azulene-opal 0.4.8

A CLI and Python library to interact with Azulene Opal

Opal Quick Start Guide:

• Opal Quick Start Guide
• Azulene-Opal
• Opal Job Types

This guide walks you through a complete working example of using Opal to submit and monitor an Absolute Binding Free Energy job using a protein and ligand file.

You will learn how to:

a. Install azulene-opal from PyPI
b. Log in
c. Place your protein + ligand files in the correct location
d. Submit an absolute_binding job (including automatic file upload)
e. Check job status and retrieve results

---

Create and activate a virtual environment (optional)

For conda

conda create -n opal-env python=3.11 -y
conda activate opal-env

For Python

# Create a virtual environment
python -m venv opal-env

# Activate the environment on Windows
opal-env\Scripts\activate

# Activate the environment on macOS / Linux
source opal-env/bin/activate

---

a. Install azulene-opal from PyPI

pip install azulene-opal

Confirm installation:

python -m opal.main --help

---

b. Log in

Run:

python -m opal.main login

The CLI will securely prompt you:

Your email: [e-mail]
Your password: **********

After this, Opal stores your auth tokens locally so you don’t need to log in again.

---

c. Example protein and ligand files

Opal ships with bundled example files you can use right away:

from opal.examples import T4_LYSOZYME_BENZENE_PDB, BENZENE_BOUND_SDF, TOLUENE_SDF

The CLI will automatically detect these as local files, upload them to Opal, and replace the paths with storage URLs.

---

d. Submit an absolute_binding job

The job type is:

absolute_binding

The required parameters are:

{
  "pdb_file": "",
  "ligand_file": "",
  "ligand_smiles": ""
}

Example 1: Using the bundled sample files

from opal import jobs
from opal.examples import T4_LYSOZYME_BENZENE_PDB, BENZENE_BOUND_SDF

result = jobs.submit(
    job_type="absolute_binding",
    input_data={
        "pdb_file": str(T4_LYSOZYME_BENZENE_PDB),
        "ligand_file": str(BENZENE_BOUND_SDF),
        "ligand_smiles": "c1ccccc1"
    }
)

print(result)

You should see something like:

📤 Uploading local files...
✅ Job submitted successfully
{
  "job_id": "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
  "status": "submitted",
  "message": "Job submitted successfully"
}

Example 2: Absolute Binding Free Energy (Ligand Already in PDB)

This example runs an absolute_binding job using:

• A protein PDB file
• A ligand inside the PDB file
• A SMILES string for the ligand
• Shortened equilibration & production lengths
• Only 1 protocol repeat

from opal import auth, jobs
from opal.examples import FKB_MODEL_PDB

# 1. Log in (Only if you haven't logged in)
auth.login(email="[e-mail]", password="yourpassword")

# 2. Submit the job
input_data = {
    "pdb_file": str(FKB_MODEL_PDB),
    "ligand_smiles": "CS(=O)C",
    "protocol_repeats": 1,
    "ligand_in_pdb_file": True,
    "complex_prod_length": 0.1,
    "solvent_prod_length": 0.1,
    "complex_equil_length": 0.02,
    "solvent_equil_length": 0.02
}

result = jobs.submit(
    job_type="absolute_binding",
    input_data=input_data
)

print(result)

---

e. Submit an Absolute Aqueous Solvation Free Energy job

The job type is:

aqueous_solvation

The required parameters are:

{
  "smiles": ""
}

Example: Using a simple SMILES (CCO)

from opal import jobs

result = jobs.submit(
    job_type="aqueous_solvation",
    input_data={
        "smiles": "CCO"
    }
)

print(result)

You should see something like:

✅ Job submitted successfully
{
  "job_id": "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
  "status": "submitted",
  "message": "Job submitted successfully"
}

f. Other useful commands

1. List your jobs

Last 5 jobs (default):

python -m opal.main jobs get-jobs

All jobs:

python -m opal.main jobs get-jobs --all

Filter by job type and status:

python -m opal.main jobs get-jobs \
  --job-type absolute_binding \
  --status completed

Filter by date:

python -m opal.main jobs get-jobs \
  --start-date 2025-12-01T00:00:00Z \
  --end-date   2025-12-05T00:00:00Z

---

2. Check a specific job

python -m opal.main jobs get --job-id YOUR_JOB_ID

This returns:

• job status
• input data
• results (if completed)
• timestamps
• any error messages

---

3. Poll running jobs

python -m opal.main jobs check-running-jobs

Use this to check on running jobs.

---

4. Cancel a job

python -m opal.main jobs cancel --job-id YOUR_JOB_ID

Only works if the job is still running.

---

Azulene-Opal

This guide shows how to:

1. Log in
2. Submit a job
3. Inspect and filter jobs
4. Get / cancel a specific job
5. Poll running jobs
6. Check service health & job types
7. Submit a batch of jobs

---

How to download OPAL

pip install azulene-opal

0. Imports (Python)

from opal import auth, jobs

---

1. Log in

from opal import auth

res = auth.login(email="[e-mail]", password="pass123")
print(res)  # {"ok": True, "message": "Logged in successfully!"}

You stay logged in via locally stored tokens until you explicitly log out.

---

2. Check who you are

from opal import auth

res = auth.whoami()
print(res)
# {
#   "ok": True,
#   "user": { ... full user object ... },
#   "slim": {
#       "email": "...",
#       "role": "...",
#       "approved": True,
#       ...
#   }
# }

---

3. Submit a single job

Example job type: generate_conformers with a SMILES and number of conformers.

from opal import jobs

res = jobs.submit(
    job_type="generate_conformers",
    input_data={"smiles": "CCO", "num_conformers": 5},  # dict
)
print(res)
# {"ok": True, "data": {"job_id": "...", "status": "submitted", ...}}

(You can also pass a JSON string instead of a dict if you want.)

---

4. List and filter jobs

By default, the server returns the last 5 jobs for the current user. You can ask for all jobs, limit, or filter by job_type, status, or date range.

from opal import jobs

# Last 5 jobs (default)
print(jobs.get_jobs())

# All jobs
print(jobs.get_jobs(all_jobs=True))

# Last 10 jobs
print(jobs.get_jobs(limit=10))

# Filter by job_type and status
print(
    jobs.get_jobs(
        job_type="generate_conformers",
        status="completed",
    )
)

# Filter by created_at date range (ISO timestamps)
print(
    jobs.get_jobs(
        start_date="2025-12-01T00:00:00Z",
        end_date="2025-12-05T00:00:00Z",
    )
)

Each call returns something like:

{"ok": True, "data": [ { "id": "...", "job_type": "...", ... }, ... ]}

---

5. Get a specific job

Once you have a job_id, you can fetch that job’s details.

from opal import jobs

res = jobs.get(job_id="YOUR_JOB_ID")
print(res)
# {"ok": True, "data": { "id": "...", "status": "...", "input_data": {...}, "results": {...}, ... }}

---

6. Cancel a job

If a job is still running, you can cancel it.

from opal import jobs

res = jobs.cancel(job_id="YOUR_JOB_ID")
print(res)
# {"ok": True, "data": {...}}

---

7. Poll running jobs

This endpoint checks any currently running jobs and update their statuses.

from opal import jobs

res = jobs.check_running_jobs()
print(res)
# {"ok": True, "data": {...}}  # depends on your backend payload

---

8. Health check

Check that the Opal backend is reachable.

from opal import jobs

res = jobs.check_health()
print(res)
# {"ok": True, "data": {...}}  on success

---

9. Discover available job types

List job types supported by the current backend.

from opal import jobs

res = jobs.get_job_types()
print(res)
# {"ok": True, "data": ["generate_conformers", "absolute_solvation_energy_aqueous", ...]}

---

10. Submit a batch of jobs (same job_type, many inputs)

You can submit multiple jobs at once for a single job_type. Each entry in the list becomes a separate job under the hood.

from opal import jobs

small_input_list = [
    {"smiles": "CCO",   "num_conformers": 5},
    {"smiles": "CCCO",  "num_conformers": 3},
    {"smiles": "CCcndO","num_conformers": 2},
]

res = jobs.submit_batch_jobs(
    job_type="generate_conformers",
    input_data=small_input_list,
)
print(res)
# {
#   "ok": True,
#   "results": [
#       {
#         "index": 0,
#         "input": {...},
#         "response": {
#             "ok": True,
#             "data": {
#                 "job_id": "...",
#                 "status": "submitted",
#                 "message": "Job submitted successfully",
#                 ...
#             }
#         }
#       },
#       ...
#   ]
# }

---

11. Log out

When you’re done, you can clear the local tokens.

from opal import auth

res = auth.logout()
print(res)  # {"ok": True}

---

TL;DR minimal workflows

from opal import auth, jobs

# 1) Log in
auth.login(email="[e-mail]", password="pass123")

# 2) Submit a job
submit_res = jobs.submit(
    job_type="generate_conformers",
    input_data={"smiles": "CCO", "num_conformers": 5},
)
print(submit_res)

# 3) List recent jobs
print(jobs.get_jobs())

# 4) Fetch that job by ID
job_id = submit_res["data"]["job_id"]
print(jobs.get(job_id=job_id))

Help Commands

python -m opal.main --help

python -m opal.main jobs --help

python -m opal.main jobs submit --help

Opal Job Types:

This document lists all currently available Opal job types, their purpose, required inputs, and example payloads.

You can fetch this list via:

python -m opal.main jobs get-job-types

or in Python:

from opal import jobs
jobs.get_job_types()

---

Overview

ID	Name	Description
generate_conformers	Generate Conformers	Generate molecular conformers from SMILES notation
mp2	MP2 Calculation	Møller–Plesset second-order perturbation theory
hartree_fock	Hartree-Fock Calculation	Self-consistent field Hartree–Fock calculation
ccsd_calculation	CCSD Calculation	Coupled Cluster Singles and Doubles
xtb_calculation	XTB Calculation	Extended tight-binding semi-empirical calculation
molecular_dynamics	Molecular Dynamics	Molecular dynamics simulation
aqueous_solvation	Absolute Aqueous Solvation Free Energy	Solvation free energy in water
relative_fe	Relative Free Energy	Relative free energy between two molecules in water
relative_fe_uaa	Relative Free Energy for (Unnatural) Amino Acids	Relative FE between two (un)natural amino acid structures
nonaqueous_solvation	Absolute Nonaqueous Solvation Free Energy	Solvation FE of a solute between two solvents
reaction_free_energy	Aqueous Reaction Free Energy	Reaction free energy in aqueous solution
deprotonation_fe	Deprotonation Free Energy	Deprotonation free energy in aqueous solution
absolute_binding	Absolute Binding Free Energy	Binding FE of a ligand to a protein in water
relative_binding	Relative Binding Free Energy	Relative binding FE between two ligands
relative_binding_uaa	Relative Binding FE for (Unnatural) Amino Acids	Relative binding FE for (un)natural amino acid ligands
lipid_permeation	Lipid Permeation Free Energy	FE of permeation through a lipid bilayer
pocket_docking	Pocket Finding and Ligand Docking	Pocket finding + docking of a ligand to a protein
upload_file	Upload File	Uploads a file and returns its storage path
boltz_prediction	Boltz-2 Affinity and Structure Prediction	Protein–ligand affinity + structure prediction using Boltz-2

---

1. Generate Conformers (generate_conformers)

Description: Generate molecular conformers from SMILES notation.

Input Schema

Field	Type	Required	Default	Description
smiles	string	yes	—	SMILES of the molecule
num_conformers	number	yes	5	Number of conformers to generate

Example Input

{
  "smiles": "CCO",
  "num_conformers": 5
}

---

2. MP2 Calculation (mp2)

Description: Møller–Plesset second-order perturbation theory.

Input Schema

Field	Type	Required	Description
atom	string	yes	Atomic coordinates in XYZ format
basis	string	yes	Basis set for the calculation

Example Input

{
  "atom": "H 0 0 0; H 0 0 0.74",
  "basis": "ccpvdz"
}

---

3. Hartree-Fock Calculation (hartree_fock)

Description: Self-consistent field Hartree–Fock calculation.

Input Schema

Field	Type	Required	Description
atom	string	yes	Atomic coordinates in XYZ format
basis	string	yes	Basis set for the calculation

Example Input

{
  "atom": "H 0 0 0; F 0 0 1.1",
  "basis": "ccpvdz"
}

---

4. CCSD Calculation (ccsd_calculation)

Description: Coupled Cluster Singles and Doubles calculation.

Input Schema

Field	Type	Required	Description
atom	string	yes	Atomic coordinates in XYZ format
basis	string	yes	Basis set for the calculation

Example Input

{
  "atom": "H 0 0 0; H 0 0 0.74",
  "basis": "ccpvdz"
}

---

5. XTB Calculation (xtb_calculation)

Description: Extended tight-binding semi-empirical calculation.

Input Schema

Field	Type	Required	Description
numbers	array	yes	Atomic numbers of the atoms
positions	array	yes	3D coordinates of the atoms

Example Input

{
  "numbers": [8, 1, 1],
  "positions": [
    [0, 0, 0],
    [0.96, 0, 0],
    [-0.24, 0.93, 0]
  ]
}

---

6. Molecular Dynamics (molecular_dynamics)

Description: Molecular dynamics simulation.

Input Schema

Field	Type	Required	Description
numbers	array	yes	Atomic numbers
positions	array	yes	Initial 3D coordinates

Example Input

{
  "numbers": [1, 1],
  "positions": [
    [0, 0, 0],
    [0.74, 0, 0]
  ]
}

---

7. Absolute Aqueous Solvation Free Energy (aqueous_solvation)

Description: Absolute solvation free energy of a molecule in water via alchemical transformations.

Key Input Fields

Field	Type	Required	Default	Description
smiles	string	yes	—	Solute SMILES
assign_protonation_states	boolean	no	false	Assign protonation states at given pH
ph	number	no	7	pH for protonation
solvent_equil_length	number	no	0.08	Solvent equilibration length (ns / replica)
solvent_prod_length	number	no	0.4	Solvent production length (ns / replica)
vacuum_equil_length	number	no	0.08	Vacuum equilibration length (ns / replica)
vacuum_prod_length	number	no	0.4	Vacuum production length (ns / replica)
platform	string	no	CUDA	OpenMM platform (CUDA, OpenCL, CPU, Reference)
protocol_repeats	integer	no	3	# of repeats for uncertainty
keep_dirs	boolean	no	True	Keep working directories

Example Input

{
  "smiles": "CCO"
}

---

8. Relative Free Energy (relative_fe)

Description: Relative FE between two molecules in water.

Key Input Fields

Field	Type	Required	Default	Description
smiles_a	string	yes	—	SMILES of molecule A
smiles_b	string	yes	—	SMILES of molecule B
assign_protonation_states	boolean	no	false	Assign protonation states at pH
ph	number	no	7	pH value
equil_length	number	no	0.08	Equilibration length (ns / replica)
prod_length	number	no	0.4	Production length (ns / replica)
platform	string	no	CUDA	OpenMM platform
protocol_repeats	integer	no	3	# of repeats
keep_dirs	boolean	no	True	Keep working dirs

Example Input

{
  "smiles_a": "CCO",
  "smiles_b": "CCC"
}

---

9. Relative Free Energy for (Unnatural) Amino Acids (relative_fe_uaa)

Description: Relative FE between two (un)natural amino acid sequences.

Key Input Fields

Field	Type	Required	Default	Description
sequence_a	string	yes	—	First peptide sequence (standard codes or UAA notation)
sequence_b	string	yes	—	Second peptide sequence
uaa_map	object	no	—	Map of placeholders (e.g. {"x": "pF-Phe"})
assign_protonation_states	boolean	no	false	Assign protonation states at pH
ph	number	no	7	pH value
equil_length	number	no	0.08	Equilibration length (ns / replica)
prod_length	number	no	0.4	Production length (ns / replica)
platform	string	no	CUDA	OpenMM platform
protocol_repeats	integer	no	3	# of repeats
keep_dirs	boolean	no	True	Keep working dirs

Example Input

{
  "sequence_a": "YGH",
  "sequence_b": "<pF-Phe>GH"
}

---

10. Absolute Nonaqueous Solvation Free Energy (nonaqueous_solvation)

Description: Solvation FE of a solute between two solvents.

Key Input Fields

Field	Type	Required	Default	Description
smiles_solute	string	yes	—	Solute SMILES
smiles_solvent_a	string	yes	—	Solvent A SMILES ("None" for vacuum)
smiles_solvent_b	string	yes	—	Solvent B SMILES ("None" for vacuum)
equil_length	number	no	0.08	Equilibration length (ns / replica)
prod_length	number	no	0.4	Production length (ns / replica)
platform	string	no	CUDA	OpenMM platform

Example Input

{
  "smiles_solute": "CCO",
  "smiles_solvent_a": "None",
  "smiles_solvent_b": "O"
}

---

11. Aqueous Reaction Free Energy (reaction_free_energy)

Description: Reaction free energy in aqueous solution.

Key Input Fields

Field	Type	Required	Description
smiles_reactant	string	yes	Reactants SMILES (comma-separated)
smiles_product	string	yes	Products SMILES (comma-separated)
stoichiometry_reactant	string	yes	Stoichiometry of reactants (comma-separated)
stoichiometry_product	string	yes	Stoichiometry of products (comma-separated)
solvent_equil_length	number	no	Solvent equilibration length
solvent_prod_length	number	no	Solvent production length
vacuum_equil_length	number	no	Vacuum equilibration length
vacuum_prod_length	number	no	Vacuum production length
platform	string	no	OpenMM platform
protocol_repeats	integer	no	# of repeats
use_xtb	boolean	no	Use xTB for gas-phase
keep_dirs	boolean	no	Keep dirs

Example Input

{
  "smiles_reactant": "C(=O)=O,O",
  "smiles_product": "OC(=O)O",
  "stoichiometry_reactant": "1,1",
  "stoichiometry_product": "1",
  "use_xtb": true
}

---

12. Deprotonation Free Energy (deprotonation_fe)

Description: Deprotonation free energy in aqueous solution.

Key Input Fields

Field	Type	Required	Description
smiles_prot	string	yes	SMILES of protonated species
smiles_deprot	string	yes	SMILES of deprotonated species
solvent_equil_length	number	no	Solvent equilibration
solvent_prod_length	number	no	Solvent production
vacuum_equil_length	number	no	Vacuum equilibration
vacuum_prod_length	number	no	Vacuum production
platform	string	no	OpenMM platform
protocol_repeats	integer	no	# of repeats
use_xtb	boolean	no	Use xTB
keep_dirs	boolean	no	Keep dirs

Example Input

{
  "smiles_prot": "C(=O)O",
  "smiles_deprot": "C(=O)[O-]",
  "use_xtb": true
}

---

13. Absolute Binding Free Energy (absolute_binding)

Description: Absolute binding FE of a ligand to a protein in water.

Key Input Fields

Field	Type	Required	Description
pdb_file	file	yes	Protein PDB (may optionally contain ligand)
ligand_file	file	no	Ligand file (SDF, PDB, or CIF format)
ligand_in_pdb_file	boolean	no	Whether ligand is in protein PDB
ligand_smiles	string	no	Ligand SMILES (esp. if ligand is only in PDB)
solvent_equil_length	number	no	Ligand solvent equilibration
solvent_prod_length	number	no	Ligand solvent production
complex_equil_length	number	no	Complex equilibration
complex_prod_length	number	no	Complex production
platform	string	no	OpenMM platform
protocol_repeats	integer	no	# of repeats
keep_dirs	boolean	no	Keep dirs

Example Input

{
  "pdb_file": "opal/examples/data/4W52_t4_lysozyme_benzene.pdb",
  "ligand_file": "opal/examples/data/toluene.sdf"
}

---

14. Relative Binding Free Energy (relative_binding)

Description: Relative binding FE between two ligands to the same protein.

