nfiacco / masterprotein

Method of Accelerated Search for Tertiary Ensemble Representatives

##this is a server component for MASTER## Method of Accelerated Search for Tertiary Ensemble Representatives

This has two components:

• a Flask based web app that serves up an API for running master on a server.
• a PyMol Plugin that provides an interface for easily sending requests to the server search api.

###prerequisites:### on osx install:

• install homebrew if you don't have it
• brew install redis
• start redis:
• redis-server /usr/local/etc/redis.conf
• pip install -r requirements.txt
• git clone [email protected]:timofei7/master_protein.git
• install master and msl in the external directory
  • precompiled MSL for osx version available here
  • master available here
• download the pdb library available at here
• edit the Settings.py file to match your paths
• edit pymol/Master/__init__.py and make sure the URL points to either:
  • http://127.0.0.1:5000/api/search for local development
  • or http://ararat.cs.dartmouth.edu:5000/api/search for hitting the "production" server.

###run it:### to run a local server simply do:

• ./run_server

This will launch a server at http://localhost:5000 which will serve up a basic html page as well as the http://localhost:5000/api/ endpoints which the PyMol module will hit.

• open PyMol and add the directory /path/to/your/repo/pymol/ to Plugin->Plugin Manager->Settings->Add New Directory. Then restart PyMol. This will autoload the plugin and if you make any code changes all you need to do is restart PyMol.

• ./kill_server

To kill the server.

###contribute to it:###

• pymol/Master contains the pymol plugin module
• testing/ contains some basic test scripts
• MasterApp.py is the main flask app with various worker classes in the same directory
• Tasks.py contains asynchronous jobs that are run by RQ which in turn uses Redis for queues
• MasterSearch logic surrounding launching background jobs and constructing master queries
• use github issues and pull requests github page

###test scripts###

test files in: testing

• testing/test.py