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2311a2f2d9
* add more checks * make precommit manual * apply formatting to pyproject.toml * add TODO * remove unneeded, add a few more * add ruff, but turn everything off * add openfe known first party * format highest-level files * first half of openfe protocols * second half of openfe protocols * openfe protocols formatting, with alyssa's fmt skips * add ruff formatter to precommit * fmt: off all vendored _rfe_utils code * addressing review comments * format openfe/utils * format openfe/setup * first batch of cli formatting * second batch of cli formatting * formatting the rest of openfecli commands * format openfecli/parameters * format openfe/storage * run precommit * Update openfecli/commands/gather.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * update example notebooks branch for v1.7.0 docs changes (#1615) * bump example notebooks branch * add ipykernel to env * roll back to fixing septop branch * i dont think we want ipykernel * bump to tmp_fix_docs branch * point to branch revert-237-v1.7_cookbooks * point to latest example notebooks release * remove colab button, point to updated example notebooks, reorg landing page (#1618) * remove colab button from example notebooks in docs * point to example notebooks 2025.10.2 * replace 'try' with CLI --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
105 lines
3.2 KiB
Python
105 lines
3.2 KiB
Python
# This code is part of OpenFE and is licensed under the MIT license.
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# For details, see https://github.com/OpenFreeEnergy/openfe
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import click
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from openfecli import OFECommandPlugin
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from openfecli.parameters import MOL, MAPPER, OUTPUT_FILE_AND_EXT
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def allow_two_molecules(ctx, param, value):
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"""click callback to require that --mol is specified exactly twice"""
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if len(value) != 2:
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raise click.BadParameter("Must specify --mol exactly twice.")
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return value
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@click.command("atommapping", short_help="Check the atom mapping of a given pair of ligands")
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@MOL.parameter(
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multiple=True,
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callback=allow_two_molecules,
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required=True,
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help=MOL.kwargs["help"] + " Must be specified twice.",
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)
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@MAPPER.parameter(required=True)
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@OUTPUT_FILE_AND_EXT.parameter(help=OUTPUT_FILE_AND_EXT.kwargs["help"] + " (PNG format)")
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def atommapping(mol, mapper, output):
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"""
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This provides tools for looking at a specific atommapping.
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"""
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# note that the text of the docstring will be the help when you run
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# `openfe atommapping --help`.
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molA_str, molB_str = mol
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molA = MOL.get(molA_str)
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molB = MOL.get(molB_str)
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mapper_cls = MAPPER.get(mapper)
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mapper_obj = mapper_cls()
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file, ext = OUTPUT_FILE_AND_EXT.get(output)
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if file:
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atommapping_visualize_main(mapper_obj, molA, molB, file, ext)
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else:
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atommapping_print_dict_main(mapper_obj, molA, molB)
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def generate_mapping(mapper, molA, molB):
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"""Utility method to extract a single mapping from a mapper.
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Parameters
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----------
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mapper : :class:`.LigandAtomMapper`
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the mapper to use to generate the mapping
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molA, molB : :class:`.SmallMoleculeComponent`
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molecules to map between
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Returns
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------
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:class:`.LigandAtomMapping` :
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the mapping generated by the mapper; errors if there is not exactly
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one mapping generated
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"""
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mappings = list(mapper.suggest_mappings(molA, molB))
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if len(mappings) != 1:
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raise click.UsageError(
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f"Found {len(mappings)} mappings; this command requires a mapper "
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"to provide exactly 1 mapping"
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)
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return mappings[0]
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def atommapping_print_dict_main(mapper, molA, molB):
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"""Main function for generating and printing out the mapping"""
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mapping = generate_mapping(mapper, molA, molB)
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print(mapping.componentA_to_componentB)
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def atommapping_visualize_main(mapper, molA, molB, file, ext):
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from rdkit.Chem import Draw
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from gufe.visualization import mapping_visualization as vis
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mapping = generate_mapping(mapper, molA, molB)
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ext_to_artist = {
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"png": Draw.rdMolDraw2D.MolDraw2DCairo(600, 300, 300, 300),
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}
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try:
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artist = ext_to_artist[ext]
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except KeyError:
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raise click.BadParameter(
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f"Unknown file format: '{ext}'. The following formats are "
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"supported: " + ", ".join([f"'{ext}'" for ext in ext_to_artist])
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)
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contents = vis.draw_mapping(
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mapping.componentA_to_componentB,
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mapping.componentA.to_rdkit(),
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mapping.componentB.to_rdkit(),
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d2d=artist,
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)
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file.write(contents)
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PLUGIN = OFECommandPlugin(
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command=atommapping,
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section="hidden",
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requires_ofe=(0, 0, 1),
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)
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