
SUMMARY
=======

This constitutes the FR3D putative module extractor part, written in Haskell.
The 'PutativeModules' executable take in the whole FR3D database and extracts
putative modules. For each module all instances in the FR3D database are
extracted. An instance is defined by equality on the extended secondary
structure. Base pairs are exchangeable based on the Leontis-Westhof notion of
base pair classes.



LICENSE
=======

This program uses many different Haskell libraries, each of these made
available under an open license, mostly BSD or GPL-3. The RNAdraw and
RNAmodules libraries and executables are available under the GPL-3 license. If
you would like to use the program or libraries under a different license,
please contact us.



AVAILABILITY
============

If possible, install directly from the hackage Haskell library database and
install using the 'cabal-dev' developer tool. This will insure that you do not
modify any global Haskell library database and keep everything self-contained.
The INSTALL process below assumes availability of cabal-dev.

Binaries are available from the authors. A binary compiled under Fedora Core 17
and GHC 7.6.2 rc1 is being shipped, too.



INSTALL
=======

This executable has been successfully built using GHC 7.6.1 and GHC 7.6.2.rc1.
We make use of many advanced features of Haskell not available in older
versions.

1. you should already be in a temporary directory if you are reading this
2. extract RNAmodules: "tar xf RNAmodules-0.1.1.0.tar.gz"
3. "cd RNAmodules-0.1.1.0"
4. "cabal-dev add-source ../RNAdraw-0.1.1.0.tar.gz"
5. "cabal update"
6. "cabal-dev install"

If everything went well, the installation should complete and a binary should
be available as "cabal-dev/bin/PutativeModules".



USAGE
=====

You need the FR3D database extracted into a directory (assumed to be "./FR3D"),
then run "./PutativeModules ./FR3D >> results" which will run for a couple of
minutes, scanning all PDB entries available in the FR3D directory.

Re-running the PutativeModules executable is only required if additional
entries are being made available by the FR3D maintainers.
