molcrafts-molrs

Python bindings for the molrs molecular modeling toolkit.

Install with pip install molcrafts-molrs and import molrs. Full docs: https://docs.molcrafts.org/molrs/.

Install

pip install molcrafts-molrs

Requires Python 3.12+.

Quick start (0.12 surface)

import numpy as np
import molrs

# SMILES → atomistic graph (class API under molrs.io)
mol = molrs.io.SmilesIR("CCO").to_atomistic()

# 3D coordinates
from molrs.conformer import Conformer

mol = Conformer().generate(mol)

# Force field: typify → pairs → potentials (no typifier.build())
from molrs.ff import MMFF94Typifier, extract_coords, intramolecular_pairs

typed = MMFF94Typifier().typify(mol)
frame = typed.to_frame()
frame["pairs"] = intramolecular_pairs(frame)
pots = MMFF94Typifier().forcefield().to_potentials(frame)
coords = extract_coords(frame)
energy, forces = pots.calc_energy_forces(coords)
assert forces.shape == (frame["atoms"].nrows, 3)

Package layout

Import	Owns
`molrs` (top level)	Core: `Frame`, `Block`, `Atomistic`, `Box`, neighbors, …
`molrs.io`	Readers/writers, `SmilesIR`
`molrs.ff`	Force fields, typifiers, potentials
`molrs.compute`	RDF, MSD, transport, dielectric, …
`molrs.conformer`	3D generation
`molrs.perceive`	Rings / aromaticity builder

Users of analysis APIs: analysis time is fs (LAMMPS real). MSD needs unwrapped coordinates. VACF is the unbiased (C(\tau)) used for Green–Kubo D and VDOS.

Development

maturin develop --release
pytest -q

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