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mattwthompson avatar mattwthompson commented on May 28, 2024

This has been completed at some point:

molecule = Molecule.from_smiles("O")
molecule.generate_conformers(n_conformers=1)
topology = molecule.to_topology()
topology.box_vectors = [4, 4, 4] * unit.nanometer

force_field = ForceField("openff-2.0.0.offxml")

interchange = force_field.create_interchange(topology)

pprint(json.loads(interchange.json()))
{
│   'positions': {
│   │   'val': [
│   │   │   [0.006112021207809448, 0.038865670561790466, 0.005890042334794998],
│   │   │   [0.07237835526466369, -0.031162935495376583, -0.0038235086947679517],
│   │   │   [-0.07849037051200866, -0.0077027328312397, -0.002066533826291561]
│   │   ],
│   │   'unit': 'nanometer'
│   },
│   'box': {'val': [[4.0, 0.0, 0.0], [0.0, 4.0, 0.0], [0.0, 0.0, 4.0]], 'unit': 'nanometer'},
│   'topology': '{"aromaticity_model": "OEAroModel_MDL", "constrained_atom_pairs": {}, "box_vectors": [4.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 4.0], "box_vectors_unit": "nanometer", "molecules": [{"name": "", "atoms": [{"atomic_number": 8, "formal_charge": 0, "is_aromatic": false, "stereochemistry": null, "name": "", "metadata": {}}, {"atomic_number": 1, "formal_charge": 0, "is_aromatic": false, "stereochemistry": null, "name": "", "metadata": {}}, {"atomic_number": 1, "formal_charge": 0, "is_aromatic": false, "stereochemistry": null, "name": "", "metadata": {}}], "bonds": [{"atom1": 0, "atom2": 1, "bond_order": 1, "is_aromatic": false, "stereochemistry": null, "fractional_bond_order": null}, {"atom1": 0, "atom2": 2, "bond_order": 1, "is_aromatic": false, "stereochemistry": null, "fractional_bond_order": null}], "properties": {}, "conformers": null, "partial_charges": [-0.834, 0.417, 0.417], "partial_charge_unit": "elementary_charge", "hierarchy_schemes": {}}]}',
│   'collections': {
│   │   'Bonds': '{"type": "Bonds", "is_plugin": false, "expression": "k/2*(r-length)**2", "key_map": {"{\\"atom_indices\\": [0, 1], \\"bond_order\\": null}": {"id": "[#8:1]-[#1:2]", "mult": null, "associated_handler": "Bonds", "bond_order": null}, "{\\"atom_indices\\": [0, 2], \\"bond_order\\": null}": {"id": "[#8:1]-[#1:2]", "mult": null, "associated_handler": "Bonds", "bond_order": null}}, "potentials": {"{\\"id\\": \\"[#8:1]-[#1:2]\\", \\"mult\\": null, \\"associated_handler\\": \\"Bonds\\", \\"bond_order\\": null}": {"parameters": {"k": "{\\"val\\": 1087.053566377, \\"unit\\": \\"kilocalorie / angstrom ** 2 / mole\\"}", "length": "{\\"val\\": 0.9716763312559, \\"unit\\": \\"angstrom\\"}"}, "map_key": null}}, "fractional_bond_order_method": "AM1-Wiberg", "fractional_bond_order_interpolation": "linear"}'
│   }
}

from openff-interchange.

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