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.
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schrodinger.application.phase.packages.shape_screen_gpu_generate.
add_jobcontrol_arguments
(parser)¶ Adds job control and standard arguments to the
parser
.
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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.
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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)
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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)
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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
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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)
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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.
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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)
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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.
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schrodinger.application.phase.packages.shape_screen_gpu_generate.
shape_generate
(args)¶ Parameters: args (argparse.Namespace) – Namespace that holds command line arguments.