Pitt Quantum Repository

This is the code for the Pitt Quantum Repository maintained by @RitwikGupta and @vonbearshark. The Pitt Quantum Repository is developed by the Hutchison and Lambrecht labs at the University of Pittsburgh Chemistry Department. Please see here for how to cite PQR.

How to install

PQR is built upon Flask, a lightweight MVC in Python. PQR also uses MongoDB. We assume that the user has MongoDB already installed and running.

To run PQR locally, do the following:

1. Clone this repository
2. Make sure you have Python 2.7.6 or Python 2.7.9
3. Install virtualenv. On Debian systems, run sudo pip install virtualenv. On Windows, pip install virtualenv
4. Make sure you are in the root of the repo, aka the same level as this README. Then, run virtualenv venv. This will create a virtual environment named venv in the root of the repo.
5. On Linux systems, run . venv/bin/activate to activate the virtual enviroment. On Windows, run .\venv\Scripts\activate.
6. Run pip install -r requirements.txt

Also ensure you scp the prq/static/data folder from the server over VPN.

Starting the Server

Production

Start the server by running uwsgi pqr.ini. Use sudo nohup uwsgi pqr.ini & to let it run in the background. If you are running for the first time, follow the steps below instead!

Development

Start the server by running ./server.py [PORT NUMBER] [dev/prod] on Linux systems. On Windows, run .\venv\Scripts\python .\server.py [PORT NUMBER] [dev/prod].

First run/Data update

The first time you run the server, or any time you update the data in the folders, you'll have to perform the following steps:

1. cd scripts/
2. (If you are updating the data only) python clear_db.py
3. python recursive_iterate.py
4. cd .. (Back to root)
5. ./server.py

Gulp

Current Tasks

• gulp less: compiles and watches less files
• gulp js: compiles and watches js files
• gulp compile: both less and js command. (Both are minified and included with sourcemaps in DEV, TEST, and PROD.)
• gulp test: runs tape testing

Install

To install the Node modules run npm install (assuming node is installed on your local machine). See package.json to see what will be installed. To install the Bower components run bower install (assuming the bower npm package is install on your local machine). See bower.json to see what will be installed.

API Calls

/api/weekly

GET Returns a plain-text response with mimetype text/plain containing all previous molecules of the week.

/api/browse/{QUERY}/{SEARCHTYPE}

GET Returns a JSON file with mimetype application/json containing all the results for QUERY given SEARCHTYPE. Valid SEARCHTYPEs are name, formula, inchi, tag, or synonym.

/api/json/{INCHIKEY}

GET
Returns a JSON file with mimetype application/json containing the data for the molecule indicated by INCHIKEY

/api/mol/{INCHIKEY}

GET Returns a MOL2 file with mimetype chemical/mol2 containing the structure for the molecule indicated by INCHIKEY

/api/inchikeys

GET Returns a plain-text response with mimetype text/plain containing every single InChIKey PQR has.

/api/status

GET Returns a JSON file with information about the application