anabiman/mmic_cg

Strategy MMIC for coarse-graining

Forcefield param assignment component

This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides a component for coarse-graining molecules.

Basic Usage

# Import main component for coarse-graining
from mmic_cg.components import CoarseComponent

# Import a molecule model that complies with MMSchema
from mmelemental.models import Molecule

# Create MMSchema molecule
mol = Molecule.from_file(path_to_file)

# Create input for coarse-graining a molecule with protoMD
cgIn = {
    "molecule": mol, 
    "method": "spacewarping",
    "keywords": {
        "kmax": 1,
        "polynomial": "legendre",
    },
}

# Execute coarse-graining
cgOut = CoarseComponent.compute(cgInput)

# Extract MMSchema CG mol
cgMol = cgOutput.mol

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.