RosettaAbinitio_scripts
__________________________________

These scripts and executables may be used with the RosettaAbinitio package. 
Perl scripts can be run without arguments for usage. Some scripts may 
require editing configuration values. The lib directory contains perl
modules that are used by some of the scripts.

An example protocol:

1. Run rosetta to generate a silent mode file.
   *Make sure the configuration values are set in rosettaAB.pl.

   ./bin/rosettaAB.pl -fasta test_.fasta -nstruct 1000

2. run cluster.pl to cluster the decoys in the resulting silent
   mode file, aatest.out, and extract the top 10 cluster centers.

   ./bin/cluster.pl -silentfile aatest.out -get_centers 10



Scripts and Executables:

./bin/cluster.pl  
Clusters silent mode file decoys and extracts cluster centers.

./src/rosetta_cluster/rosetta_cluster
Clustering executable.

./bin/make_fragments_from_server.pl
Makes fragment libraries from the robetta fragment server.
*Requires libwww-perl (http://search.cpan.org/search?dist=libwww-perl)
 or individual modules, HTTP and LWP, for HTTP requests.
*THIS SCRIPT IS NOT FOR COMMERCIAL USE!!
 If you are a commercial user and would like to make fragment libraries, 
 get a license to use the Rosetta Fragment Selection (NNMAKE) package.

./bin/reconstruct_PDB_by_index
Decoy extraction executable. 
*Requires the GNU Scientific Library (http://www.gnu.org/software/gsl/).
 Shared libraries must be installed in /usr/lib/.

./bin/rosettaAB.pl
RosettaAbinitio wrapper. Generates a silent mode file with nstruct decoys.

./bin/findhomologues.pl
Gets homologs from a psi-blast search against the NCBI NR database.
*Make sure the configuration values are set to point to blastpgp executable
 and the NCBI non-redundant database (nr).



