schrodinger.application.desmond.stage.app.absolute_binding.struc module¶
Absolute binding FEP structure module.
Copyright Schrodinger, LLC. All rights reserved.
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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.
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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 theFEP_HASH_ID
andFEP_ORIGINAL_TITLE
properties.
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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
.
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schrodinger.application.desmond.stage.app.absolute_binding.struc.
make_dummy
(ct: schrodinger.structure._structure.Structure)¶ Mark structure as the dummy and add a dummy atom. This is needed for the solvent leg to run as a relative calculation.
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schrodinger.application.desmond.stage.app.absolute_binding.struc.
is_dummy_ligand
(ct: schrodinger.structure._structure.Structure) → bool¶