suns-cmd is a command line client to the Suns protein search engine.
Install the Haskell Platform.
$ cabal update $ cabal install
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
$ ~/.cabal/bin/suns-cmd -d results/ -r 0.2 < test/figure2/search1.pdb
-d parameter tells the program to store all results in the
$ 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.
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
To run benchmarks:
cabal configure --enable-benchmarks cabal build cabal bench
You can optionally provide benchmark options, using the
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)
To report bugs, request features, or ask for support, contact the official
mailing list at
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.