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