README.md

In PengGroup/indoortransformer: Predict Indoor Transformation Products

indoortransformer

The indoortransformer package is designed to extend the functionality of existing commercial chemical databases by predicting likely indoor transformation products. The current build is designed to be used only for organophosphorus compounds (OPCs).

Installation

The ChemmineR package is required to use indoortransformer. You can install ChemmineR with:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChemmineR")

The latest version of Rtools is also required in order to install packages directly from Github.

You can install the current version of indoortransformer from GitHub with:

install.packages("devtools")
devtools::install_github("toxicpeng/indoortransformer")

Troubleshooting

If the package does not install correctly, first make sure that your version of R is up to date (>= 4.1.2).

If you encounter the following error while trying to install this package, you may need to update/re-install Java on your computer.

# Error: .onLoad failed in loadNamespace() for 'rJava', details:
#   call: fun(libname, pkgname)
#   error: JAVA_HOME cannot be determined from the Registry

Download the appropriate version of the Java SDK for your system here. Close and reopen R. You will then need to set “JAVA_HOME” to the directory on your computer which contains the file “jvm.dll”.

# Example file path:
Sys.setenv(JAVA_HOME = 'C:\\Program Files\\Java\\jdk-17.0.1\\bin\\server')

If you are still unable to install indoortransformer, use the following instead, then try to install indoortransformer again.

Sys.setenv(JAVA_HOME = '')

Example

The trans.Products() function accepts a character vector of molecules in SMILES (Simplified Molecular-Input Line-Entry System) format. For example:

x <- c("CO[P](=S)(OC)Oc1ccc(cc1)[S](=O)(=O)N(C)C","CO[P](=O)(OC)OC=C(Cl)Cl")
y <- trans.Products(x)'
View(y)

PengGroup/indoortransformer documentation built on May 21, 2022, 12:05 a.m.