schrodinger.application.phase.packages.shape_screen_arg_utils module

Does argument parsing and validation for shape_screen_driver.py. For clarity, the term “fast” is synonymous with the default way of screening, wherein the fast_shape.cpp backend is invoked. This in contrast to “classic” screens, wherein the shape_screen.cpp backend is invoked.

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schrodinger.application.phase.packages.shape_screen_arg_utils.add_alignment_args(parser: argparse.ArgumentParser) → None

Adds arguments that override the default method of aligning structures.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_conf_treatment_args(parser: argparse.ArgumentParser) → None

Adds options for conformer generation and treatment.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_database_screening_args(parser: argparse.ArgumentParser) → None

Adds arguments that are supported only when screening a Phase database.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_file_screening_args(parser: argparse.ArgumentParser) → None

Adds arguments that control perception of conformers when Maestro or SD files are screened.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_filtering_args(parser: argparse.ArgumentParser) → None

Adds arguments that control the elimination of output alignments.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_jobcontrol_args(parser: argparse.ArgumentParser) → None

Adds job control arguments.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_reporting_args(parser: argparse.ArgumentParser) → None

Adds arguments that control the output of alignments and other information that’s reported.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_required_args(parser: argparse.ArgumentParser) → None

Adds required arguments.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_shape_treatment_args(parser: argparse.ArgumentParser) → None

Adds arguments that control the manner in which the shape of a structure is represented.

schrodinger.application.phase.packages.shape_screen_arg_utils.add_sim_algorithm_args(parser: argparse.ArgumentParser) → None

Adds arguments that control the basic algorithm used to compute similarities.

schrodinger.application.phase.packages.shape_screen_arg_utils.get_parser() → argparse.ArgumentParser

Creates argparse.ArgumentParser with supported command line options.

schrodinger.application.phase.packages.shape_screen_arg_utils.is_core_hopping_job(shape: str) → bool

Returns True if the provided shape is a Maestro or SD file that contains SHAPE_CORE_HOPPING_PROPERTY. Raises a phase_utils.MissingInputFileError if shape is a Maestro or SD file that doesn’t exist.

schrodinger.application.phase.packages.shape_screen_arg_utils.must_run_classic_screen(args: argparse.Namespace) → bool

Returns True if a classic shape screen must be run. Raises a phase_utils.MissingInputFileError if a call to is_core_hopping_job() is made and the shape query file isn’t found. This can happen before argument validation, which isn’t ideal, but it’s a necessary evil since the screening mode must be determined before argument validation can be done.

schrodinger.application.phase.packages.shape_screen_arg_utils.prepare_for_backend(argv: List[str], classic: bool) → List[str]

Given a command line generated by prepare_for_parsing() and whether a classic job is being run, this function generates arguments that can be used to invoke either the fast_shape or shape_screen C++ binary. The supplied command should have already undergone validation unless the returned command will be supplied to the applicable binary with the -check flag (i.e., to validate).

schrodinger.application.phase.packages.shape_screen_arg_utils.prepare_for_parsing(argv: List[str]) → List[str]

Given a raw command line that does not include the shape_screen wrapper script, this function generates arguments that can be safely parsed using the ArgumentParser returned by get_parser().

schrodinger.application.phase.packages.shape_screen_arg_utils.validate_args(argv: List[str], classic: bool) → Tuple[bool, str]

Given a command line generated by prepare_for_parsing() and whether a classic job is to be run, this function validates the command line by invoking the fast_shape or shape_screen C++ binary with the -check flag. Returns a tuple of validity and a non-empty error message if not valid.