Get started

This page takes you from nothing to a running job in a few minutes, using either the command line or Python.

Install

pip install azulene-opal

This gives you the opal command line tool and the Python package (imported as opal).

Log in

opal login

Sign in with your email and password, or with Google. Your session is saved, so you only do this once.

Run an example

The quickest way to see a result is to run one of the curated examples.

From the command line:

opal examples show                   # examples for every tool
opal examples show absolute_binding  # examples for one tool only
opal examples submit absolute_binding hif2a-belzutifan

opal examples show lists the available examples for every tool. Pass a tool name (for example absolute_binding) to see only that tool’s examples. opal examples submit downloads the example inputs and submits the job for you.

From Python:

from opal import examples

examples.show()                    # examples for every tool
examples.show("absolute_binding")  # examples for one tool only
examples.submit("absolute_binding", example_id="hif2a-belzutifan")

Run with your own data

When you are ready, submit your own protein and ligand instead of an example.

From the command line:

opal jobs submit --job-type absolute_binding \
  --input-data '{"pdb_file": "/path/to/your/protein.pdb", "ligand_smiles": "CC(=O)Oc1ccccc1C(=O)O", "ph": 7.0}'

From Python:

from opal import jobs

jobs.submit(
    job_type="absolute_binding",
    input_data={
        "pdb_file": "/path/to/your/protein.pdb",
        "ligand_smiles": "CC(=O)Oc1ccccc1C(=O)O",
        "ph": 7.0,
    },
)

Each tool page lists the exact inputs that tool expects. See Absolute Binding Free Energy for a full example.

Track your jobs

opal jobs get-jobs                # list your jobs
opal jobs cancel --job-id <id>    # cancel a running job

Run opal jobs --help to see every job command.

Questions

If you have questions or run into a problem, contact the Azulene team at support@azulenelabs.com. We are happy to help.