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
- LoadOptionalRestartFiles()¶
Load the restart files for the possible restarting of the running node.
- Returns
list of filenames
- Type
list(str) or None
- LoadOptionalRestartFilesDict()¶
Load a dict of the optional restart files. The dictionary maps the jobname of the subjob to a list of optional files for restarting the subjob.
- Returns
dict of optional files
- Return type
{str: list}
- static LoadPreviousNodes(restart_file)¶
Load nodes that were finished in previous job.
- Parameters
restart_file (str) – filename of the AL .pkl restart file
- Returns
Nodes that were finished in previous job.
- Return type
OrderedDict that maps node name to node instance.
- addOptionalRestartFilesDict()¶
Pass variable optional_restart_files_dict to the restart dictionary. Dump the restart dictionary as a pickle file.
- checkOSFileLimit()¶
Check the system file descriptors limit.
- configure()¶
Prepare the active learning job.
- getInitialInputs()¶
Get the inputs for the runNode() method of the first node in the workflow.
- Returns
dict that contains the keyword arguments and values for the runNode() of the first node.
- Return type
dict{keyword argument: value}
- getLocalArgs()¶
- Returns
arguments on local machine.
- Return type
argparse.Namespace
- static getNodeClasses(use_known_score, al_node_supplier)¶
Return a list of node classes to run based on the job type.
- Parameters
use_known_score (bool) – Use known scores in score_file to obtain the score.
al_node_supplier (ActiveLearningNodeSupplier) – Supplier of active learning nodes
- Returns
a list of ActiveLearningNode subclass
- Return type
list
- getNodesToRun()¶
Return nodes to run and finished nodes for current active learning job.
- getPilotScoreFile()¶
Reorder the columns in the pilot ligand score file for the use of machine learning model training input.
- Returns
name of reorder .csv file.
- Return type
str
- getRestartNode()¶
Get the node for restarting the workflow.
- Returns
last finished node
- Return type
- postprocessing()¶
Combine the log files of all subjobs.
- property restart_files¶
Get all the necessary files for restarting the workflow from finished nodes.
- Returns
a set of files for restarting.
- Return type
set(str)
- runNodes()¶
Run all the ActiveLearningNode instances in self.nodes_to_run.
- property scored_csv_file_list¶
Get all the .csv files that contain scored ligands from ScoreProviderNode.
- Returns
list of .csv files contain score ligands.
- Return type
list(str)
- splitInputfiles()¶
Separate the input files into small blocks randomly.
- 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()¶