MolPy is a Python toolkit for the full molecular-system workflow — parsing, building, editing, typing, analyzing, packing, and reading/writing simulation formats.

Under active development. Public APIs may change between minor releases.

Vision

Molecular modeling is fragmented. Every simulation code has its own file formats and conventions; every task — parsing, building, typing, analysis, visualization — lives in a separate library; and moving a system between them means writing throwaway glue.

molpy aims to be the common foundation beneath that workflow: one explicit, programmable representation of a molecular system that every stage can share. Parse a structure into it, build on it, type and analyze it — then hand the same object onward, with no conversion step in between.

That representation is meant to be built on, not just used. It is the data model the MolCrafts ecosystem extends — visualization, experiment management, agent access — and it reads the same whether a human writes it or an agent calls it.

Capabilities

Each row is one src/molpy/ module — parse or build a structure, edit and type it, analyze or minimize it, then read and write it across formats.

Install

pip install molcrafts-molpy

# Browser (Pyodide) — needs molcrafts-molrs Pyodide wheel on PyPI:
# await micropip.install("molcrafts-molrs")
# await micropip.install("molcrafts-molpy")

Core dependencies: NumPy, python-igraph, Lark, Pint, and molrs (the Rust numerical core). Optional: RDKit (3D geometry), AmberTools (GAFF charges).

Nightly builds. Bleeding-edge snapshots are published to the separate project molcrafts-molpy-nightly (versioned X.Y.Z.devN) on every push to the nightly branch. Install with pip install --pre molcrafts-molpy-nightly. It imports as molpy, so it cannot be installed alongside the stable molcrafts-molpy (same as tensorflow vs tf-nightly).

git clone https://github.com/MolCrafts/molpy.git
cd molpy
pip install -e ".[dev]"   # includes tox (gate driver)
prek install
# optional manual gates (same as prek/CI):
#   uv run --extra dev tox -e lint
#   uv run --extra dev tox -e py
pytest tests/ -m "not external"

git clone https://github.com/MolCrafts/molrs.git
cd molrs
pip install maturin
maturin develop -m molrs-python/Cargo.toml --release   # installs `molrs` editable
cd ../molpy
pip install -e ".[dev]"                                # resolves molrs from the local build

Quick start

Parse a SMILES string, assign OPLS-AA types, and write LAMMPS input files:

import molpy as mp

mol   = mp.parser.parse_molecule("CCO")          # ethanol from SMILES
ff    = mp.io.read_xml_forcefield("oplsaa.xml")  # bundled OPLS-AA
typed = mp.typifier.OplsAtomisticTypifier(ff).typify(mol)

mp.io.write_lammps_system("output/", typed.to_frame(), ff)
# → output/system.data  output/system.in

More workflows — packed solvent boxes, virtual-site models, polymer chains and networks (the stress test for MolPy's editing machinery), AmberTools parameterization — are in the Example Gallery and the task-oriented Guides.

Documentation

Full documentation, including executable notebooks: molpy.molcrafts.org

• Getting Started — install and first example
• Example Gallery — short copy-paste workflows
• Guides — task-oriented notebooks
• Concepts — data model deep dives
• API Reference — full API

MolCrafts ecosystem

Contributing

Issues and pull requests are welcome — see Contributing.

License

BSD-3-Clause — see LICENSE.

MolPy ports or adapts code, algorithms, and data from other projects (freud, foyer, OpenMM, moltemplate, RDKit, and others). All third-party attributions and their license terms are consolidated in Third-Party Attributions.