Note: the most recent version of this tutorial can be found here and a short overview slide show here.

1 Introduction

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project (O’Boyle, Morley, and Hutchison 2008; O’Boyle et al. 2011). OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR (Cao et al. 2008; Backman, Cao, and Girke 2011; Wang et al. 2013) as an add-on package rather than used directly.

2 Installation

To use the ChemmineOB package on Linux or Mac, OpenBabel 2.3.0 or greater needs to be installed on a system. On Linux systems, the OpenBabel header files are also required in order to compile ChemmineOB. The windows distribution will include its own version of OpenBabel. The OpenBabel site (http://openbabel.org/wiki/Get_Open_Babel) provides excellent instructions for installing the OpenBabel software on Mac or Linux systems. The ChemmineR and ChemmineOB packages can be installed from within R with:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("ChemmineR", "ChemmineOB")) 
library("ChemmineR") 
library("ChemmineOB")

If the installation fails on Linux, you may need to manually set the locations of the open babel libraries and header files. This is best done through configure flags. For example, at the command prompt do:

$ R CMD INSTALL --configure-args='--with-openbabel-include=...  --with-openbabel-lib=...' <ChemmineOB package file>

where the ‘…’ are replaced by the relevant paths. See the README file for more details.

3 User Manual in ChemmineR Vignette

Detailed instructions for using ChemmineOB are provided in the vignette of the ChemmineR package instead of this document. The main reason for consolidating the documentation in one central document rather than distributing it across several vignettes is that it helps minimizing duplications and inconsistencies. It also is the more suitable format for providing a task-oriented description of functionalities for users. To obtain an overview of the OpenBabel utilities supported by ChemmineOB, we recommend consulting the OpenBabel Functions section of the ChemmineR vignette. To open the ChemmineR vignette from R, one can use the following command.

 vignette("ChemmineR")

4 SWIG Interface (For R developers)

ChemmineOB now includes wrapper functions for all of OpenBabel, as genereted by SWIG. We still maintain our own set of functions to provide better integration with R in general and ChemmineR specifically.

If you are familiar with the Open Babel API, using the SWIG wrapper should be similar, once you know a few conventions used. You can look at the R code in this package to see examples of these.

  • New objects are created with a function with the same name as the object you want to construct. So instead of
OBConversion *x = new OBConversion(...)

in R you would have:

x = OBConversion(...)
  • Methods on objects are called through a function whose name is the name of the object type concatenated with the method name, separated by an underscore. Then the first argument of this method is the instance of the object. For example, instead of:
x->AddOption(...)

we have:

OBConversion_AddOption(x,...)
  • If you need a char* you can create one in R with the stringp function. The char* pointer can be accessed with the cast slot. The value can be retrieved from the value slot. For example:
result = stringp()
OBDescriptor_GetStringValue(... , result$cast())
stringValue = result$value()
  • STL vectors of various types are available via functions named as “vector{TYPE NAME}”. For example, a vector of unsigned int is created wit the function “vectorUnsignedInt”. You can get the size of this vector with “vectorUnsignedInt_size(vectorVariable)”.

There are still many special cases however. The SWIG documentation can help, as well as browsing the generated R code in R/ChemmineOB.R.

5 Version Information

sessionInfo()

R version 4.2.0 RC (2022-04-19 r82224) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS: /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB
[4] LC_COLLATE=C LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] ChemmineOB_1.33.2 BiocStyle_2.23.1

loaded via a namespace (and not attached): [1] bookdown_0.26 codetools_0.2-18 digest_0.6.29 R6_2.5.1
[5] jsonlite_1.8.0 magrittr_2.0.3 evaluate_0.15 zlibbioc_1.41.0
[9] stringi_1.7.6 rlang_1.0.2 cli_3.2.0 jquerylib_0.1.4
[13] bslib_0.3.1 rmarkdown_2.13 tools_4.2.0 stringr_1.4.0
[17] xfun_0.30 yaml_2.3.5 fastmap_1.1.0 compiler_4.2.0
[21] BiocManager_1.30.16 htmltools_0.5.2 knitr_1.38 sass_0.4.1

6 Funding

This software was developed with funding from the National Science Foundation: ABI-0957099, 2010-0520325 and IGERT-0504249.

References

Backman, T W, Y Cao, and T Girke. 2011. “ChemMine tools: an online service for analyzing and clustering small molecules.” Nucleic Acids Res 39 (Web Server issue): 486–91. https://doi.org/10.1093/nar/gkr320.

Cao, Y, A Charisi, L C Cheng, T Jiang, and T Girke. 2008. “ChemmineR: a compound mining framework for R.” Bioinformatics 24 (15): 1733–4. https://doi.org/10.1093/bioinformatics/btn307.

O’Boyle, Noel, Michael Banck, Craig James, Chris Morley, Tim Vandermeersch, and Geoffrey Hutchison. 2011. “Open Babel: An Open Chemical Toolbox.” Journal of Cheminformatics 3 (1): 33. https://doi.org/10.1186/1758-2946-3-33.

O’Boyle, Noel, Chris Morley, and Geoffrey Hutchison. 2008. “Pybel: A Python Wrapper for the Openbabel Cheminformatics Toolkit.” Chemistry Central Journal 2 (1): 5. https://doi.org/10.1186/1752-153X-2-5.

Wang, Y, T W Backman, K Horan, and T Girke. 2013. “fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R.” Bioinformatics, August. https://doi.org/10.1093/bioinformatics/btt475.