bundled-skills-rowan

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SKILL.md

Rowan: Cloud-Based Quantum Chemistry Platform

Routing Boundary

Use this skill only for explicit Rowan context, including Rowan, rowan-python, labs.rowansci.com, the Rowan API, or a Rowan-specific chemistry workflow. Do not use it for generic chemistry, RDKit, PubChem, ChEMBL, docking, pKa, conformer search, quantum chemistry, molecular machine learning, Boltz, or Chai-1 unless explicit Rowan context is present.

Overview

Rowan is a cloud-based computational chemistry platform that provides programmatic access to quantum chemistry workflows through a Python API. It enables automation of complex molecular simulations without requiring local computational resources or expertise in multiple quantum chemistry packages.

Key Capabilities:

Molecular property prediction (pKa, redox potential, solubility, ADMET-Tox)
Geometry optimization and conformer searching
Protein-ligand docking with AutoDock Vina
AI-powered protein cofolding with Chai-1 and Boltz models
Access to DFT, semiempirical, and neural network potential methods
Cloud compute with automatic resource allocation

Why Rowan:

No local compute cluster required
Unified API for dozens of computational methods
Results viewable in web interface at labs.rowansci.com
Automatic resource scaling

Installation and Authentication

Installation

uv pip install rowan-python

Authentication

Generate an API key at labs.rowansci.com/account/api-keys.

Option 1: Direct assignment

import rowan
rowan.api_key = "your_api_key_here"

Option 2: Environment variable (recommended)

export ROWAN_API_KEY="your_api_key_here"

import rowan

# Check authentication
user = rowan.whoami()
print(f"Logged in as: {user.username}")
print(f"Credits available: {user.credits}")

import rowan
import stjames

# Create molecule from SMILES
mol = stjames.Molecule.from_smiles("c1ccccc1O")  # Phenol

# Submit pKa workflow
workflow = rowan.submit_pka_workflow(
    initial_molecule=mol,
    name="phenol pKa calculation"
)

# Wait for completion
workflow.wait_for_result()
workflow.fetch_latest(in_place=True)

# Access results
print(f"Strongest acid pKa: {workflow.data['strongest_acid']}")  # ~10.17

import rowan
import stjames

mol = stjames.Molecule.from_smiles("CCCC")  # Butane

workflow = rowan.submit_conformer_search_workflow(
    initial_molecule=mol,
    name="butane conformer search"
)

workflow.wait_for_result()
workflow.fetch_latest(in_place=True)

# Access conformer ensemble
conformers = workflow.data['conformers']
for i, conf in enumerate(conformers):
    print(f"Conformer {i}: Energy = {conf['energy']:.4f} Hartree")

import rowan
import stjames

mol = stjames.Molecule.from_smiles("CC(=O)O")  # Acetic acid

workflow = rowan.submit_basic_calculation_workflow(
    initial_molecule=mol,
    name="acetic acid optimization",
    workflow_type="optimization"
)

workflow.wait_for_result()
workflow.fetch_latest(in_place=True)

# Get optimized structure
optimized_mol = workflow.data['final_molecule']
print(f"Final energy: {optimized_mol.energy} Hartree")

import rowan

# First, upload or create protein
protein = rowan.create_protein_from_pdb_id(
    name="EGFR kinase",
    code="1M17"
)

# Define binding pocket (from crystal structure or manual)
pocket = {
    "center": [10.0, 20.0, 30.0],
    "size": [20.0, 20.0, 20.0]
}

# Submit docking
workflow = rowan.submit_docking_workflow(
    protein=protein.uuid,
    pocket=pocket,
    initial_molecule=stjames.Molecule.from_smiles("Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1"),
    name="EGFR docking"
)

workflow.wait_for_result()
workflow.fetch_latest(in_place=True)

# Access docking results
docking_score = workflow.data['docking_score']
print(f"Docking score: {docking_score}")

import rowan

# Protein sequence
protein_seq = "MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL"

# Ligand SMILES
ligand = "CCC(C)CN=C1NCC2(CCCOC2)CN1"

# Submit cofolding with Chai-1
workflow = rowan.submit_protein_cofolding_workflow(
    initial_protein_sequences=[protein_seq],
    initial_smiles_list=[ligand],
    name="kinase-ligand cofolding",
    model="chai_1r"  # or "boltz_1x", "boltz_2"
)

workflow.wait_for_result()
workflow.fetch_latest(in_place=True)

