suns-cmd v1.0.0

suns-cmd is a command line client to the Suns protein search engine.

Quick Start

Install the Haskell Platform.

$ cabal update
$ cabal install

To use suns-cmd, just create a directory to store the results:

$ mkdir results

... and feed in the motif to search to the program's standard input. This source package provides example motifs in the test/ subdirectory:

$ ~/.cabal/bin/suns-cmd -d results/ -r 0.2 < test/figure2/search1.pdb

The -d parameter tells the program to store all results in the results/ directory:

$ ls results
1tqg_0.pdb   1v7w_2.pdb  2fr5_1.pdb  3a6r_0.pdb   3cuz_1.pdb  3fke_0.pdb
1tqg_1.pdb   1v7w_3.pdb  2fr5_2.pdb  3a6r_1.pdb   3cuz_2.pdb  3fke_1.pdb
...

Each result is labeled by the structure name followed by a number which distinguishes results originating from the same structure. These results are already aligned to the original search query.

Testing

If you want to run tests before installation, then use the following installation sequence instead:

cabal update                    # Updates Hackage metadata
cabal configure --enable-tests  # Enable tests
cabal build                     # Compile the executable and tests
cabal test                      # Run the test suite
cabal copy                      # Copy the executable to ~/.cabal/bin

This test requires a network connection because it sends the searches to the official search engine hosted at suns.degradolab.org. You can find the test input structures in the test directory.

Benchmarking

To run benchmarks:

cabal configure --enable-benchmarks
cabal build
cabal bench

You can optionally provide benchmark options, using the --benchmark-options flag:

cabal bench --benchmark-options="--hostname 127.0.01"

These are the full set of available options:

Usage: bench [--hostname STRING] [-r|--rmsd DOUBLE] [-n|--num INT]
  Send search requests and store results as PDB files

Available options:
  -h,--help                Show this help text
  --hostname STRING        Search engine address (default: suns.degradolab.org)
  -r,--rmsd DOUBLE         Override RMSD cutoff (default: 1.0)
  -n,--num INT             Number of results (default: 100)

Support

To report bugs, request features, or ask for support, contact the official mailing list at suns-search@googlegroups.com.

License (BSD 3-clause)

Copyright (c) 2013 Gabriel Gonzalez All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

• Neither the name of Gabriel Gonzalez nor the names of other contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.