#----------------------------------------------------------------------------------------#
#            MUSTANG (v0.3): A MUltiple STuructural AligNment alGorithm.                 #
#            Authors:        A S Konagurthu,  J Whisstock, and P J Stuckey, A M Lesk.    #
#            Written by:     A S Konagurthu.                                             #
#----------------------------------------------------------------------------------------#

<=------------------------------------------------------------------------
MUSTANG LINUX/UNIX or MAC INSTALLATION:

    * Extract using: tar -zxvf MUSTANG_v.3.tgz
    * then, cd MUSTANG_v.3
    * run gmake or make
    * Test the installation using:
      ./bin/MUSTANG_v.3 -f ./data/test/test_zf-CCHH
      This should produce the following files:
      -- results.html
      -- results.pdb
    * For other command line options, run: ./bin/MUSTANG_v.3 --help


MUSTANG WINDOWS INSTALLATION: SO HELP HIM GOD!
-----------------------------------------------------------------------=>


<=------------------------------------------------------------------------
MUSTANG COMMAND LINE OPTIONS:

 CmdLine Option           Arguments                 Description
 --------------           ---------                 -----------


-p              <path>

                                             Path to the directory holding the (PDB) structures
                                              to be aligned.

-i              <struct-1> <struct-2> ...

                                             Input structures to be aligned. Note: if -p option
                                              is used in the command line, supply only the file
                                              names of the structures; if not give the absolute/relative
                                              path of each of the input structures.

-f              <description file>

                                             This option is used to AVOID entering the path (-p)
                                              and file name (-i) details in the command line.
                                              Instead, to keep the command line short, the user
                                              can enter the path and file name details in a "description"
                                              file and supply it in the command line.
                                              The format of the "description file" is given in
                                              the 'MUSTANG DESCRIPTION FILE FORMAT' part of this file (see below).    
					      Note: the options { -p , -i} and
                                              {-f} are mutually exclusive.

-o              <output identifier>

                                             A common identifier for various outputs of the program.
                                              Appropriate extentions (e.g. <identifier>.html,
                                              <identifier>.pdb, <identifier>.msf) will be added
                                              to this identifier depending on the options the
                                              user specifies in the command line. DEFAULT output
                                              identifier: 'results'

-F              one or more of {<html> <pir> <fasta> <msf>}

                                             Alignment output format. The choices are: 'html', 'fasta',
                                              'pir', 'msf'.  DEFAULT format: 'html'

-D              [CA-CA diameter]

                                             Produce an HTML file where the the residues are reported
                                              in lower case with grey background when the
                                              aligned(superposed) CA-CA diamter of residues in a
                                              column of alignment is > the CA-CA diameter threshold.-s


-s              [<ON>/<OFF>]

                                             Generate a PDB file containing optimal superposition
                                              of all the structures based on the alignment.  DEFAULT:
                                               'ON'

--help

                                             display this help and exits.

--version

                                             output version information and exits.
-----------------------------------------------------------------------=>


<=-----------------------------------------------------------------------
MUSTANG DESCRIPTION FILE FORMAT" ( see -f CmdLine option)

To keep the command line short the user can write the path and file names into a  (description) file and
supply the description file at the command line using the '-f' option. For example see the
file used to test the installation: './data/test/test_zf-CCHH' 

FORMAT:

PATH should have a prefix '>'. When the program parses this file, it looks for the line
starting with '>' symbol (whitespaces are ignored before and after the symbol). The PATH
containing the PDB files of the structures to be aligned should follow. See for example:
'./data/test/test_zf-CCHH'

FILENAMES should have a prefix '+' (whitespaces are ignored before and after this symbol).
If PATH is specified then only the filenames should be provided after the '+' symbol. 
However, if PATH line is NOT provided, then the absolute/relative paths of the structure 
files should be provided.  './data/test/test_zf-CCHH'
-----------------------------------------------------------------------=>
