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devtools: add script to update Settings in data files

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This commit is contained in:
richard gowers
2024-02-19 21:30:32 +00:00
parent 208a5400eb
commit 7cd609332f
2 changed files with 21 additions and 7 deletions
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26
devtools/data/gen-serialized-results.py → devtools/data/gen_serialized_results.py
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@@ -76,20 +76,25 @@ def execute_and_serialize(dag, protocol, simname):
json.dump(outdict, zipfile, cls=JSON_HANDLER.encoder)
def generate_md_json(smc):
def generate_md_settings():
settings = PlainMDProtocol.default_settings()
settings.simulation_settings.equilibration_length_nvt = 0.01 * unit.nanosecond
settings.simulation_settings.equilibration_length = 0.01 * unit.nanosecond
settings.simulation_settings.production_length = 0.01 * unit.nanosecond
settings.forcefield_settings.nonbonded_method = "nocutoff"
protocol = PlainMDProtocol(settings=settings)
return settings
def generate_md_json(smc):
protocol = PlainMDProtocol(settings=generate_md_settings())
system = openfe.ChemicalSystem({"ligand": smc})
dag = protocol.create(stateA=system, stateB=system, mapping=None)
execute_and_serialize(dag, protocol, "MDProtocol")
def generate_ahfe_json(smc):
def generate_ahfe_settings():
settings = AbsoluteSolvationProtocol.default_settings()
settings.solvent_equil_simulation_settings.equilibration_length_nvt = 10 * unit.picosecond
settings.solvent_equil_simulation_settings.equilibration_length = 10 * unit.picosecond
@@ -114,7 +119,11 @@ def generate_ahfe_json(smc):
settings.vacuum_engine_settings.compute_platform = 'CPU'
settings.solvent_engine_settings.compute_platform = 'CUDA'
protocol = AbsoluteSolvationProtocol(settings=settings)
return settings
def generate_ahfe_json(smc):
protocol = AbsoluteSolvationProtocol(settings=generate_ahfe_settings())
sysA = openfe.ChemicalSystem(
{"ligand": smc, "solvent": openfe.SolventComponent()}
)
@@ -127,12 +136,17 @@ def generate_ahfe_json(smc):
execute_and_serialize(dag, protocol, "AHFEProtocol")
def generate_rfe_json(smcA, smcB):
def generate_rfe_settings():
settings = RelativeHybridTopologyProtocol.default_settings()
settings.simulation_settings.equilibration_length = 10 * unit.picosecond
settings.simulation_settings.production_length = 250 * unit.picosecond
settings.forcefield_settings.nonbonded_method = "nocutoff"
protocol = RelativeHybridTopologyProtocol(settings=settings)
return settings
def generate_rfe_json(smcA, smcB):
protocol = RelativeHybridTopologyProtocol(settings=generate_rfe_settings())
a_smcB = align_mol_shape(smcB, ref_mol=smcA)
mapper = KartografAtomMapper(atom_map_hydrogens=True)