README

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)