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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>
97 lines
3.2 KiB
Python
97 lines
3.2 KiB
Python
import pathlib
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import click
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from openfecli import OFECommandPlugin
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from openfecli.parameters import MOL_DIR, YAML_OPTIONS, OUTPUT_FILE_AND_EXT, NCORES, OVERWRITE
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YAML_HELP = """
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Path to a YAML file specifying the method to use to charge the molecules
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(any atom mapper or network generation options will be ignored).
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Supported partial charge method choices are:
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- ``am1bcc``
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- ``am1bccelf10`` (only possible if ``off_toolkit_backend`` is ``openeye``)
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- ``nagl`` (must have openff-nagl installed)
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- ``espaloma`` (must have espaloma_charge installed)
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``settings`` allows for passing in any keyword arguments of the method's corresponding Python API.
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For example:
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::
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partial_charge:
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method: am1bcc
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settings:
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off_toolkit_backend: ambertools
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"""
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@click.command("charge-molecules", short_help="Generate partial charges for a set of molecules.")
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@MOL_DIR.parameter(required=True, help=MOL_DIR.kwargs["help"] + " Any number of sdf paths.")
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@YAML_OPTIONS.parameter(multiple=False, required=False, default=None, help=YAML_HELP)
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@OUTPUT_FILE_AND_EXT.parameter(
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help="The name of the SDF file the charged ligands should be written to.",
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required=True,
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type=click.Path(exists=False, path_type=pathlib.Path),
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)
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@NCORES.parameter(help=NCORES.kwargs["help"], default=1)
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@OVERWRITE.parameter(help=OVERWRITE.kwargs["help"], default=OVERWRITE.kwargs["default"], is_flag=True) # fmt: skip
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def charge_molecules(molecules, yaml_settings, output, n_cores, overwrite_charges):
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"""
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Generate partial charges for the set of input molecules and write them to file.
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"""
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from openfecli.utils import write
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if output.exists():
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raise FileExistsError(
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f"The output file {output} already exists, choose a new file to write the charged ligands to"
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)
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write("SMALL MOLECULE PARTIAL CHARGE GENERATOR")
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write("_________________________________________")
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write("")
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from openfe.protocols.openmm_utils.charge_generation import bulk_assign_partial_charges
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write("Parsing in Files: ")
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# INPUT
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write("\tGot input: ")
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small_molecules = MOL_DIR.get(molecules)
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write("\t\tSmall Molecules: " + " ".join([str(sm) for sm in small_molecules]))
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yaml_options = YAML_OPTIONS.get(yaml_settings)
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partial_charge = yaml_options.partial_charge
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write("Using Options:")
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write("\tPartial Charge Generation: " + str(partial_charge.partial_charge_method))
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if overwrite_charges:
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write("\tOverwriting partial charges")
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write("")
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charged_molecules = bulk_assign_partial_charges(
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molecules=small_molecules,
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overwrite=overwrite_charges,
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method=partial_charge.partial_charge_method,
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toolkit_backend=partial_charge.off_toolkit_backend,
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generate_n_conformers=partial_charge.number_of_conformers,
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nagl_model=partial_charge.nagl_model,
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processors=n_cores,
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)
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write("\tDone")
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write("")
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# OUTPUT
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write("Output:")
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write(f"\tSaving to: {output}")
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with output.open(mode="w") as output:
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for mol in charged_molecules:
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output.write(mol.to_sdf())
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PLUGIN = OFECommandPlugin(command=charge_molecules, section="Miscellaneous", requires_ofe=(0, 3))
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