BAZOO

So much to do, so little time

Trying to squeeze sense out of chemical data

rinchi – An R package to generate InChI’s and InChI Keys

with 4 comments

While trying to update rcdk on CRAN it was pointed out to me that usage of the library resulted in modifications to the users home directory. Specifically, this occurred when generating InChI‘s. The CDK makes use of jni-inchi, which in turn depends on JNATI¬†which enables Java code to work with native libraries in a platform independent fashion. As part of this, it creates $HOME/.jnati – which is a no-no for CRAN packages. To resolve this, the latest version of rcdklibs excludes the InChI module and its dependencies. Hopefully rcdk and rcdklibs will now pass CRAN QC.

To access InChI functionality in R you can use the rinchi package which is hosted on Github. Since it will modify the users home directory, it cannot be hosted on CRAN. However, it’s easy enough to install

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library(devtools)
install_github("cdkr", "rajarshi", subdir="rinchi")

Importantly, if all you need is to go from SMILES to InChI, there is no need to install rcdk as well. So the following works

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inchi <- get.inchi('CCC')
inchik <- get.inchi.key('CCC')

But if you do have a molecule object obtained via rcdk, you can also pass that in to get an InChI or InChI key representation.

Written by Rajarshi Guha

August 30th, 2014 at 6:23 pm

Posted in cheminformatics,software

Tagged with , , , , ,

4 Responses to 'rinchi – An R package to generate InChI’s and InChI Keys'

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  1. Hi Rajarshi,

    Another possibility is to use the nestedvm inchi jar (see JChemPaint/Rich Apodaca post). Just incase you missed it – the RInChI is also the name of the reaction InChI – http://www.jcheminf.com/content/5/1/45.

    J

    John

    2 Sep 14 at 11:20 am

  2. Hmm just seen your rinchi actually came first…

    John

    2 Sep 14 at 11:21 am

  3. My mistake – was looking at the whole repo dates.

    John

    2 Sep 14 at 11:22 am

  4. Yes, I was aware of the name clash, but figured that referring to the rinchi package would be sufficient for disambiguation …

    Rajarshi Guha

    4 Sep 14 at 12:47 pm

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