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