schrodinger.application.livedesign.ld_glide_utils module

LiveDesign Glide protocol utils

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.livedesign.ld_glide_utils.write_result_row(st: structure.Structure, lig_file: str, prot_file: str, status: str, lid_file: str, show_strain: bool, is_reflig: bool) → dict[str, str]

Write a result row

Parameters

  • st – Ligand structure for properties

  • lig_file – Ligand MAE file

  • prot_file – Protein MAE file

  • status – Status string

  • lid_file – LID PNG/SVG file

  • show_strain – Whether to show the docking strain

  • is_reflig – Whether the input is a reference ligand

Returns

A dict of the result row

schrodinger.application.livedesign.ld_glide_utils.parse_glide_results(glide_outfile: str, glide_keywords: schrodinger.application.glide.glide.Dock, poses_per_ligand: int, ref_st_file: str, remaining_corp_ids: set, show_reflig: bool, backend: schrodinger.job.jobcontrol._Backend, sch_ver: str) → tuple[list[dict[str, str]], set]

Parse the Glide PV structure file, extract the desired properties and create a Maestro file and LID for each ligand

Parameters

  • glide_outfile – Filename of the Glide PV structure file

  • glide_keywords – All Glide keywords

  • poses_per_ligand – Number of poses to keep per ligand title

  • ref_st_file – File containing a reference structure

  • remaining_corp_ids – Set of corporate IDs after LigPrep/LigFilter stages

  • show_reflig – Include the reference ligand in the results

  • backend – the _Backend object of Jobcontrol

  • sch_ver – Schrodinger suite version

Returns

List of dictionaries containing the results for each input ligand and a set of compound IDs that failed the Glide stage

schrodinger.application.livedesign.ld_glide_utils.filter_glide_results(glide_pv_file: str, dedup_pv_file: str, poses_per_ligand: int) → None

Run glide_blocksort on the input PV file and sort/filter based on the number of poses to keep for each title

Parameters

  • glide_pv_file – Maestro PV file

  • dedup_pv_file – Maestro PV file that has been filtered

  • poses_per_ligand – Number of poses to keep per ligand title

schrodinger.application.livedesign.ld_glide_utils.get_optimal_atom_mapping(smarts: str, ref_st: structure.Structure, lig_st: structure.Structure) → tuple[list[int], list[int]]

For a SMARTS for a substructure that is common to two structures, return atom mapping for a common match between the structures.

SMARTS patterns can return multiple matches for a given structure and relying on the first SMARTS match can result in incorrect atom mappings between a ligand and reference. This in turn, can given rise to incorrect LIDs. The function identifies the optimal mapping between the reference and ligand atoms that match the SMARTS pattern by identifying the mapping that has the lowest RMSD

Parameters

  • smarts – RDKit SMARTS string

  • ref_st – Reference structure

  • lig_st – Ligand structure

Returns

List of atom indices for the ligand and reference structure in their optimal order for mapping

schrodinger.application.livedesign.ld_glide_utils.create_implicit_smarts(glide_smarts: str) → str

The implicit SMARTS are need to generate the optimal heavy-atom mapping between the ligand and reference molecules in order to create an aligned LID. Using the SMARTS pattern from the docking, create a RDKit RWMol, remove all hyrdogens and generate am implicit, heavy-atom only SMARTS.

Parameters

glide_smarts – SMARTS pattern from Glide

Returns

Implicit SMARTS string for the Glide substructure

schrodinger.application.livedesign.ld_glide_utils.create_lid(rec_st: schrodinger.structure._structure.Structure, lig_st: schrodinger.structure._structure.Structure, glide_keywords: schrodinger.application.glide.glide.Dock, ref_st: schrodinger.structure._structure.Structure) → PyQt6.QtGui.QImage

Create a LID for each docking pose. If specified, use the reference structure to align the LID using the alignment settings from Glide

Parameters

  • rec_st – Receptor structure

  • lig_st – Docked pose

  • glide_keywords – All Glide keywords

  • ref_st – Reference structure

Returns

LID image