schrodinger.application.phase.packages.shape_creation_logic module¶
Creation of “binary shape files” from several kind of sources (PHASE-2070).
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schrodinger.application.phase.packages.shape_creation_logic.add_arguments(p)¶ Adds shape-creation-specific arguments to the parser.
Parameters: p (argparser.ArgumentParser) – Parser-like instance.
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schrodinger.application.phase.packages.shape_creation_logic.validate_args(args)¶ Validates command-line arguments added by
add_arguments.Parameters: args (argparse.Namespace) – Namespace holding command line options. Returns: Tuple of validation success and error message. Return type: (bool, str)
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schrodinger.application.phase.packages.shape_creation_logic.runtimize_paths(args)¶ Runtimizes input file paths for the command line arguments.
Parameters: args (argparse.Namespace) – Namespace populated with command line arguments.
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schrodinger.application.phase.packages.shape_creation_logic.get_input_files(args)¶ Identifies input files among arguments (for job control purposes).
Parameters: args (argparse.Namespace) – Namespace populated with command line arguments.
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schrodinger.application.phase.packages.shape_creation_logic.get_jobname_and_outfile(args)¶ Returns the job name and job name-derived output file name. If job name is not provided it gets derived from the input file name.
Parameters: args (argparse.Namespace) – Namespace populated with command line arguments. Returns: job name, output file name Return type: str, str
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class
schrodinger.application.phase.packages.shape_creation_logic.ShapeCreator(args)¶ Bases:
object-
__init__(args)¶ Expects validated and runtimized command line arguments.
Parameters: args (argparse.Namespace) – Namespace populated with command line arguments.
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getMetadata()¶ Returns JSON-able representation of the
self.
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schrodinger.application.phase.packages.shape_creation_logic.validate_shape_data_file_metadata(meta)¶ Validates shape data file metadata.
Parameters: meta (dict) – Shape data file metadata. Returns: Validation outcome and complain (if any). Return type: (bool, str)
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schrodinger.application.phase.packages.shape_creation_logic.validate_shape_data_file_metadata_compatibility(meta1, meta2)¶ Validates shape data file metadata compatibility.
Parameters: - meta1 (dict) – Validated shape data file metadata #1.
- meta2 (dict) – Validated shape data file metadata #2.
Returns: Validation outcome and complain (if any).
Return type: (bool, str)
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schrodinger.application.phase.packages.shape_creation_logic.execute(args)¶ The “main” subroutine for the “create” task.
Parameters: args (argparse.Namespace) – Namespace populated with command line arguments.