Prepare Complex

Protein-ligand complex preparation module for the Rush Python client.

This module builds on the protein preparation workflow to prepare complexes by extracting ligands from PDB inputs, adding hydrogens, and merging ligand data with prepared protein TRC data for downstream computations.

rush.prepare_complex.prepare_complex(input_path, ligand_names, 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)

  • ligand_names (list[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)

Return type:

TRC | RunError