schrodinger.application.phase.packages.shape_screen_oned_driver_utils module¶
Provides supporting functionality for shape_screen_oned_driver.py.
Copyright Schrodinger LLC, All Rights Reserved.
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.add_confgen_args(parser: argparse.ArgumentParser) None ¶
Adds conformer generation arguments.
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.add_jobcontrol_args(parser: argparse.ArgumentParser) None ¶
Adds job control arguments.
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.add_reporting_args(parser: argparse.ArgumentParser) None ¶
Adds reporting arguments.
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.add_required_args(parser: argparse.ArgumentParser) None ¶
Adds required arguments.
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.add_screening_args(parser: argparse.ArgumentParser) None ¶
Adds screening arguments.
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.get_conformer_reader(args)¶
Returns a reader that runs LigPrep on and generates conformers for the 1D hits in the file <subjob_name>.csv.gz.
- Parameters
args (argparse.Namespace) – Command line arguments for a subjob
- Returns
Conformer reader attached to <subjob_name>.csv.gz
- Return type
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.get_distributed_shape_screen_commands(args, nsub)¶
Returns commands for the quick_shape shape screen subjobs.
- Parameters
args (argparse.Namespace) – Command line arguments
nsub (int) – Number of shape screen subjobs
- Returns
quick_shape subjob commands
- Return type
list[list[str]]
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.get_oned_screen_command(args)¶
Returns the command that should be used to run oned_screen.
- Parameters
args (argparse.Namespace) – Command line arguments
- Returns
oned_screen command
- Return type
list(str)
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.get_parser()¶
Creates argparse.ArgumentParser with supported command line options.
- Returns
Argument parser object
- Return type
argparse.ArgumentParser
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.get_shape_generator(args)¶
Constructs a ShapeGenerator from the provided subjob arguments.
- Parameters
args (argparse.Namespace) – Command line arguments for a subjob
- Returns
Shape generator
- Return type
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.get_shape_queries(args)¶
Constructs shape queries from the provided subjob arguments.
- Parameters
args (argparse.Namespace) – Command line arguments for a subjob
- Returns
Shape queries
- Return type
list(shape.ShapeQuery)
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.merge_oned_hits_files(hits_files_in, hits_file_out)¶
Merges a list of gzipped CSV files, creating an output gzipped CSV file with only unique SMILES/name combinations, a master set of properties and no query row.
- Parameters
hits_files_in (list(str)) – List of gzipped CSV hits files to merge
hits_file_out (str) – Output gzipped CSV hits file
- Returns
Number of merged hits written
- Return type
int
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.split_queries(shape_file)¶
Splits the shape queries into separate files <jobname>_query_<i>.<ext> for each query <i>, where <ext> is maegz or phypo. The names of the created files are returned.
- Parameters
shape_file (str) – The Maestro, SD or hypothesis file containing the shape queries
- Returns
List of query files created
- Return type
list[str]
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.validate_shape_screen_report_args(args)¶
Raises a ValidationError if the arguments for generating a shape screen report are invalid.
- Parameters
args (argparse.Namespace) – argument namespace with command line options
- Raise
ValidationError if validation fails
- schrodinger.application.phase.packages.shape_screen_oned_driver_utils.validate_args(args)¶
Checks the validity of command line arguments.
- Parameters
args (argparse.Namespace) – Command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
tuple[bool, str]