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.

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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()