SOAN

Subsets Of Adjacent Nodes - A program for rapidly computing suboptimal paths in a protein dynamic network.

How to use SOAN from the command line

SOAN is written in Python and is designed to be called from the command line. Here is a example

python soan.py -i adjM.dat -s 19 -t 235 -l 1 -k 1000 -o paths.txt

At any point, the list of command line parameters and default values can be viewed by,

python soan.py -h

usage: soan.py [-h] [-i INPUT] [-s SOURCE] [-t TARGET] [-l LEVEL] [-k NPATHS] [-o OUTPUT] [-m MAXLEVEL]

optional arguments:

-h, --help show this help message and exit

-i INPUT path to adjacency matrix input file, default='network.dat'

-s SOURCE source node (can be multiple sources), default=1

-t TARGET target node, default=1

-l LEVEL level of neighbors to expand to, default=1

-k NPATHS number of paths to find, default=1000

-o OUTPUT output file name, default='paths.txt'

-m MAXLEVEL Max level to expand to (default=5), this should only be changed if the calculation fails