MolPy is a Python toolkit for the full molecular-system workflow — parsing, building, editing, typing, analyzing, and reading/writing simulation formats. Packing a box is the job of the companion package molpack.

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

Every name is reached through import molpy as mp, and molpy is a thin layer over the native core (molrs): every native name is the molrs object. Every molrs subsystem is mirrored by a molpy module (mp.core for molrs.core — stores, graphs, box, neighbour search and units — then mp.io, mp.ff, mp.perceive, mp.compute, mp.builder, …). The core data classes you handle directly (mp.Frame, mp.Block, mp.Trajectory, mp.Box, mp.Atomistic, …) are promoted to the root, as the same objects.

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 and molrs on molpy's own major.minor line (molpy X.Y.* needs molcrafts-molrs>=X.Y.0,<X.(Y+1); import molpy checks it) plus the MolCrafts logging/config packages. Optional: RDKit (adapter example), AmberTools (AM1-BCC charges and AMBER polymer chains; GAFF typing itself is native).

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
uv sync --extra dev
pre-commit install --hook-type pre-commit --hook-type pre-push
# the two gates (same as the hooks / CI):
uv run --no-project --with 'tox>=4.23' --with ruff==0.16.1 --with ty==0.0.65 tox -e lint
uv run --extra dev python -m pytest tests/ -n auto

Quick start

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

import molpy as mp

from pathlib import Path

mol       = mp.io.smiles.SmilesIr("CCO").to_atomistic()     # ethanol from SMILES
mol3d, _  = mp.conformer.Conformer(seed=42).generate(mol)   # hydrogens + 3D coordinates

typifier  = mp.ff.typifier.OplsAaTypifier()          # carries the OPLS-AA library
typed     = typifier.typify(mol3d)
ff        = typifier.forcefield()                 # parameters of the assigned types

system    = typed.to_frame()
system.box = mp.Box.cube(30.0)
system["atoms"]["mol_id"] = mp.Topology.from_frame(system).connected_components() + 1

# the pair cutoff is a run setting: you declare it, molpy never invents one
ff.get_style("pair", "lj/cut")["cutoff"] = 10.0
ff.get_style("pair", "coul/cut")["cutoff"] = 10.0

out = Path("output"); out.mkdir(exist_ok=True)
mp.io.write_lammps_data(out / "system.data", system)
mp.io.write_lammps_forcefield(out / "system.ff", ff, system)

More workflows — packed solvent boxes, virtual-site models, polymer architectures (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: docs.molcrafts.org/molpy

• 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.