schrodinger.application.desmond.stage.app.absolute_binding.struc module¶

Absolute binding FEP structure module.

schrodinger.application.desmond.stage.app.absolute_binding.struc.prepare_input_structures(input_sts: List[schrodinger.structure._structure.Structure]) → Tuple[List[schrodinger.structure._structure.Structure], List[schrodinger.structure._structure.Structure]]¶

Prepare and return the input ligand and receptor structures for absolute binding fep. Also include the solvent and membrane structures if present. Raises a ValueError if no receptor or ligands were found.

Parameters: input_sts – The list of input structures containing at least one receptor and one or more ligands. It may also include solvent or membrane as separate structures.
Returns: List of environment structures and list of ligands used in the simulation.

schrodinger.application.desmond.stage.app.absolute_binding.struc.prepare_md_structures(cts: List[schrodinger.structure._structure.Structure], ligand_hash_id: str) → List[schrodinger.structure._structure.Structure]¶: Extracts the environment cts, the ligand ct that matches the given ligand_hash_id and update annotate with the FEP_HASH_ID and FEP_ORIGINAL_TITLE properties.

schrodinger.application.desmond.stage.app.absolute_binding.struc.filter_fep_structures(sts: List[schrodinger.structure._structure.Structure], leg: str) → List[schrodinger.structure._structure.Structure]¶: Extract the structures with the matching leg.

schrodinger.application.desmond.stage.app.absolute_binding.struc.make_dummy(ct: schrodinger.structure._structure.Structure) → schrodinger.structure._structure._StructureAtom¶: Mark structure as the dummy and add a dummy atom. This is needed for the solvent leg to run as a relative calculation.

schrodinger.application.desmond.stage.app.absolute_binding.struc.is_dummy_ligand(ct: schrodinger.structure._structure.Structure) → bool¶