README file for assignment

The program was developed by Matthias Trautwein in the group of Thomas Exner at the University of Tuebingen for the automated assignment of NMR chemical shifts in proteins based on a known 3D structure and 4D [1H,15N]-HSQC-NOESY-[1H,15N]-HSQC spectra. More information is available in manual.pdf.

It can be compiled with the following command: 
g++ -O2 -Wall -o assignment assignment.cc 

Usage: assignment [-h][-p <file>][-n <file>][-f <file][-l <file>][-m <int>][-t <int>][-s <float>]
    [-h]          : This helpscreen
    [-p <file>]   : Pdb-file (default: "1D3Z.pdb")
    [-n <file>]   : NOESY peaklist (default: "NOESY.peaks")
    [-l <file>]   : Log-file (default: "logfile")
    [-c <file>]   : Chemical shifts file (optional parameter: no default value)
	 [-f <file>]   : Fix chemical shifts (default: no default value) 
    [-s <float>]  : Safety distance added to restraints (default: 0.2)
    [-m <int>]    : Maximum number of Cycles (default: 100) 
    [-t <int>]    : Number of threads used by openmp (default: 4)
    [-r <bool>]   : Call referencing routine, 0 = FALSE, 1 = TRUE (default: 0)
    [-d <bool>]   : Call identify doublepeaks routine, 0 = FALSE, 1 = TRUE (default: 0)


All default values are set for the Ubiquitin example, so the user can start the program without any flags. 
In the current version the -t and -m are included but have no effect (parallelization and maximum number of cycles not supported yet). These flags are provided for further developments.