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.