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 argument 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_input_files(args)
schrodinger.application.phase.packages.shape_screen_gpu_generate.get_jobname_and_outfile(args)
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_shapes_file_stats(filename)

Returns number of entries (molecules) and number of shapes stored in filename.

Parameters:filename (str) – Shape file name.
Returns:Number of entries, number of shapes
Return type:(int, int)
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, and not ‘-source’.
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, subjob_argv, nstructs, disable_smart_distribution=False)

Splits input and runs subjobs for each piece.

Returns:Subjob names.
Return type:list(str)
schrodinger.application.phase.packages.shape_screen_gpu_generate.estimate_shape_data_size(args)

Estimates number of bytes occupied on average by shapes/conformers of a single input molecule.

Parameters:args (argparse.Namespace) – Namespace that holds (validated) command line arguments.
Returns:Shape data size for a single molecule (in bytes).
Return type:int
schrodinger.application.phase.packages.shape_screen_gpu_generate.distribute_one(args, be_argv)

The “main” function for the first-level distributed execution: slice input into chunks to limit resulting shape file sizes.

Parameters:
  • args (argparse.Namespace) – Namespace that holds (validated) command line arguments.
  • be_argv (list(str)) – Backend command line arguments (not parsed).
schrodinger.application.phase.packages.shape_screen_gpu_generate.distribute_two(args, be_argv)

The “main” function for the second-level distributed execution: slice input to maximize throughput, merge shapes returned by the subjobs.

Parameters:
  • args (argparse.Namespace) – Namespace that holds (validated) command line arguments.
  • be_argv (list(str)) – Backend command line arguments (not parsed).
schrodinger.application.phase.packages.shape_screen_gpu_generate.shape_generate(args)