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girke-lab / ChemmineOB

OpenBabel wrapper package for R
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make inchi strings available on windows #9

Closed khoran closed 7 years ago

khoran commented 10 years ago

requires either making a dynamic lib work on windows or forcing the inchi shared lib to be included in the static lib via symbol name mangling. Either method will take a long time and be very painful.

stanstrup commented 7 years ago

Hi. @TylerBackman I almost forgot our conversation in Dublin. You mentioned that it would be possible to have this fallback to pulling it from your online service or something like that?

TylerBackman commented 7 years ago

@stanstrup I added a feature to the ChemMine Tools web service to generate InChI strings, which you can use directly with the ChemmineR ChemMine Tools interface. This doesn't overload the chemmineOB feature, but you can now use it immediately, without updating your R packages, as the function list is grabbed remotely by ChemmineR.

Here is a code example:

library(ChemmineR)
data(sdfsample)
sdf <- sdfsample
job <- launchCMTool('InChI Strings',sdf)
inchiResult <- result(job)

The full API is documented here: https://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html#chemmine-tools-r-interface

stanstrup commented 7 years ago

Thanks! Would it also be possible to get InChIKeys? In the RMassBank project I referenced above I think that is what they need to get rid of direct calls to openbabel.

TylerBackman commented 7 years ago

@stanstrup, I have now added InChIkeys. The interface is the same, there is just now and extra column on the returned data.frame

stanstrup commented 7 years ago

Fantastic! Thanks. I'll pass it along.