schrodinger.application.phase.packages.hypo_refine.option_utils module¶

Module with phase_hypo_refine option parsing and validation functionality.

schrodinger.application.phase.packages.hypo_refine.option_utils.add_project_creation_options(parser)¶

Adds project creation options to the provided parser.

Parameters:	parser (argparser.ArgumentParser) – Argument parser object.

schrodinger.application.phase.packages.hypo_refine.option_utils.add_refinement_options(parser)¶

Adds hypothesis refinement options to the provided parser.

Parameters:	parser (argparser.ArgumentParser) – Argument parser object.

schrodinger.application.phase.packages.hypo_refine.option_utils.get_parser()¶

Creates argparse.ArgumentParser with supported command line options.

Returns:	Argument parser object
Return type:	argparser.ArgumentParser

schrodinger.application.phase.packages.hypo_refine.option_utils.validate_actives_decoys(args)¶

Checks the validity of <actives>, <decoys>, and, if applicable, <actives2> and <decoys2>.

Parameters:	args (argparser.Namespace) – argparser.Namespace with command line arguments
Returns:	tuple of validity and non-empty error message if not valid
Return type:	bool, str

schrodinger.application.phase.packages.hypo_refine.option_utils.validate_args(args)¶

Checks the validity of command line arguments.

Parameters:	args (argparser.Namespace) – argparser.Namespace with command line arguments
Returns:	tuple of validity and non-empty error message if not valid
Return type:	bool, str

schrodinger.application.phase.packages.hypo_refine.option_utils.validate_hypo(args)¶

Checks the validity of hypothesis.

Parameters:	args (argparser.Namespace) – argparser.Namespace with command line arguments
Returns:	tuple of validity and non-empty error message if not valid
Return type:	bool, str

schrodinger.application.phase.packages.hypo_refine.option_utils.validate_project_creation_options(args)¶

Checks the validity of project creation options.

Parameters:	args (argparser.Namespace) – argparser.Namespace with command line arguments
Returns:	tuple of validity and non-empty error message if not valid
Return type:	bool, str

schrodinger.application.phase.packages.hypo_refine.option_utils.validate_project_fd(project_path, hypo_path)¶

Validates that the feature definitions in the provided zipped project are equivalent to those in the provided hypothesis.

Parameters:	project_path (str) – Path to zipped project file hypo_path (str) – Path to hypothesis file
Returns:	tuple of validity and non-empty error message if not valid
Return type:	bool, str

schrodinger.application.phase.packages.hypo_refine.option_utils.validate_project_sites(project_path)¶

Validates that the provided zipped project contains pharmacophores sites.

Parameters:	project_path (str) – Path to zipped project file
Returns:	tuple of validity and non-empty error message if not valid
Return type:	bool, str

schrodinger.application.phase.packages.hypo_refine.option_utils.validate_refinement_options(args)¶

Checks the validity of hypothesis refinement options.

Parameters:	args (argparser.Namespace) – argparser.Namespace with command line arguments
Returns:	tuple of validity and non-empty error message if not valid
Return type:	bool, str