Prepare Protein

Protein preparation module for the Rush Python client.

This module supports system preparation workflows such as converting PDB inputs to TRC, protonating and optimizing hydrogen positions, and augmenting structures with connectivity and formal charge information before downstream calculations.

rush.prepare_protein.prepare_protein(input_path, ph=None, naming_scheme=None, capping_style=None, truncation_threshold=None, debump=None, run_spec=RunSpec(), run_opts=RunOpts(), collect=False)[source]

Run prepare-protein on a PDB or TRC file and return the separate T, R, and C files.

Parameters:

  • input_path (Path | str)

  • ph (float | None)

  • naming_scheme (Literal['AMBER', 'CHARMM'] | None)

  • capping_style (Literal['never', 'truncated', 'always'] | None)

  • truncation_threshold (int | None)

  • debump (bool | None)

  • run_spec (RunSpec)

  • run_opts (RunOpts)

rush.prepare_protein.save_outputs(res)[source]
Parameters:

res (list[dict] | tuple[dict, dict, dict] | RunError)

Return type:

tuple[Path, Path, Path] | RunError