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        "author": "David Martin",
        "author_email": "d.m.a.martin@dundee.ac.uk",
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        "description": "David's useful Unimod Wrapper\r\n=============================\r\n\r\n\r\nThis is a simple python module to wrap the Unimod XML file in a readily \r\naccessible form for python programemrs. \r\nA copy of the unimod.xml file is included.\r\n\r\nDependencies\r\n============\r\nNo dependencies that are not in a standard >2.4 python distribution.\r\n\r\nUsage\r\n=====\r\n\r\n1. simple usage. Use the built in file. \r\n\r\n>>> import Unimod.unimod\r\n>>> db=Unimod.unimod.database\r\n\r\n2. Use your own file\r\n>>> import Unimod.Database\r\n>>> db=Unimod.Database.Database(file=\"my unimod file\")\r\n\r\n3.  Getting element info\r\nUse the get_element(label) method and a dictionary is returned.\r\n>>> db.get_element('H')\r\n{'avge_mass': '1.00794', 'title': 'H', 'full_name': 'Hydrogen', 'mono_mass': '1.007825035'}\r\n\r\nAll labels are supported, and additionally the common isotopes as labels as well\r\n\r\n>>> db.get_element('O')\r\n{'avge_mass': '15.9994', 'title': 'O', 'full_name': 'Oxygen', 'mono_mass': '15.99491463'}\r\n>>> db.get_element('18O')\r\n{'avge_mass': '17.9991603', 'title': '18O', 'full_name': 'Oxygen18', 'mono_mass': '17.9991603'}\r\n>>> db.get_element('16O')\r\n{'avge_mass': '15.9994', 'title': 'O', 'full_name': 'Oxygen', 'mono_mass': '15.99491463'}\r\n\r\n4. getting modification info\r\n\r\nUse the get_label(modification) method\r\n>>> db.get_label('Phospho')\r\n{'delta_mono_mass': '79.966331',\r\n'group_of_poster': 'admin', \r\n'delta_avge_mass': '79.9799', \r\n'username_of_poster': 'unimod', \r\n'title': 'Phospho', \r\n'delta_composition': 'H O(3) P', \r\n'sites': {\r\n    'C': {'position': 'Anywhere', 'hidden': 'true', 'site': 'C', 'classification': 'Post-translational', 'spec_group': '5'}, \r\n    'D': {'position': 'Anywhere', 'hidden': 'true', 'site': 'D', 'classification': 'Post-translational', 'spec_group': '3'}, \r\n    'H': {'position': 'Anywhere', 'hidden': 'true', 'site': 'H', 'classification': 'Post-translational', 'spec_group': '4'}, \r\n    'K': {'position': 'Anywhere', 'hidden': 'true', 'site': 'K', 'classification': 'Other', 'spec_group': '7'}, \r\n    'S': {'position': 'Anywhere', 'hidden': 'false', 'site': 'S', 'classification': 'Post-translational', 'spec_group': '1'}, \r\n    'R': {'position': 'Anywhere', 'hidden': 'true', 'site': 'R', 'classification': 'Post-translational', 'spec_group': '6'}, \r\n    'T': {'position': 'Anywhere', 'hidden': 'false', 'site': 'T', 'classification': 'Post-translational', 'spec_group': '1'}, \r\n    'Y': {'position': 'Anywhere', 'hidden': 'false', 'site': 'Y', 'classification': 'Post-translational', 'spec_group': '2'}\r\n}, \r\n'spec_group': {\r\n    '1': ['T', 'S'], \r\n    '3': ['D'], \r\n    '2': ['Y'], \r\n    '5': ['C'], \r\n    '4': ['H'], \r\n    '7': ['K'], \r\n    '6': ['R']\r\n}, \r\n'date_time_posted': '2002-08-19 19:17:11', \r\n'date_time_modified': '2011-11-25 10:55:54', \r\n'full_name': 'Phosphorylation', \r\n'record_id': '21', \r\n'approved': 'true'\r\n}\r\n\r\nIn this dictionary are two fields, 'sites' which contains info for each amino acid, and 'spec_group' which contains the specificity grouping for the modification.\r\n\r\n5. Searching for labels\r\nPass a regular expression in text form to the list_labels method.\r\n\r\n>>> db.list_labels('.*Phospho.*')\r\n['Phosphoguanosine', 'Phosphopantetheine', 'PhosphoHex', 'Phosphopropargyl', 'PhosphoribosyldephosphoCoA', 'PhosphoHexNAc', 'Phosphoadenosine', 'PhosphoUridine', 'Phosphogluconoylation', 'Label:13C(9)+Phospho', 'Phospho'] \r\n\r\nAuthor\r\n======\r\n\r\nDr David Martin, University of Dundee, UK. d.m.a.martin@dundee.ac.uk\r\n\r\nCopyright\r\n=========\r\n\r\n(c) David Martin 2012\r\n\r\nLicense\r\n=======\r\n\r\nUnimod data is redistributed under the terms of the licensing described on the \r\nUnimod website http://www.unimod.org - in short you can redistribute the data \r\nincluded as long as you permit unrestricted subsequent redistribution.\r\n\r\nThe software code is licensed under the Creative Commons Attribution License \r\nhttp://creativecommons.org/licenses/by/3.0/ You may use, alter and publish work\r\nbased on the code as long as you acknowledge the use of the code with an \r\nappropriate statement such as this in the copyright/attribution/help text: \"Includes the python Unimod wrapper by Dr David Martin, University of Dundee\".\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n",
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