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OpenFreeEnergy / feflow

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
MIT License
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`NonEquilibriumCyclingSettings` can not be round tripped to JSON #87

Closed jthorton closed 1 month ago

jthorton commented 1 month ago

In ASAP-Alchemy we are trying to add support for the NonEquilibriumCyclingProtocol which involves building a schema that inherits from NonEquilibriumCyclingSettings to store the settings used in a run for provenance. However we have found that it is not possible to round trip NonEquilibriumCyclingSettings to JSON due to the forcefield_settings type hint defined in the base gufe model here. See the example below, this can be fixed by updating the hint as is done in the RelativeHybridTopologyProtocolSettings.

import json
from gufe.tokenization import JSON_HANDLER

from feflow.protocols import NonEquilibriumCyclingProtocol
from feflow.settings import NonEquilibriumCyclingSettings
from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol
from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocolSettings

# round trip the relative protocol
rel_settings = RelativeHybridTopologyProtocol.default_settings()
ref_json = json.dumps(rel_settings.dict(), cls=JSON_HANDLER.encoder)
# load a new settings from the JSON
rel_settings_2 = RelativeHybridTopologyProtocolSettings.parse_obj(json.loads(ref_json, cls=JSON_HANDLER.decoder))
assert rel_settings == rel_settings_2

# try with NEQ
neq_settings = NonEquilibriumCyclingProtocol.default_settings()
neq_json = json.dumps(neq_settings.dict(), cls=JSON_HANDLER.encoder)
neq_settings_2 = NonEquilibriumCyclingSettings.parse_obj(json.loads(neq_json, cls=JSON_HANDLER.decoder))
assert neq_settings == neq_settings_2

pydantic.error_wrappers.ValidationError: 7 validation errors for NonEquilibriumCyclingSettings forcefield_settings -> constraints extra fields not permitted (type=value_error.extra) forcefield_settings -> forcefields extra fields not permitted (type=value_error.extra) forcefield_settings -> hydrogen_mass extra fields not permitted (type=value_error.extra) forcefield_settings -> nonbonded_cutoff extra fields not permitted (type=value_error.extra) forcefield_settings -> nonbonded_method extra fields not permitted (type=value_error.extra) forcefield_settings -> rigid_water extra fields not permitted (type=value_error.extra) forcefield_settings -> small_molecule_forcefield extra fields not permitted (type=value_error.extra)