-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathREADME.Rmd
127 lines (85 loc) · 5.74 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# volcalc <a href="https://meredith-lab.github.io/volcalc/"><img src="man/figures/logo.PNG" alt="volcalc website" align="right" height="120"/></a>
<!-- badges: start -->
[](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml) [](https://zenodo.org/badge/latestdoi/425022983) [](https://doi.org/10.3389/fmicb.2023.1267234) [](https://www.repostatus.org/#active) [](https://app.codecov.io/gh/Meredith-Lab/volcalc?branch=master) [](https://cct-datascience.r-universe.dev/volcalc) [](https://CRAN.R-project.org/package=volcalc)
<!-- badges: end -->
## 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](https://doi.org/10.5194/acp-8-2773-2008)) and a modified version used in [Meredith et al. (2023)](https://doi.org/10.3389/fmicb.2023.1267234).
`volcalc` works with either .mol files or [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system) strings as input, and supports downloading .mol files directly from [KEGG](https://www.kegg.jp/).
## Installation
Install from CRAN with
``` r
install.packages("volcalc")
```
You can install the development version of `volcalc` from GitHub with
``` r
# install.packages("pak")
pak::pkg_install("Meredith-Lab/volcalc")
```
Or from r-universe with
``` r
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
``` r
pak::pkg_install("Meredith-Lab/[email protected]")
```
Installation of `volcalc` requires the system libraries [OpenBabel](https://open-babel.readthedocs.io/) 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:
``` bash
brew install open-babel
```
For Ubuntu Linux:
``` bash
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](https://open-babel.readthedocs.io/en/latest/Installation/install.html) and `ChemmineOB` [install guide](https://github.com/girke-lab/ChemmineOB/blob/master/INSTALL)
## 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](https://www.genome.jp/dbget-bin/www_bget?C16181), are C16181, and C00042.
```{r}
library(volcalc)
```
```{r}
out_path <- tempdir()
# download a .mol file from KEGG
files <- get_mol_kegg(c("C16181", "C00042"), dir = out_path)
calc_vol(files$mol_path)
#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")
```
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](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
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](https://github.com/Meredith-Lab/volcalc/issues/new) on GitHub.
## How to cite
If you use this package in your published work, please cite it using the reference below:
```{r}
citation("volcalc")
```
### 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>