docking_scripts
---------------

This is a collection of scripts used with the RosettaDock package.
Some are essential (such as post-processing tools), others are handy
for working with or creating Rosetta input and output files, and
others are obscure routines for dealing with specific types of, say,
calibration runs.

If you add files:
1-enter descriptions here
2-all scripts should have a help message if arguments are not entered properly
3-comment scripts and list an author/email

Enjoy


STARTERS

rrun.sh			  main script for invoking Rosetta in dock mode
ppk.bash		  Creates a prepacked starting structure
rosettarc		  Setup file for using RosettaDock
testrun.bash		  Mike Daily's example script for testing a
			  dock run

POST-PROCESSING ROUTINES for large runs on computing clusters:

pp_pdb2.sh		  Second half of post-processing, usually done
			  on the lab intranet where R is present
pp_pdb.sh		  Post-processes a docking run.  Calls several
			  other pp_ scripts.  Usually done on the
			  cluster, then data files are pushed to a
			  desktop machine for further processing.
pp_compile_scorefiles.sh  Merges multiple scorefiles (aa,ab...)
			  together for an analysis of the superset
pp_extract_set.sh	  Extracts topN structures from multiple subdirectories
pp_push_set.sh		  Pushes top decoy sets off the cluster
pp_cluster_set.sh	  Create clusters of decoys (uses R)
pp_calc_contacts.bash	  Calculate the number of correct residue-residue 
			  contacts (obsolete now that Fnat is
			  calculated by Rosetta)
pp_dwindle_byfile.sh	  Observe how many correct structures pass
			  various filters
pp_dwindle.sh		  same as above
pp_set.sh		  calls pp_pdb.sh for all targets in the
			  current directory
pp_summarize_clusters.sh  Details the results from clustering
pp_summarize_lowscores.sh Details the results from final score
pp_zip_pdb.sh		  Zips up completed sets of runs.


HANDY SCRIPTS for looking at scorefile output

filter_bumps.pl           Remove structures with bad bumps
filter_column.pl	  Filter a scorefile on a particular column
			  (by column number)
filter_on.pl		  Filter by a particular score (by name) 
sort_on.bash		  Sort by a particular score (by name)
findColumn.pl		  Find the column number for a particular score
findIndex.pl		  Find the column number for a particular score
find_max.pl		  Find the max value in a particular column
find_min.pl		  Find the min value in a particular column
find_percent.pl		  Filter at a cretain percentage
findRank.pl		  Determine rank of first decoy fullfilling a criterion
checkCol.pl		  be sure all lines of a scorefile have the
			  same specified number of columns
column_filter.pl	  Remove scorefile lines with the wrong
			  number of columns
column_unfilter.pl	  Show offending scorefile lines with the
			  wrong number of columns
		

MISCELLANEOUS and supporting scripts

analyzeclusters.sh	    Contacts and relative rms of top clusters
calc_score_for_cluster.pl   Finds the best scoring decoy in a cluster
clean_scratch.sh	    Removes temp files from computer cluster
			    scratch drives
docking_make_scorefilter.sh Find cutoff values for filtering decoys by score
do_voids.sh		    Calculate voids at interfaces using voidoo
energy_diff.py		    Determine energy changes from ppk
			    structure (monomer) to bound (decoy) structure
getAllscores_complete.pl    Combine scorefiles from calibration
			    (perturbation) runs for input into R for 
			    regressions
getAllscores_withTargets.pl, getAllscores.pl: ditto above
histjoin.pl		    Join two histograms
makeprefix.sh		    Convert a number to a two-letter code
			    (useful for large runs)
pdb_dir_maker.pl	    Create output directories for dock runs
adddirs.pl		    From a list of decoys, add prefix subdirectories
rms2avglink.csh		    For clustering, calculate rms between all
			    pairs of decoys
rms2.pl			    Clustering guts


also:

pdb_scripts/ contains scripts for manipulating pdbs, including
	     preparation for docking runs
R_scripts/   contains scripts for plotting scores from scorefiles and
	     fitting weights from scorefiles

JJG 4/21/2004
Revisions:
