Documentation

Installation

Get started with BioQL in seconds using pip:

pip install bioql

Requirements

• Python 3.8 or higher
• Qiskit 1.3.0+ (automatically installed)
• NumPy, Matplotlib (dependencies handled)

pip install bioql[vina,viz,quantum_chemistry]

Quick Start

bioql_test_8a3f9d2c1e5b4f7a9c2d6e1f8b3a5c7d

Your first quantum drug discovery computation in 3 lines:

from bioql import quantum

# Example 1: Molecular Docking
result = quantum(
    "dock aspirin to COX-1 receptor",
    backend='ionq_simulator',
    api_key='bioql_test_8a3f9d2c1e5b4f7a9c2d6e1f8b3a5c7d',
    shots=4096
)

print(f"Binding Energy: {result.binding_energy} kcal/mol")

# Example 2: Create Quantum Entanglement
result = quantum(
    "create a bell state with two qubits and measure both",
    backend='ionq_simulator',
    api_key='bioql_test_8a3f9d2c1e5b4f7a9c2d6e1f8b3a5c7d',
    shots=1000
)

# Example 3: Drug Simulation with VQE
result = quantum(
    "simulate aspirin molecule using variational quantum eigensolver "
    "with 4 qubits to find ground state energy",
    backend='ionq_simulator',
    api_key='bioql_test_8a3f9d2c1e5b4f7a9c2d6e1f8b3a5c7d',
    shots=2048
)

What Just Happened?

1. Natural Language Parsing: Your request was analyzed using 164B+ patterns and converted to a quantum circuit
2. Algorithm Selection: BioQL automatically chose VQE for molecular simulation
3. Quantum Execution: Circuit ran on IonQ simulator with error mitigation
4. Results Returned: Binding energy, affinity metrics, and quantum advantage calculated

30-Second Demo

Run this one-liner to test BioQL:

pip install bioql && python -c "from bioql import quantum; print(quantum('create bell state', backend='ionq_simulator', api_key='bioql_test_8a3f9d2c1e5b4f7a9c2d6e1f8b3a5c7d'))"

Authentication

BioQL uses API keys for authentication. Get yours at the pricing page.

Using Environment Variables

# .env file
BIOQL_API_KEY=bioql_your_api_key_here
IBM_QUANTUM_TOKEN=your_ibm_token_here
IONQ_API_KEY=your_ionq_key_here

from bioql import quantum
import os

result = quantum(
    "predict ADME properties for ibuprofen",
    backend='ibm_quantum',
    api_key=os.getenv('BIOQL_API_KEY')
)

Natural Language Interface

BioQL understands over 164 billion natural language patterns across drug discovery, quantum chemistry, and bioinformatics. No quantum gates knowledge required!

"dock aspirin to COX-1"
"dock ligand SMILES CC(=O)OC... to protein PDB 1PTK"
"bind ibuprofen to cyclooxygenase"
"calculate binding affinity"

"predict ADME properties for ibuprofen"
"calculate bioavailability and half-life"
"analyze toxicity of compound"
"optimize drug-target interaction"

"simulate water molecule using VQE"
"calculate dipole moment with 4 qubits"
"find ground state energy of H2"
"compute bond angles and lengths"

"design CRISPR guide for ATCGATCG"
"optimize guide RNA with minimal off-targets"
"predict editing efficiency"
"analyze PAM sequence compatibility"

"create bell state with 2 qubits"
"apply grover search on 3 qubits"
"run QAOA optimization"
"implement quantum fourier transform"

"fold protein sequence MKLLVLCL"
"predict protein stability"
"analyze protein-ligand interaction"
"calculate binding free energy"

Drug Discovery Pipeline

Complete workflow from molecular docking to toxicity prediction:

from bioql import run_complete_pipeline

results = run_complete_pipeline(
    molecule_smiles="CC(=O)OC1=CC=CC=C1C(=O)O",
    target_protein_pdb="cox1.pdb",
    backend='simulator',
    api_key='your_api_key'
)

# Results include:
print(f"1. Docking Score: {results.docking.best_energy}")
print(f"2. Binding Affinity Kd: {results.affinity.kd} nM")
print(f"3. ADME Bioavailability: {results.adme.bioavailability}%")
print(f"4. Toxicity Risk: {results.toxicity.overall_risk}")
print(f"5. Drug-likeness: {results.lipinski_compliant}")

VSCode/Cursor Agent

Interactive AI agent extension for Visual Studio Code and Cursor that generates quantum code with automatic visualizations and error correction.

Key Features

Installation

# Step 1: Download the VSIX file above (📥 Download Extension button)

# Step 2: Install via command line
code --install-extension bioql-assistant-4.13.5.vsix

# Or via Command Palette in VS Code/Cursor:
# 1. Press Cmd+Shift+P (Mac) or Ctrl+Shift+P (Windows/Linux)
# 2. Type: "Extensions: Install from VSIX"
# 3. Select the downloaded bioql-assistant-4.13.5.vsix file

Configuration

// settings.json
{
  "bioql.apiKey": "your_bioql_api_key",
  "bioql.defaultBackend": "simulator",
  "bioql.enableQEC": false,
  "bioql.enableVisualizations": true,
  "bioql.defaultShots": 1000
}

Usage Examples

# Generate code with keyboard shortcut
# Cmd+Shift+G (Mac) / Ctrl+Shift+G (Windows)

# Chat interface
@bioql create a bell state with surface code QEC
@bioql dock metformin to AMPK with 4096 shots
@bioql optimize this quantum circuit for AWS Braket
@bioql explain this VQE implementation

# Commands
# - BioQL: Generate Code (Cmd+Shift+G)
# - BioQL: Fix Code (Cmd+Shift+F)
# - BioQL: Explain Code
# - BioQL: Run on Quantum Computer

Examples

Changelog

v5.7.5 (Current - October 2025)

• ✅ Complete drug discovery pipeline with 7 modules
• ✅ De novo drug design module for novel molecule generation
• ✅ CRISPR-QAI module for gene editing optimization
• ✅ IBM Quantum Torino (133 qubits) support
• ✅ Advanced error mitigation (ZNE, PEC)
• ✅ 21 CFR Part 11 compliance logging
• ✅ Real Vina docking integration

v5.6.0 (September 2025)

• Added bioisosteric replacement database (12+ replacements)
• Similarity search across ChEMBL and PubChem
• Off-target screening panel (30+ proteins)
• Resistance profiling for mutations

View complete changelog →