============================ * JH PROGRAM SUITE * ==============================
============================= * PROCEDURE DICK * ===============================
Version 1.00 for Android (ARM)
Compiled 2018-02-17 using X11-BASIC
(C) Alan Liska & Veronika Ruzickova, 2018
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A. BATCH USE
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I. Input file

The standard input contains individual lines describing the type and number
of amino acid fragments included in the calculated molecule as in the example of
polypeptide (saved as JH-Dick.inp to /mnt/sdcard/JH/Program/Dick/):

Ala;2
Asp;2
Ser;1
Gly;5
Glu;2
Phe;1
Leu;1
Val;1
Arg;1

(please note that the fragment definition is the same as in the database file
JH-Dick.dat).

II. Parameter file

General layout of the parameter file JH-Dick.par is as follows:

Amino acid fragment (0/+/-);Gibbs energy contribution;Enthalpy contribution;
Entropy contribution

(all refer to formation process from the elements in their standard states,
polypeptide is in the standard state of aqueous solution)
Units: kcal.mol-1 (G and H), cal.K-1.mol-1 (S)

III. Database and other files

The program comes along with some additional files which must be present
in the same folder as JH-Dick.b when performing calculations. 
These are (including their structure):

essential:

JH-Dick.b (the standalone program)

JH-Dick.dat

fragment;G;H;S

JH-Dick.inp
(this file is modified to obtain the desired results)

and as an example

JH-Dick.out
(not necessary to be present, it is generated as a result of the
calculation). 

If the requested fragment is not present in the database file 
JH-Dick.dat, it is possible to add manually the missing data. 
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B. INTERACTIVE MODE
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As most of programs which deal with structural input data, JH-Dick.b does
not support interactive mode as well. It is necessary to input data through the
file named JH-Dick.inp present in the same folder as other files. 
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C. TROUBLESHOOTING, FEEDBACK
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Once you input element that is/are not present in the datasheets, the error 
message is generated and the program terminated. Its necessary to repeat the 
input procedure with correct data again. 
In case of bugs, any report sent to the authors (alan.liska@jh-inst.cas.cz)
is welcomed. 
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D. DISCLAIMER, LICENSE
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This program is being developed as a freeware with ABSOLUTELY NO WARRANTY
concerning the correct functionality of the software and the reliability of the
predicted data. The authors CARRY NO RESPONSIBILITY for any kind of situation
connected to use of this software as well as ARE NOT OBLIGED to provide any 
kind of support. 
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E. REVISION HISTORY
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1.00 Primary version.
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REFERENCES:
[1] J. M. Dick, D. E. LaRowe, H.C. Helgeson, Biogeosciences 3 (2006) 311-336.
[2] J. M. Dick, D. E. LaRowe, H. C. Helgeson, Biogeosciences Discussions 2
 (2005) 1515-1615.
[3] Jan P. Amend, Harold C. Helgeson, Biophysical Chemistry 84 (2000) 105-136.
[4] Allen J. Bard, Roger Parsons, Joseph Jordan: Standard Potentials in Aqueous
 Solution. Marcel Dekker, New York and Basel 1985.
ACKNOWLEDGEMENTS
Markus Hoffmann: X11-BASIC, Version 1.25, 1997-2018, x11-basic.sourceforge.net
(Interpreter & Compiler)
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