schrodinger.application.phase.packages.shape_screen_oned_driver_utils module¶

Provides supporting functionality for shape_screen_oned_driver.py.

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: conformer_reader.ConformerReader

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: shape_generator.ShapeGenerator

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]