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: schrodinger.structure._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.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

schrodinger.application.livedesign.ld_glide_utils.update_required_licenses(glide_infiles: list[str], schro_licenses: set) → set

Add additional required licenses based on the Glide input files

Parameters

  • glide_infiles – List of Glide input files

  • schro_licenses – Initial required licenses

Returns

Completed set of required licenses