molssi / mmic_parmed

Tactic MMIC translator for ParmEd/MMSchema

ParmEd translator for MMSchema

This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides translators between MMSchema and ParmEd.

mmic_parmed provides 4 classes of translators for: molecules, forcefields, trajectories (incomplete), and simulation (incomplete).

Models

from mmic_parmed.models import ParmedMol

# Convert MMSchema to ParmEd molecule
pa_mol = ParmedMol.from_schema(mm_mol) -> parmed.structure.Structure

# Convert ParmEd to MMSchema molecule
mm_mol = ParmedMol.to_schema(pa_mol) -> mmelemental.models.molecule.Molecule

Components

The from_schema and to_schema methods in the ParmedMol model use translation components provided by mmic_parmed and MMElemental to convert between MMSchema and ParmEd.

from mmic_parmed.components import ParmedToMolComponent, MolToParmedComponent
from mmic_parmed.models.import ParmedMol
from mmelemental.models.molecule import Molecule

MMSchema to ParmEd molecule

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

# Create translation input
inp = {
    "schema_object": mm_mol,
    "schema_version": 1,
}

# Run translator compute
outp = MolToParmedComponent.compute(inp)

# Extract parmed structure
pa_mol = outp.data_object.data

ParmEd to MMSchema molecule

# Create ParmEd input
pa_struct = parmed.load_file(path_to_file)
pa_mol = mmic_parmed.models.ParmedMol(mol=pa_struct)

# Create translation input
inp = {
    "data_object": pa_mol
}

# Running translator compute
outp = Translator.compute(inp)

# Extract MMSchema molecule
mm_mol = outp.schema_object

Copyright

Copyright (c) 2021, MolSSI

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.5.

mmic_parmed's Issues

Missing fudgeLJ and fudgeQQ in GMX file

Current implementation does read/write fudgeLJ or fudgeQQ needed in .top files.

Support polarizable force fields

Need to support reading polarizable force fields in FFToParmedComponent

PSF files not working with PDB/XYZ files

Investigate the underlying problem with this behavior:

>>> parmed.load_file(mm_data.ffs["dialanine.psf"], xyz=mm_data.mols["dialanine.pdb"]) 
... TypeError: parse() got an unexpected keyword argument 'xyz'

Support for improper dihedrals

Need to support improper periodic dihedrals (funct = 4 in gmx) in both FFToParmedComponent and ParmedToFFComponent.

Inconsistent hashing [unspecified velocity_units]

Inconsistent hash found in model reconstruction when using the mmic_parmed molecule converter.

Code snippet

import mmelemental

mol = mmelemental.models.Molecule.from_file(some_file, translator="mmic_parmed")
mol2 = mmelemental.models.Molecule(**mol.dict())

returns

Model data inconsistent with stored hash code! (type=assertion_error)

Expected behaviour

mol.get_hash() == mol2.get_hash()
False

For some reason, the generated hash code is inconsistent with the original model hash code.