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Cheminformatics tools in R | ERD's website #1

Open utterances-bot opened 1 year ago

utterances-bot commented 1 year ago

Cheminformatics tools in R | ERD's website

https://riveradelgado.com/post/2021/04/18/chemistry-in-r/

dfaberjob commented 1 year ago

I have been trying to find something that walks me how to configure this stuff in R and this is perfect. Challenge I run into is below:

rcdk::view.molecule.2d(caffeine) Error in rcdk::view.molecule.2d(caffeine) : java.lang.NoSuchMethodError:

rJava is running and I believe all my packages are up to date

JC-swEng commented 1 year ago

@dfaberjob I tried for a whole day to use rcdk and it was the most frustrating experience. I was unable to get any molecules to render. I tried ChemmineR for a couple hours and was immediately able to get what I needed. I suggest switching to ChemmineR. It's as simple as:

library(shiny) library("ChemmineR") library("ChemmineOB") sdf <- smiles2sdf('CN1C=NC2=C1C(=O)N(C(=O)N2C)C') openBabelPlot(sdf[1])

darekb94 commented 6 months ago

Dear Edgardo Rivera-Delgado, I have read your report "Using QSAR for predictions in drug delivery" with a great interest. I tried to find a web app you described in your pre-print, but I did not manage to do it. I found a repository qsar-app on your github profile (https://github.com/eriveradelgado/qsar-app) but I am unable to launch the app. Could you help me?

eriveradelgado commented 6 months ago

Hi @darekb94,

Were you able to resolve your issue with the launch of the app? If you let me know the errors you are encountering I can help you resolve the issue.

Best, Edgardo