Python 3decision REST API Wrapper

This is a small python wrapper for the 3decision REST API. Feel free to use it if you want. Else you can find a full documentation of the current official 3decision REST API here

Set up

Clone this repository to your computer. Make sure the path to this folder is available in your python path so you can load the module, and install the packages specified in the requirements.txt file

Programmatic access to 3decision

Depending on how you access 3decision, using the public cloud or an on-premises installation you have to get your access token from 3decision and adapt the settings.py with your data.

Example settings

Here an example to access the 3decision public cloud server:

    params = {
        'base_url'          : 'https://3decision.discngine.cloud',
        'api_path'          : '/api/v2',
        'auth_type'         : 'cloud', // or 'on_prem'
        'x_api_secret'      : 'myFancySecretKeyIgotFrom3decisionForCloudAuthentication',
        'mail'              : '[email protected]',
        'user'              : 'myUsername',
        'password'          : 'passwordForOnPremInstallationsOnly',
        'verifySSL'         : True
    }

Note, only for on-prem installations you need to provide your password. Specify an email address if you want to get notified with details on the progress of longer structure registration jobs (POST structure endpoint). For cloud authentication, you will need to generate an API Secret Key.

How do I get the API Secret?

Connect to 3decision and go to your user preferences. Open API and generate a new key. You can set a custom expiration period.

More documentation on the secret key and token management is available

Example usage

from api_python_3decision import api

# Structure endpoints:

response = api.get_structure('1uyd')
response = api.get_structure_metadata('1uyd')
response = api.get_structure_ligands('1uyd')
response = api.reanalyze_structure('1uyd')
response = api.post_structure('pathtoarchive.zip')
response = api.delete_structure('structureCodeIWantToDelete')

# Project endpoints:

response = api.get_project_ids('My New Project')
project_id = 1
response = api.get_project(project_id)

# Ligand endpoints
response = api.get_ligand_search('exact', 'smiles', 'CCCCn1c(Cc2cc(OC)c(OC)c(OC)c2Cl)nc2c(N)ncnc12')

Endpoints

Post Structure Endpoint

In order to register one or several structures you can use the post_structure function. You should specify a zip file containing all information required for such an upload. More information on how the specifications of that zip file can be found in the POST Structure endpoint documentation. You can also download a sample zip file to get you started.

When using the example archive, you will need to unzip it, change the user specified in the CREATED BY field by your own username, and rebuild the archive. Make sure to have the configuration file at the root of the archive :

Make a Python package

From folder where settings.py lives pip install wheel pip install .

Install the conda environment

conda env create -f conda_env.yml
conda activate 3decision_api

Running unit tests (for developers only)

Activate your conda environment and run the following command: pytest