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