schrodinger.application.phase.packages.shape_screen_gpu_generate module

Utility to generate Shape data files (.bin) suitable for GPU Shape screening. Shape data files include representation of molecular shapes along with the corresponding chemical structures.

schrodinger.application.phase.packages.shape_screen_gpu_generate.add_jobcontrol_arguments(parser)

Adds job control and standard arguments to the parser.

schrodinger.application.phase.packages.shape_screen_gpu_generate.add_generate_arguments(parser)

Adds shape generation arguments to the parser.

Parameters:parser (argparse.ArgumentParser) – Command line arguments parser.
schrodinger.application.phase.packages.shape_screen_gpu_generate.validate_jobcontrol_args(args)

Checks job control command line arguments.

Parameters:args (argparse.Namespace) – Namespace holding the command line options.
Returns:Tuple of validation success and error message.
Return type:(bool, str)
schrodinger.application.phase.packages.shape_screen_gpu_generate.validate_generate_args(args)

Checks generate task command line arguments.

Parameters:args (argparse.Namespace) – Namespace holding the command line options.
Returns:Tuple of validation success and error message.
Return type:(bool, str)
schrodinger.application.phase.packages.shape_screen_gpu_generate.get_shapes_file_metadata(filename)

Reads metadata from shape data file and parses it from JSON.

Parameters:filename (str) – Shape file name.
Returns:Deserialized shape file metadata.
Return type:dict
schrodinger.application.phase.packages.shape_screen_gpu_generate.get_backend_argv(argv=None)

Isolates backend command line arguments.

Parameters:argv (list(str)) – Command line arguments (not including script name).
Returns:Arguments that are not job-control related, not ‘-source’, ‘-shape_data_dir’, or ‘-shape_data_treatment’.
Return type:list(str)
schrodinger.application.phase.packages.shape_screen_gpu_generate.echo_log_files(subjobnames)

Echoes subjob log files content.

Parameters:subjobnames (list(str)) – Names of the subjobs to consider.
schrodinger.application.phase.packages.shape_screen_gpu_generate.split_input_and_run_subjobs(args, nstructs)

Splits input and runs subjobs for each piece.

Returns:Subjob names.
Return type:list(str)
schrodinger.application.phase.packages.shape_screen_gpu_generate.run_distributed(args, nstructs)
Parameters:
  • args (argparse.Namespace) – Namespace that holds (validated) command line arguments.
  • nstructs (int) – Number of structures per subjob.
schrodinger.application.phase.packages.shape_screen_gpu_generate.shape_generate(args)
Parameters:args (argparse.Namespace) – Namespace that holds command line arguments.