schrodinger.application.phase.packages.shape_screen_al_driver module¶
Implementation of screening large library with Shape Screen active learning scheme.
Shape screen active learning scheme 1. Select N ligands from the library 2. Shape Screen the selected portion of the library. 3. Train a ligand_ml model with the Shape CPU screening scores. 4. Evaluate the whole library with the generated ligand_ml model. 5. Pick N from the top M best ligands predicted by the ligand_ml model. 6. Shape Screen the ligands picked in step 5 and repeat step 3 until it reaches num_iter.
Copyright Schrodinger Inc, All Rights Reserved.
- class schrodinger.application.phase.packages.shape_screen_al_driver.ActiveLearningShapeScreenJob(args, al_node_supplier)¶
Bases:
schrodinger.active_learning.al_driver.ActiveLearningJob
- __init__(args, al_node_supplier)¶
Initialize the ActiveLearningShapeScreenJob from the cmd arguments.
- Parameters
args (argparse.Namespace) – argument namespace with command line options
- schrodinger.application.phase.packages.shape_screen_al_driver.parse_input_file(args)¶
Parse the input file. Some inter-keyword dependencies and validation are handled here.
- Parameters
args (argparse.Namespace) – argument namespace (modified in place!)
- schrodinger.application.phase.packages.shape_screen_al_driver.get_parser()¶
Creates argument parser for shape_screen active learning job.
- Returns
configured argument parser
- Return type
argparse.ArgumentParser
- schrodinger.application.phase.packages.shape_screen_al_driver.parse_args(argv=None)¶
Parses and validates command-line arguments.
- Parameters
argv (list(str)) – argument list
- Returns
argument namespace with command line options
- Return type
argparse.Namespace
- schrodinger.application.phase.packages.shape_screen_al_driver.validate_args(args)¶
Validate command-line arguments
- Parameters
args (argparse.Namespace) – argument namespace with command line options
- Returns
(validation outcome, error message)
- Return type
(bool, str)
- schrodinger.application.phase.packages.shape_screen_al_driver.check_license()¶
Check for the existence of the ACTIVE_LEARN license and exit with an error message if it doesn’t.
- schrodinger.application.phase.packages.shape_screen_al_driver.get_job_spec_from_args(argv)¶
Register input files with jobcontrol.
- Parameters
argv (List[str]) – Argument list
- schrodinger.application.phase.packages.shape_screen_al_driver.main()¶