mkt.databases.cli.generate_pymol_files
CLI for generating PyMOL visualization files for kinase structures.
Functions
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Generate PyMOL visualization files for kinase structures. |
- mkt.databases.cli.generate_pymol_files.main(gene: ~typing.Annotated[str, <typer.models.OptionInfo object at 0x7754019d6260>] = 'ABL1', config_type: ~mkt.databases.app.schema.Annotated[~mkt.databases.app.schema.StandardConfigChoice, <typer.models.OptionInfo object at 0x7754019d63b0>] = StandardConfigChoice.KLIFS_IMPORTANT, output_dir: ~typing.Annotated[~pathlib.Path | None, <typer.models.OptionInfo object at 0x7754019d63e0>] | None = None, json_mutations: ~typing.Annotated[~pathlib.Path | None, <typer.models.OptionInfo object at 0x7754019d64d0>] | None = None, indices: ~typing.Annotated[str | None, <typer.models.OptionInfo object at 0x7754019d6500>] | None = None, colors: ~typing.Annotated[str | None, <typer.models.OptionInfo object at 0x7754019d6590>] | None = None, transparency: ~typing.Annotated[float, <typer.models.OptionInfo object at 0x7754019d6620>] = 0.3, verbose: ~typing.Annotated[bool, <typer.models.OptionInfo object at 0x7754019d66b0>] = False) None[source]
Generate PyMOL visualization files for kinase structures.
- Examples:
# Generate KLIFS pocket visualization for ABL1 generate_pymol_files –gene ABL1 –config KLIFS_IMPORTANT
# Generate phosphosite visualization generate_pymol_files –gene EGFR –config PHOSPHOSITES
# Generate mutation visualization (requires JSON file) generate_pymol_files –gene ABL1 –config MUTATIONS_KLIFS –json-mutations mutations.json
# Generate group-averaged mutations generate_pymol_files –gene ABL1 –config MUTATIONS_GROUP –json-mutations mutations.json
# Generate KLIFS regions (semi-transparent cartoon) with custom stick residues generate_pymol_files –gene ABL1 –config KLIFS_CUSTOM –indices 315,317 –colors red,blue