LengthOverBreadthDescriptor (geometrical)
  • MomentOfInertiaDescriptor (geometrical)
  • VABCDescriptor (topological)
  • WHIMDescriptor (hybrid)
  • extractDrugPetitjeanShapeIndex (for feature geomShape )

[MohammedFCIS]

• CPSADescriptor needs 3D structure
• Converting smiles to 3d molecules (rcdk solution did not work)

[MohammedFCIS]

• There is a solution.
• It needs a refinement
• I will add these descriptors later when I finish
• The analysis code is:

suppressMessages(library(dplyr))
# 1. get targets drugs
drugs_with_targets <- unique(dbdataset::Targets_Drug$parent_key)
smiles <- dbdataset::Calculated_Properties_Drug %>%
   filter(kind == "SMILES", parent_key %in% drugs_with_targets) %>% select(value) %>% pull()
sdf <- ChemmineR::smiles2sdf(smiles[1])
sdf <- ChemmineR::generate3DCoords(sdf)
tmpdest <- tempfile(pattern='xxx')
ChemmineR::write.SDF(sdf, tmpdest)
farr <- rJava::.jarray(tmpdest, contents.class = 'S')
molecules <- rJava::.jcall('org/guha/rcdk/util/Misc', '[Lorg/openscience/cdk/interfaces/IAtomContainer;',
                    'loadMolecules', farr, T, T, T,
                    check=FALSE)
#smile 13 causes issue (byro7 ma byrga3shi)
=========================================
which.desc <- "org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor"
featurea <- rcdk::eval.desc(molecules, which.desc)

[MohammedFCIS]

check other descriptors with that solution