molcrafts-molrs 0.9.3

Python bindings for molrs molecular simulation library

molcrafts-molrs

Python bindings for the molrs molecular modeling toolkit.

This package is the first public preview of the Python API. Install with pip install molcrafts-molrs and import it as molrs.

Full documentation lives at https://molcrafts.github.io/molrs/. The Python API reference is rendered at https://molcrafts.github.io/molrs/reference/python/.

Install

pip install molcrafts-molrs

Quick start

import numpy as np
import molrs

# Parse SMILES and generate 3D coordinates
ir = molrs.parse_smiles("CCO")
mol = ir.to_atomistic()
result = molrs.generate_3d(mol, molrs.EmbedOptions(speed="fast", seed=42))
frame = result.mol.to_frame()

# Build a system from scratch
frame = molrs.Frame()
atoms = molrs.Block()
atoms.insert("x", np.array([0.0, 0.96, -0.24], dtype=np.float64))
atoms.insert("y", np.array([0.0, 0.0, 0.93], dtype=np.float64))
atoms.insert("z", np.zeros(3, dtype=np.float64))
atoms.insert("element", ["O", "H", "H"])
frame["atoms"] = atoms

Support

• Python 3.9+
• pip install molcrafts-molrs
• import molrs
• Offline API help is available with help(molrs.Frame) and related symbols

API

Data model

• Frame — dict-like container of named Blocks + optional Box
• Block — column store backed by numpy arrays
• Box — simulation box with periodic boundaries

I/O

• molrs.read_pdb(path) / molrs.read_xyz(path) → Frame
• molrs.parse_smiles(smiles) → SmilesIR → .to_frame()

Neighbor search and analysis

nq = molrs.NeighborQuery(box, positions, cutoff=5.0)
nlist = nq.query_self()

from molrs.compute.density import RDF
rdf = RDF(100, 5.0)
result = rdf.compute(frame, nlist)

Force field

typifier = molrs.MMFF94Typifier()
potentials = typifier.build(atomistic)

Development

maturin build
pip install target/wheels/*.whl
pytest -q

Component	Version
Python	3.9+
PyO3	Managed by molrs-python/Cargo.toml
maturin	1.x

License

BSD-3-Clause