schrodinger.application.phase.packages.phase_screen_utils module¶
Module with common functionality for Phase screening backends.
Copyright Schrodinger LLC, All Rights Reserved.
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schrodinger.application.phase.packages.phase_screen_utils.
add_database_options
(parser)¶ Adds database screening options to the provided parser and returns the argument group object that holds those options.
Parameters: parser (argparser.ArgumentParser) – Argument parser object Returns: Argument group object Return type: argparse._ArgumentGroup
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schrodinger.application.phase.packages.phase_screen_utils.
add_reporting_options
(parser, sort_prop)¶ Adds reporting options to the provided parser and returns the argument group object that holds those options.
Parameters: - parser (argparser.ArgumentParser) – Argument parser object
- sort_prop (str) – Sort property name to display in help message
Returns: Argument group object
Return type: argparse._ArgumentGroup
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schrodinger.application.phase.packages.phase_screen_utils.
combine_hit_files
(hit_files_in, hit_file_out, max_hits=None, sort_prop=None)¶ Combines a list of hit files.
Parameters: - hit_files_in (list(str)) – Hit files to combine (Maestro format)
- hit_file_out – Destination hit file (Maestro or SD format)
- max_hits – Maximum number of sorted hits, or None if not sorting
Sort_prop: CT-level property for decreasing sort, or None if not sorting
Type: sort_prop: str
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schrodinger.application.phase.packages.phase_screen_utils.
get_max_hits
(args)¶ Returns the maximum number of hits to keep.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line options Returns: Maximum number of hits Return type: int
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schrodinger.application.phase.packages.phase_screen_utils.
get_subset_file
(args)¶ Returns the name of the input subset file if -isub was specified on the the command line. The leading path to the subset file is not modified. Returns an empty string if -isub was not specified.
Parameters: args (argparse.Namespace) – Command line arguments Returns: Subset file name or empty string Return type: str
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schrodinger.application.phase.packages.phase_screen_utils.
run_glide_sort
(hit_files, hit_file_out, max_hits, sort_prop)¶ Invokes glide_sort to sort subjob hit_files by decreasing group fitness.
Parameters: - hit_files (list(str)) – Subjob hit files in Maestro format
- hit_file_out (str) – Output hit file (*.maegz)
- max_hits (int) – Number of hits to keep
- sort_prop (str) – CT-level property for decreasing sort
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schrodinger.application.phase.packages.phase_screen_utils.
validate_source_dbs
(source_dbs)¶ Checks the validity of Phase databases to be screened. Existence is checked only if the current process is running under job control.
Parameters: source_dbs (list(str)) – Phase database names Returns: tuple of validity and error message if not valid Return type: bool, str
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schrodinger.application.phase.packages.phase_screen_utils.
validate_subset
(args)¶ Checks for the existence of the input subset file, where we allow it to be missing at startup time only if it’s specified using an absolute path.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line options Returns: tuple of validity and error message if required file is missing Return type: bool, str