drugforge.modeling.modeling.spruce_protein

drugforge.modeling.modeling.spruce_protein(initial_prot: openeye.oechem.OEGraphMol, protein_sequence: str = None, loop_db: Path = None) → openeye.oechem.OEGraphMol[source]

Applies the OESpruce protein preparation pipeline to the given protein structure.

Parameters:

  • initial_prot (oechem.OEMol) – The input protein structure to be prepared.

  • protein_sequence (str, optional) – The sequence of the protein for a single change. If provided, this will be added to the Structure Metadata before applying the OESpruce pipeline. Default is None.

  • loop_db (str, optional) – The filename of the loop database to be used by the OESpruce pipeline. If provided, the pipeline will include the loop building step. Default is None.

Returns:

(success – Returns a tuple of: a boolean for whether sprucing was successful a string of the error message if sprucing failed the prepared protein structure.

Return type:

bool, spruce_error_msg: str, initial_prot: oechem.OEMol)