Development

Flow Chart

Web Server 

option file: smoothdock/lib/smoothdock_option_webserver.txt

python PyMM/bin/do_SmoothServer_Daemon_PDZ_WebServer.py smoothdock/lib/smoothdock_option_webserver.txt pdz 60

Docker Computing Cluster

Daemon:

do_SmoothServer_Daemon_PDZ_Docker.py smoothdock/lib/smoothdock_option_docker.txt pdz 15 

 PDZ job location: ~/jobs/pdz

For example job #24:

qsub 24_queue.sh
do_PDZDB_ResultData_LowestPath.py data.seq.txt assemble -560 320 5 9 20 PSD95-PDZ3 final -9.58
do_PDZDB_Reconstruct.py assemble final final/PSD95-PDZ3.-560.320.entropy.lowestpath.txt  5 9 -9.58 15

The results are in the "final/" and "assemble/"

To Do List

Online User Input

Online Result Output

Job Management

1. Damon on Docker

    *.  submitted job to queuing system              Done

    *.  Running the job                                           Done (but using test bb library for debugging)

    *   preparing the pathway                                Done

    *.  checking the results and send results back to web server                                    Done

2. Daemon on Web Server

    *. submit the jobs                                              Done    

    *. read the results and draw the free energy pathway

    *. send the results back to user.

SmoothPDZ package