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OpenBabel R bindings
=====================
This module provides an R interface to the Open Babel chemistry library.
Open Babel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing anyone
to search, convert, analyze, or store data from molecular modeling,
chemistry, solid-state materials, biochemistry, or related areas.
The code is generated using the SWIG package and provides access to
almost all of the Open Babel interfaces via R, including the base
classes OBMol, OBAtom, OBBond, and OBResidue, as well as the
conversion framework OBConversion, fingerprints, and descriptors.
There are two ways to use this binding. You can either build an
R package which wraps the C++ library (see examples directory for such
a package) and then import it into your R code, or you can use the
generated openbabelR.R and openbabel-R.cpp files directly in your
own package.
To use the first Method, copy the openbabelR directory from the examples
directory somewhere. In the R subdirectory place a copy of or a link to
the openbabelR.R file (found in <build dir>/scripts/R/openbabelR.R).
In the src subdirectory, do the same for the openbabel-R.cpp file (found
in <source dir>/scripts/R/openbabel-R.cpp). You then need to edit
the file src/Makevars to point to the open babel include and lib
directories. Finally, install the package with "R CMD INSTALL openbabelR".
You can then use this library in your code by calling "library(openbabelR)".
To use the second method, copy the .R and .cpp files into an existing R
package, in the same way as the first method. You will also need to
edit the .R file to replace all occurances of "PACKAGE=openbabelR"
with "PACKAGE=<your package name>". I recommend using search and
replaceAll for this as there are a few thousand occurances.
You also need to copy the file examples/openbabelR/R/init.R into
your packages R directory. The key thing is that the library be
loaded with LOCAL=FALSE, otherwise openbabel will not be able to
access any of its plugins.
Finally, if OpenBabel has not been installed globally, ensure
the following environment variables are set:
export LD_LIBRARY_PATH=<openbabel build dir>/lib
export BABEL_DATADIR=<openbabel source dir>/data
export BABEL_LIBDIR=$LD_LIBRARY_PATH
You can test the first method with the test.R script in the
examples directory. Run is as: R --vanilla --slave < test.R .
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