volcalc

Overview

The volcalc package allows you to automate calculating estimates of volatility for chemical compounds.

volcalc supports “group contribution” methods for estimating volatility that rely on molecular properties such as molecular weight, numbers of certain atoms, and counts of certain functional groups. Currently, the only methods implemented are SIMPOL.1 (Pankow & Asher 2008) and a modified version used in Meredith et al. (2023).

volcalc works with either .mol files or SMILES strings as input, and supports downloading .mol files directly from KEGG.

Installation

You can install the development version of volcalc from GitHub with

# install.packages("pak")
pak::pkg_install("Meredith-Lab/volcalc")

Or from r-universe with

install.packages("volcalc", repos = c("https://cct-datascience.r-universe.dev", getOption("repos")))

You can install the ‘legacy’ version used in Meredith et al. (2023) with

pak::pkg_install("Meredith-Lab/[email protected]")

Installation of volcalc requires the system libraries OpenBabel and Eigen3 (requirements of the ChemmineOB package, which volcalc depends on). pak will take care of the installation of these libraries for you on some systems, but you may need to install them manually on some operating systems.

For macOS, they can be installed via homebrew by running the following shell command:

brew install open-babel

For Ubuntu Linux:

sudo apt-get install libopenbabel-dev
sudo apt-get install libeigen3-dev

For windows, OpenBabel is included in the ChemmineOB binary and does not need to be installed separately.

For other installation options see the OpenBabel documentation and ChemmineOB install guide

Basic Usage

This is a basic example which shows you how to get an estimated relative volatility index (rvi) for two example compounds beta-2,3,4,5,6-Pentachlorocyclohexanol, and Succinate. The KEGG compound identifiers for the compounds, as found on the compound’s KEGG page, are C16181, and C00042.

library(volcalc)

out_path <- tempdir()
# download a .mol file from KEGG
files <- get_mol_kegg(c("C16181", "C00042"), dir = out_path)
calc_vol(files$mol_path)
#> # A tibble: 2 × 5
#>   mol_path                                          formula name    rvi category
#>   <chr>                                             <chr>   <chr> <dbl> <fct>   
#> 1 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T… C6H7Cl… beta…  6.98 high    
#> 2 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T… C4H6O4  Succ…  2.57 high

#alternatively, supply a SMILES representation
calc_vol(c("C1(C(C(C(C(C1Cl)Cl)Cl)Cl)Cl)O",  "C(CC(=O)O)C(=O)O"), from = "smiles")
#> # A tibble: 2 × 5
#>   smiles                        formula  name    rvi category
#>   <chr>                         <chr>    <chr> <dbl> <fct>   
#> 1 C1(C(C(C(C(C1Cl)Cl)Cl)Cl)Cl)O C6H7Cl5O <NA>   6.98 high    
#> 2 C(CC(=O)O)C(=O)O              C4H6O4   <NA>   2.57 high

This returns a tibble with columns specifying general info about the compound, and the compound’s calculated volatility and corresponding volatility category. The functional group counts underlying the volatility can be additionally returned with return_fx_groups = TRUE, and the intermediate calculation steps with return_calc_steps = TRUE.

Code of Conduct

Please note that the volcalc project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

How to contribute

We appreciate many kinds of feedback and contributions to this R package. If you find a bug, are interested in an additional feature, or have made improvements to the package that you want to share, feel free to file an issue on GitHub.

How to cite

If you use this package in your published work, please cite it using the reference below:

citation("volcalc")
#> To cite volcalc in publications please use:
#> 
#>   Riemer K, Scott E, Meredith L (2023). _volcalc: Calculate Volatility
#>   of Chemical Compounds_. doi:10.5281/zenodo.8015155
#>   <https://doi.org/10.5281/zenodo.8015155>, R package version
#>   2.1.2.9000.
#> 
#> Please also cite the related manuscript:
#> 
#>   Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L,
#>   LeBauer D, Tfaily M, Krechmer J (2023). "Automating methods for
#>   estimating metabolite volatility." _Frontiers in Microbiology_.
#>   doi:10.3389/fmicb.2023.1267234
#>   <https://doi.org/10.3389/fmicb.2023.1267234>.
#> 
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.

References

Pankow, J.F., Asher, W.E., 2008. SIMPOL.1: a simple group contribution method for predicting vapor pressures and enthalpies of vaporization of multifunctional organic compounds. Atmos. Chem. Phys. https://doi.org/10.5194/acp-8-2773-2008

Meredith, L.K., Ledford, S.M., Riemer, K., Geffre, P., Graves, K., Honeker, L.K., LeBauer, D., Tfaily, M.M., Krechmer, J., 2023. Automating methods for estimating metabolite volatility. Frontiers in Microbiology 14. https://doi.org/10.3389/fmicb.2023.1267234