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jade.basic.path.get_database_testing_path()[source]¶ Get the path to the database testing file. :return:
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jade.basic.path.get_decoy_extension(decoy)[source]¶ Return the extension of the decoy. .pdb, .pdb.gz, .cif, .cif.gz, etc. :param decoy: str :rtype: str
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jade.basic.path.get_decoy_name(decoy)[source]¶ Get the decoy name from path or name, whether .pdb, .pdb.gz or no extension. :param decoy: :rtype:str
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jade.basic.path.get_decoy_path(decoy, alternate_paths=None)[source]¶ Search .pdb, .pdb.gz, .cif, .cif.gz, .xml, .xml.gz In addition, Search alternative search paths. Return found path or NONE.
Parameters: - decoy –
- alternate_paths –
:rtype:str
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jade.basic.path.get_directories_recursively(inpath)[source]¶ Get a list of directories recursively in a path. Skips hidden directories. :param inpath: str :rtype: list
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jade.basic.path.get_file_paths(pattern, dir, ext='.pdb')[source]¶ Get file paths matching the exact pattern and extension. :param pattern: :param dir: :param ext: :return:
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jade.basic.path.get_make_get_dirs(root, dirs)[source]¶ Recursively make dirs and return the final path :param root: :param dirs: :rtype: str
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jade.basic.path.get_matching_pdbs(directory, pattern, ext='.pdb')[source]¶ Get pdbs in a directory matching a pattern. :param directory: :param pattern: :param ext: :return:
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jade.basic.path.get_rosetta_features_root()[source]¶ Get the path to Rosetta features directory through set ROSETTA3_DB env variable. :rtype: str
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jade.basic.path.get_rosetta_features_run_script()[source]¶ Get the path to Rosetta features script dir through the set ROSETTA3_DB env variable. :rtype: str
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jade.basic.path.get_testing_inputs_path()[source]¶ Get the path to testing inputs (PDBs,fasta,etc.) :rtype:str
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jade.basic.path.get_xml_scripts_path()[source]¶ Get the path to the Rosetta xml script directory. Useful for variable substitutions. :rtype: str