CCD

CCD stands for Crystallisation Construct Designer.

CCD is a web application that facilitates protein crystallography experiments. In this repository you can find the core of the application.

You can visit the complete site https://ccd.rhpc.nki.nl

Basic web software used in this project:

• Flask
• JQuery
• AJAX
• Google Material Design
• Bootstrap

Docker image run

If you do not have Docker you can install it in Ubuntu following these steps:

https://docs.docker.com/engine/install/ubuntu/

You can run the Docker image from the Docker Hub like this:

docker run -d -p 8888:5000 --name ccd_container gdamaskos/ccdimg

Then visit the address:

http://localhost:8888

Enjoy! You can also find the Dockerfile in this repository's root directory.

Installation for development on your computer

Prerequisites

First of all, you must be running a Debian Operating System like Ubuntu.

The following prerequisites are required by CCD and must be installed manually if not present:

• predator (already uploaded in this repository's deps directory)
• uipred (already uploaded in this repository's deps directory)
• ncoils (e.g. apt-get install ncoils on a Debian-like OS)
• muscle (e.g. apt-get install muscle on a Debian-like OS)
• git (e.g. apt-get install git on a Debian-like OS)
• python 3.8, follow this tutorial to prepare https://www.digitalocean.com/community/tutorials/how-to-install-python-3-and-set-up-a-programming-environment-on-ubuntu-20-04-quickstart

Steps for setting up the development environment

Clone the repository from github and go to the ccd directory:

git clone https://github.com/gdamaskos/flask_with_ajax_and_matrix_visualization.git

cd flask_with_ajax_and_matrix_visualization

Create a python3.8 virtual environment containing the dependences found in requirements.txt:

python3 -m venv ~/virtual_environments/ccd3
source ~/virtual_environments/ccd3/bin/activate

Install python dependencies:

pip install wheel
pip install -r requirements.txt

Modify the settings in config/settings.example to your needs and rename the file to config/ccd_settings.cfg. Make sure you generate a new secret key, and fill in a valid email to allow Uniprot to notify you in case of problems.

The secret key can be generated using a python shell, for example:

$ python
>>> import os
>>> os.urandom(96)

Run the tests

./test.sh

Start the app!

./run_autoreload.sh

Visit the address:

http://localhost:5000

Further options for deployment

If you would like to create systemd services to run CCD automatically see the config/celery.service and config.ccd3.service.

As an alternative, you can use python supervisor and use the config/supervisor.conf to make a system service ccd managed by supervisor (edit where necessary).

If you need to configure a reverse proxy with apache check config/xxx-ccd.conf to see an example.

The contact page (available only on developer versions for ccd.rhpc.nki.nl) requires a working Google maps API. (see https://developers.google.com/maps/api-key-best-practices for how to obtain and configure one) In short:

1. Generate an API key
2. Restrict it by HTML referrer to the website you are running CCD from + /contact (e.g. ccd.rhpc.nki.nl/contact)
3. Enable "Map Javascript API".
4. Add your API key to contact.html template in the place of the current key.