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66ac2bdc64
* updates to cli from_json * replacing dump instances with to_json * Remove unnecessary imports of JSON_HANDLER * addressing review --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Co-authored-by: David L. Dotson <dotsdl@gmail.com>
55 lines
1.8 KiB
Python
55 lines
1.8 KiB
Python
"""
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Write out the file that is used to test the quickrun command.
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This will need to be run if the serialized transformation changes such that
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the old file can't be read.
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USAGE:
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python write_transformation_json.py ../data/
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(Assuming you run from within this directory.)
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"""
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import gufe
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import openfe
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import json
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import argparse
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import pathlib
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from gufe.tests.conftest import benzene_modifications
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from gufe.tests.test_protocol import DummyProtocol, BrokenProtocol
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parser = argparse.ArgumentParser()
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parser.add_argument('directory')
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opts = parser.parse_args()
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directory = pathlib.Path(opts.directory)
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if not directory.exists() and directory.is_dir():
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raise ValueError(f"Bad parameter for directory: {directory}")
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benzene_modifications = benzene_modifications.__pytest_wrapped__.obj()
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benzene = gufe.SmallMoleculeComponent.from_rdkit(benzene_modifications['benzene'])
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toluene = gufe.SmallMoleculeComponent.from_rdkit(benzene_modifications['toluene'])
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solvent = gufe.SolventComponent(positive_ion="K", negative_ion="Cl")
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benz_dict = {'ligand': benzene}
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tol_dict = {'ligand': toluene}
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solv_dict = {'solvent': solvent}
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solv_benz = gufe.ChemicalSystem(dict(**benz_dict, **solv_dict))
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solv_tol = gufe.ChemicalSystem(dict(**tol_dict, **solv_dict))
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mapper = openfe.setup.LomapAtomMapper()
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mapping = list(mapper.suggest_mappings(benzene, toluene))[0]
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protocol = DummyProtocol(settings=DummyProtocol.default_settings())
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transformation = gufe.Transformation(solv_benz, solv_tol, protocol, mapping)
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bad_protocol = BrokenProtocol(settings=BrokenProtocol.default_settings())
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bad_transformation = gufe.Transformation(solv_benz, solv_tol,
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bad_protocol, mapping)
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transformation.to_json(directory / "transformation.json")
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bad_transformation.to_json(directory / "bad_transformation.json")
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