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Maximum Common Substructure
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HOW TO INSTALL First run configure: ./configure If you want to build python module and/or R package, use one of: ./configure --enable-R ./configure --enable-python ./configure --enable-R --enable-python Now you can build it: make If you encounter 'swig error', you can use force to use the bundled the files: touch python/src/py_wrap.c R/mcs/src/r_wrap.c If you choose to make python module, cd the `python' folder and install it: cd python python2.4 setup.py install If you choose to make a R package, cd the `R' folder and install it: cd R R CMD INSTALL mcs HOW TO USE To use the C library, consult examples in folder `tests': - test.c: the most simple example - tes-longresult.c: simple test that loads full match result - sdf_mcs.cc: example that reads SDF instead of graph file - test-timed.c: calculation with timeout control - batch.c: batch processing To use the python module, consult file tests/calc_mcs.py. To use the R package, follow the following instructions: 1) to parse SDF, use `graph.from.sdffile'. The only argument is a URL to sdf or path to a local fle. z <- graph.from.sdffile("http://bioweb.ucr.edu/ChemMineV2/compound/Aurora/6000/sdf") zz <- graph.from.sdffile("mycompound.sdf") 2) to calculate mcs, invoke mcs match <- mcs(z, zz) the return value are the size, and the lists of matched atoms in both compounds. If the calculation takes too long, you may set a timeout: match <- mcs(z, zz, timeout=30) The search will run at most 30 seconds in this case. 3) to get the matched substructure, use subsdf: subsdf(z, match$sub1)
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