Key Input Fields

Field	Type	Required	Description
pdb_file	file	yes	Protein PDB
ligand_file_a	file	no	First ligand file (SDF, PDB, or CIF format)
ligand_file_b	file	no	Second ligand file (SDF, PDB, or CIF format)
ligand_in_pdb_file_a	boolean	no	First ligand in protein PDB
ligand_in_pdb_file_b	boolean	no	Second ligand in protein PDB
smiles_a	string	no	SMILES of ligand A
smiles_b	string	no	SMILES of ligand B
assign_protonation_states	boolean	no	Assign protonation states
ph	number	no	pH value
equil_length	number	no	Equilibration length
prod_length	number	no	Production length
platform	string	no	OpenMM platform
protocol_repeats	integer	no	# of repeats
keep_dirs	boolean	no	Keep dirs

Example Input

{
  "pdb_file": "protein.pdb",
  "ligand_file_a": "ligandA.sdf",
  "ligand_file_b": "ligandB.sdf"
}

---

15. Relative Binding FE for (Unnatural) Amino Acids (relative_binding_uaa)

Description: Relative binding FE between two (un)natural amino acid ligands.

Key Input Fields

Field	Type	Required	Description
sequence_a	string	yes	First peptide sequence
sequence_b	string	yes	Second peptide sequence
pdb_file	file	yes	PDB file (e.g. from previous job)
uaa_map	object	no	Map placeholders to UAA names/SMILES
assign_protonation_states	boolean	no	Assign protonation states
ph	number	no	pH value
equil_length	number	no	Equilibration
prod_length	number	no	Production
platform	string	no	OpenMM platform
protocol_repeats	integer	no	# of repeats
keep_dirs	boolean	no	Keep dirs

Example Input

{
  "sequence_a": "YGH",
  "sequence_b": "xGH",
  "pdb_file": "protein.pdb",
  "uaa_map": "{\"x\": \"pF-Phe\"}"
}

---

16. Lipid Permeation Free Energy (lipid_permeation)

Description: Free energy of a molecule permeating through a lipid bilayer.

Key Input Fields

Field	Type	Required	Description
smiles	string	yes	Solute SMILES
lipid_type	string	yes	Lipid type (DPPC, DMPC, DOPC, DLPE, DLPC, POPE, POPC)
equil_length	number	no	Equilibration length
prod_length	number	no	Production length
platform	string	no	OpenMM platform
keep_dirs	boolean	no	Keep dirs

Example Input

{
  "smiles": "O",
  "lipid_type": "POPC"
}

---

17. Pocket Finding and Ligand Docking (pocket_docking)

Description: Find the binding pocket and dock a ligand to a protein.

Key Input Fields

Field	Type	Required	Description
pdb_file	file	yes	Protein PDB
ligand_smiles	string	yes	Ligand SMILES
ph	float	no	pH value (default: 7)

Example Input

{
  "pdb_file": "protein.pdb",
  "ligand_smiles": "CC1=CC=CC=C1"
}

---

18. Upload File (upload_file)

Description: Uploads a file and returns its storage path.

Input Schema

Field	Type	Required	Description
file_path	file	yes	Local file path to upload

Example Input

{
  "file_path": "examples/input.txt"
}

---

19. Boltz-2 Affinity and Structure Prediction (boltz_prediction)

Description: Boltz-2 based affinity and structure prediction.

Input Schema

Field	Type	Required	Description
protein_sequence	string	yes	Protein sequence (one-letter amino acid code)
ligand_smiles	string	yes	Ligand SMILES

Example Input

{
  "protein_sequence": "MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAK",
  "ligand_smiles": "CC1=CC=CC=C1"
}

---

For live job type info directly on Opal, always refer to:

python -m opal.main jobs get-job-types

or see the API_Reference.md for usage patterns and CLI/Python examples.

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