A program to calculate elemental compositions for a given mass.
Run the HR2 programs with the batch programs, which also will mark timestamps (before & after).
To work place this folder in the C directory or modify the batch program (Line 2 - cd C:/HR2_program_testing)
The all-res versions are from Seven Golden Rules v46 (http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software/). The rebuilt and mod versions were compiled in Visual Studio Express 2012 (with /Ox optimization).
The short mass list is a subset of the allCHO_HR2 mass list. The longer list is all "valid" CHO formulae within 150-1000 Da.
The Test_Run_Short batch program uses the shortened mass list, and will run in less than 30 minutes. The Test_Run batch file will take a long time (hours). The NoOuput batch file does not create output files.
The order of versions in the batch programs are 1)original, 2)rebuilt, 3)mod, and 4)original-count. There are 5 timestamps, which when subtracted are the elapsed time (for example the origial elapsed time = timestamp#2 - timestamp#1).
The source code for the modified HR2 program is HR2_mod.c.
The prior readme in general applies to all versions. The modified version may not exactly replicate the original version, and it handling of ion masses is turned off.
HR2 (not the Seven Golden Rules itself) is based on code of HiRes from Joerg Hau which is published under the GPL
HR2 compiles under Windows with Visual C++ Express (freely available) at: http://msdn.microsoft.com/vstudio/express/
There are two versions: a) a formula generator which generates output, by using ">" the results can be written into a file b) a counting only version
A) hr2-all-res -C "ActinomycinD-5ppm" -m 1254.629124 -t 6.278182 -C 1-95 -H 1-190 -N 0-20 -O 0-80 -P 0-12 -S 0-9 *** Result: 2274 formulas found in 14 seconds by evaluating 689753865 formulae.
hr2-all-res -c "BrClS-10_1000Da_20ppm_20iae" -m 1000 -t 20 -C 38-84 -H 0-188 -N 0-40 -O 0-63 -P 0-12 -S 0-12 -F 0-12 -L 0-14 -B 0-10 -I 0-0
*** Result: 130812 formulas found in 33 seconds by evaluating 434674243 formulae.
B) the counting version starts with a low mass (-m) but uses a large mass limit (-t) hr2-fast-all-res-count -c "test" -m 1 -t 1000000 -C 1-78 -H 1-126 -N 0-25 -O 0-27 -P 0-9 -S 0-14 *** Result: 30077741 formulas found in 23 seconds by evaluating 240065734 formulae.
Syntax: -C : comment -m : accurate isotopic mass -t : mass limit (mmu) (not ppm!) -C : is number or range of chlorine atoms -H : is number or range of hydrogen atoms -N : is number or range of nitrogen atoms -O : is number or range of oxigene atoms -P : is number or range of phosphorous atoms -S : is number or range of sulfur atoms -F : is number or range of fluorine atoms -L : is number or range of chlorine atoms -B : is Brom (not Bor) (!) -I : is silicon not iodine (!)
LICENSE for HR2 (not the Seven Golden Rules itself)
This program and its documentation are Copyright (c) 1992-2005 by Joerg Hau.
This program is free software; you can redistribute it and/or modify it under the terms of version 2 of the GNU General Public License ("GPL") as published by the Free Software Foundation. See the file LICENSE for details.
If you use this program (or any part of it) in another application, note that the resulting application becomes also GPL. In other words, GPL is a "contaminating" license.