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

Absolute binding FEP structure module.

Copyright Schrodinger, LLC. All rights reserved.

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]][source]

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][source]

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][source]

Extract the structures with the matching leg.

schrodinger.application.desmond.stage.app.absolute_binding.struc.make_dummy(ct: schrodinger.structure._structure.Structure)[source]

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[source]