refactor get_fx_groups to be independent of KEGG. Uses SDFset as input

Meredith-Lab / volcalc

volcalc: Calculate Volatility of Chemical Compounds

https://meredith-lab.github.io/volcalc/

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refactor get_fx_groups to be independent of KEGG. Uses SDFset as input #38

Closed Aariq closed 1 year ago

Aariq commented 1 year ago

Re-factors calc_vol() and get_fx_groups() to be fully independent of KEGG
Pulls out the SIMPOL.1 algorithm part into its own function for future extensibility of calc_vol()
Output of calc_vol() not has a column with the input to calc_vol() to help users merge data
vectorizes functions so multiple compounds can be used as input (superseding calc_vol_pathway(), which is removed)

Aariq commented 1 year ago

I already let this PR get too big, sorry. I'll stop now and wait for some feedback.

KristinaRiemer commented 1 year ago

Review steps:

ran devtools::check locally after pulling down PR -- good
install volcalc from PR -- good
outside of volcalc project, ran get_mol_kegg examples to get a couple of individual mol files and all files for a pathway
ran calc_vol on both individual mol files, with two "return" arguments individually set as TRUE -- good
ran calc_vol on all mol pathway files w/ pathway_ex <- calc_vol(input = list.files("Users/kristinariemer/Desktop/map00253/", full.names = TRUE)) -- good

Aariq commented 1 year ago

Pretty sure this is failing on r-devel because of #54. Looks like it's installing a newer version of ChemmineR on that runner only (because it's building from source because there isn't a binary yet)

I may end up merging this and fixing #54 in a separate PR if the fix is more than a couple lines.

Aariq commented 1 year ago

Yeah, going to merge this and prioritize work on #54 in a different PR. Unfortunately getting volcalc to work with both old and new versions of ChemmineR is going to be a bit of a pain.