MolPy — A programmable toolkit for molecular simulation workflows

MolPy is under active development. Public APIs may change between minor releases.

MolPy is a Python toolkit for building, editing, typing, and exporting molecular systems. It keeps topology, force fields, numerical frames, and engine I/O explicit and composable in Python.

Polymer construction and reactive topology editing are core strengths, but MolPy is built for broader molecular simulation workflows, from system preparation and topology transformation to force-field assignment and export.

Representative Workflows

Small molecule — parse, type, export:

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

Polymer chain — G-BigSMILES to LAMMPS in one call:

import molpy as mp

# PEO chain with degree of polymerization = 10, built with 3D coordinates
peo   = mp.tool.polymer("{[<]CCOCC[>]}|10|")
ff    = mp.io.read_xml_forcefield("oplsaa.xml")
typed = mp.typifier.OplsAtomisticTypifier(ff).typify(peo)
mp.io.write_lammps_system("output/", typed.to_frame(), ff)

Polydisperse melt — Schulz-Zimm distribution, fully atomistic:

import molpy as mp

# Mn = 1500 Da, Mw = 3000 Da, total mass ≈ 500 kDa
chains = mp.tool.polymer_system(
    "{[<]CCOCC[>]}|schulz_zimm(1500,3000)||5e5|",
    random_seed=42,
)
print(f"Built {len(chains)} chains")   # reproducible chain population

frames = [c.to_frame() for c in chains]
packed = mp.pack.pack(frames, box=[80, 80, 80])
mp.io.write_lammps_system("peo_bulk/", packed, ff)

AmberTools pipeline — GAFF2 parameters, partial charges, AMBER topology:

import molpy as mp

eo = mp.tool.PrepareMonomer().run("{[<]CCOCC[>]}")  # BigSMILES → 3D + ports

result = mp.tool.polymer(
    "{[#EO]|20}",
    library={"EO": eo},
    backend="amber",   # runs antechamber + parmchk2 + tleap
)
# result.prmtop_path, result.inpcrd_path, result.pdb_path

---

Core Capabilities

Area	Capability
Parsing	Native support for SMILES, BigSMILES, CGSmiles, and G-BigSMILES
Polymer construction	Linear, branched, and cyclic assembly from notation-driven specifications
Polydispersity	Schulz-Zimm, Poisson, Flory-Schulz, and uniform chain-length distributions
Reactive topology editing	Anchor and leaving-group selectors, bond-forming reactions, and LAMMPS fix bond/react template generation
Force-field assignment	OPLS-AA and GAFF/GAFF2 typing through SMARTS/SMIRKS matching
External parameterization	AmberTools interfaces for antechamber, parmchk2, prepgen, and tleap
Packing and export	Packmol-based packing and export to LAMMPS, PDB, XYZ, AMBER, GRO, and HDF5
Simulation interfaces	Input generation for LAMMPS and CP2K
Interoperability	RDKit and OpenBabel adapters for conversion and structure preparation
Explicit data model	Distinct Atomistic, Frame/Block, and ForceField representations
Agent interface	Source-introspection MCP server provided by the molmcp gateway (local or hosted)

---

Architecture

SMILES / BigSMILES / CGSmiles / G-BigSMILES
           │
           ▼ parser
      Atomistic                  ← editable graph: Atom, Bond, Angle, Dihedral
      (topology graph)
           │
    ┌──────┴──────┐
    ▼             ▼
reacter        builder           ← reactions, polymer assembly
    └──────┬──────┘
           │
           ▼ typifier
    Typed Atomistic              ← SMARTS pattern matching assigns ForceField types
           │
           ▼ .to_frame()
         Frame                   ← columnar NumPy arrays; Box; metadata
           │
    ┌──────┴──────┐
    ▼             ▼
   pack          io / engine     ← Packmol packing; LAMMPS / CP2K / AMBER export

Each boundary is an explicit function call. State transitions remain visible throughout the workflow; no hidden coupling or monkey-patching is required.

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Installation

pip install molcrafts-molpy

Core dependencies: NumPy, igraph, Lark. Optional: RDKit (3D geometry), AmberTools (GAFF charges).

For development:

git clone https://github.com/MolCrafts/molpy.git
cd molpy
pip install -e ".[dev]"
pre-commit install
pytest tests/ -m "not external"

---

Documentation

Full documentation, including executable notebooks: https://molcrafts.github.io/molpy

• Getting Started — install and first example
• Guides — task-oriented notebooks
• Concepts — data model deep dives
• API Reference — full API

---

MolCrafts Ecosystem

Project	Role
MolPy	Python toolkit — this repo
MolVis	WebGL molecular visualization and interactive editing
MolRS	Rust backend: typed array structures and fast compute kernels (native + WASM)

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Contributing

Issues and pull requests are welcome. See Contributing.

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License

BSD-3-Clause — see LICENSE.