# Access structure predictions
print(f"Predicted TM Score: {workflow.data['ptm_score']}")
print(f"Interface pTM: {workflow.data['interface_ptm']}")

import rowan
from rdkit import Chem

# Create RDKit molecule
mol = Chem.MolFromSmiles("c1ccccc1O")

# Compute pKa directly
pka_result = rowan.run_pka(mol)
print(f"pKa: {pka_result.strongest_acid}")

# Batch processing
mols = [Chem.MolFromSmiles(smi) for smi in ["CCO", "CC(=O)O", "c1ccccc1O"]]
results = rowan.batch_pka(mols)

for mol, result in zip(mols, results):
    print(f"{Chem.MolToSmiles(mol)}: pKa = {result.strongest_acid}")

# List recent workflows
workflows = rowan.list_workflows(size=10)
for wf in workflows:
    print(f"{wf.name}: {wf.status}")

# Filter by status
pending = rowan.list_workflows(status="running")

# Retrieve specific workflow
workflow = rowan.retrieve_workflow("workflow-uuid")

# Submit multiple workflows
workflows = rowan.batch_submit_workflow(
    molecules=[mol1, mol2, mol3],
    workflow_type="pka",
    workflow_data={}
)

# Poll status of multiple workflows
statuses = rowan.batch_poll_status([wf.uuid for wf in workflows])

# Create folder for project
folder = rowan.create_folder(name="Drug Discovery Project")

# Submit workflow to folder
workflow = rowan.submit_pka_workflow(
    initial_molecule=mol,
    name="compound pKa",
    folder_uuid=folder.uuid
)

# List workflows in folder
folder_workflows = rowan.list_workflows(folder_uuid=folder.uuid)

import rowan
import stjames

smiles_list = ["CCO", "c1ccccc1O", "CC(=O)O"]

# Submit all pKa calculations
workflows = []
for smi in smiles_list:
    mol = stjames.Molecule.from_smiles(smi)
    wf = rowan.submit_pka_workflow(
        initial_molecule=mol,
        name=f"pKa: {smi}"
    )
    workflows.append(wf)

# Wait for all to complete
for wf in workflows:
    wf.wait_for_result()
    wf.fetch_latest(in_place=True)
    print(f"{wf.name}: pKa = {wf.data['strongest_acid']}")

import rowan

# Upload protein once
protein = rowan.upload_protein("target.pdb", name="Drug Target")
protein.sanitize()  # Clean structure

# Define pocket
pocket = {"center": [x, y, z], "size": [20, 20, 20]}

# Screen compound library
for smiles in compound_library:
    mol = stjames.Molecule.from_smiles(smiles)
    workflow = rowan.submit_docking_workflow(
        protein=protein.uuid,
        pocket=pocket,
        initial_molecule=mol,
        name=f"Dock: {smiles[:20]}"
    )

import rowan
import stjames

mol = stjames.Molecule.from_smiles("complex_molecule_smiles")

# Generate conformers
conf_wf = rowan.submit_conformer_search_workflow(
    initial_molecule=mol,
    name="conformer search"
)
conf_wf.wait_for_result()
conf_wf.fetch_latest(in_place=True)

# Analyze lowest energy conformers
conformers = sorted(conf_wf.data['conformers'], key=lambda x: x['energy'])
print(f"Found {len(conformers)} unique conformers")
print(f"Energy range: {conformers[0]['energy']:.4f} to {conformers[-1]['energy']:.4f} Hartree")

import rowan

try:
    workflow = rowan.submit_pka_workflow(
        initial_molecule=mol,
        name="calculation"
    )
    workflow.wait_for_result(timeout=3600)  # 1 hour timeout

    if workflow.status == "completed":
        workflow.fetch_latest(in_place=True)
        print(workflow.data)
    elif workflow.status == "failed":
        print(f"Workflow failed: {workflow.error_message}")

except rowan.RowanAPIError as e:
    print(f"API error: {e}")
except TimeoutError:
    print("Workflow timed out")

bundled-skills-rowan

Summary

SKILL.md

Rowan: Cloud-Based Quantum Chemistry Platform

Routing Boundary

Overview

Installation and Authentication

Installation

Authentication

Verify Setup

Core Workflows

1. pKa Prediction

2. Conformer Search

3. Geometry Optimization

4. Protein-Ligand Docking

5. Protein Cofolding (AI Structure Prediction)

RDKit-Native API

Workflow Management

List and Query Workflows

Batch Operations

Folder Organization

Computational Methods

Reference Documentation

Common Patterns

Pattern 1: Property Prediction Pipeline

Pattern 2: Virtual Screening

Pattern 3: Conformer-Based Analysis

Best Practices

Error Handling

Additional Resources

Related skills