## 
##  Copyright 1989 John Overington
##  
##  Permission to use, copy, modify, and distribute this software
##  and its documentation for academic purposes is hereby granted without fee,
##  provided that the above copyright notice appear in all copies and that
##  both that copyright notice and this permission notice appear in
##  supporting documentation, and that the names of John Overington,
##  Birkbeck College, Pfizer, or the ICRF not be used in advertising or
##  publicity pertaining to distribution of the software without specific,
##  written prior permission. John Overington makes no representations about
##  the suitability of this software for any purpose. It is provided "as is"
##  without express or implied warranty.
##  
##  JOHN OVERINGTON DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS
##  SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
##  FITNESS, IN NO EVENT SHALL JOHN OVERINGTON BE LIABLE FOR ANY SPECIAL,
##  INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
##  FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
##  OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
##  OR PERFORMANCE OF THIS SOFTWARE.
##  
##  Primary author:
##  	Dr. John Overington
##      Imperial Cancer Research Fund
##  	Lab. of Structural Molecular Biology
##  	Dept. of Crystallography
##      Birkbeck College
##      Univ. of London
##      Malet St.
##      London, WC1E 7HX
##      U.K.
##
## present address:
##
## Computational Chemistry
## Pfizer Central Research
## Ramsgate Rd
## Sandwich 
## Kent
## CT13 9NJ
## U.K.
##
##      telephone U.K. + 1304 - 618467
##      fax       U.K. + 1304 - 618463
##  	email     overingtonj@pfizer.com
##
## Please send any improvements, bug fixes, useful modifications, and comments
## to overingtonj@pfizer.com
##
##

  The software distribution consists of joy itself, and a series of support
programs, organised in a series of subdirectories, as follows.

 bvalplot/	plot temperature factors from a pdb file (using troff package)
 caplot/	plot contact matrix from a pdb file (using troff package)
 compo/		plot sequence composition from a pir file (using troff package)
 dotplot/	plot a dot plot from two pir files (using troff package)
 grcons/	plot conservation from an alignment file (using troff package)
 hbond/		calculate hydrogen bonds from a pdb file
 hbplot/	plot hydrogen bonds from a pdb file (using troff package)
 hydplot/	plot hydrophobicity values from a pir file (using troff package)
 jank/		a simple pdb file checking utility
 joy/		joy itself
 joylib/	general support utilities
 kitschorder/	reorder an alignment file according to a tree
 mds/		perform multidimensional scaling on distance data
 ms/		calculate a mass from a pir file
 ooiplot/	plot contact numbers from a pdb file (using troff package)
 pI/		plot pI curve from pir file (using troff package)
 psa/		calculate solvent accessibility parameters from pdb file
 psaplot/	plot temperature factors from a pdb file (using troff package)
 ramaplot/	plot temperature factors from a pdb file (using troff package)
 rmsplot/	plot temperature factors from a pdb file (using troff package)
 site/		extract residues forming binding site for ligand
 sstruc/	calculate secondary structure, etc from pdb file
 summer/	calculate exchange matrices from joy output

The above programs are primarily the work of the author, with the exception of

jank: Frank Eisenmenger
psa: see source for attribution
sstruc: David K. Smith and Janet Thornton (contact Janet for right to use)

