File	Date	Author	Commit
RASP	2013-07-19	Chris MacRaild	[2fad8a] Fix triplet constructuion bug causing inconsist...
example	2013-07-19	Chris MacRaild	[2fad8a] Fix triplet constructuion bug causing inconsist...
MANIFEST.in	2013-07-18	Chris MacRaild	[82f9df] More unit tests
README	2013-07-08	Chris MacRaild	[3a7fdf] README and example data
rasp	2013-07-19	Chris MacRaild	[56cfb7] Catch errors during GRASP optimisation to outpu...
setup.py	2013-07-18	Chris MacRaild	[82f9df] More unit tests

Read Me

RASP: Resonance assignment by chemical shift prediction
(c) 2012-2013 Chris MacRaild

RASP uses structure-based chemical shift predictions to solve the backbone 
resonance assignment problem in protein NMR spectroscopy. This enables rapid 
determination of highly accurate assignments on the basis of minimal 
experimental datasets, even for spectroscopically challenging proteins.

RASP runs on the command-line:

> rasp.py [options]

Run without any command-line options, RASP will read predicted chemical shifts 
from a file named rasp_pred.tab and experimental spin systems from rasp_ss.tab. 
100 RASP iterations will be run, and the calculated assignment ensemble will be 
output to rasp_ss.out and rasp_res.out (organised by spin system and by residue, 
respectively). This can be expected to run for minutes for a small protein up to 
a day or two for very large/difficult problems.

Predicted chemical shifts can be read directly from the output of Shiftx2 (run 
with the –f BMRB flag), Sparta+, or camshift. The file format for spin system 
input is the same as that used by MARS: each spin system is listed on a single 
line: the first field is a unique integer spin system identifier, followed by 
the list of shifts associated with that spin system. The first line is a header, 
listing the chemical shift types, in the order they appear in each subsequent 
line.

The resulting assignment ensemble will be output in two files. rasp_ss.out lists 
the assignment ensemble by spin system. Each line presents the assignment results 
for a single spin system. A leading asterisk (*) denotes spin system assignments 
that are considered robustly determined. The next term is the spin system 
identifier from the input file. Subsequent terms are residue numbers to which 
that spin system is assigned, followed by (in brackets) the frequency of that 
assignment in the ensemble.

The 'example' folder contains the input files and results for a RASP calculation 
on Ubiquitin. The calculation can be run as:

> rasp.py -n ubiq

A more typical invocation of RASP might be:

> rasp.py –n runname –nproc 6 –w

a summary of frequently used options follows.
For more details see: http://sourceforge.net/p/raspnmr/wiki

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -v, --verbose         very detailed output to log file for debugging. Use 0
                        or 1 iterations

  File IO options:
    -n NAME, --name=NAME
                        base name for input and output files [rasp]
    -p FILE, --predicted=FILE
                        read predicted chemical shifts from FILE
                        [NAME_pred.tab]
    -e FILE, --spinSystems=FILE
                        read experimental spin systems from FILE
                        [NAME_expt.tab]
    -o OUTNAME, --output=OUTNAME
                        base name for ouput files [NAME]
    -w, --write_state   write final program state

  Algorithm control options:
    -f FILE, --fix=FILE
                        Fix assignments read from FILE
    -i NITER, --iterations=NITER
                        Run NITER RASP iterations [100]
    --nproc=NPROC       run NPROC rasp processes in parallel [1]