from glypy.composition.structure_composition import substituent_compositions from glypy.composition.composition_transform import has_derivatization, derivatize from glypy.io import format_constants_map from glypy.io.nomenclature import identity from glypy.utils import invert_dict from glypy.io.file_utils import ParserInterface, ParserError # A static copy of monosaccharide names to structures for copy-free comparison monosaccharide_reference = {k: v for k, v in named_structures.monosaccharides.items()} anomer_map_from = dict(format_constants_map.anomer_map) anomer_map_from['?'] = anomer_map_from.pop('x') anomer_map_to = invert_dict(anomer_map_from) anomer_map_from['beta'] = anomer_map_from['b'] anomer_map_from['alpha'] = anomer_map_from['a'] Stem = constants.Stem Configuration = constants.Configuration Modification = constants.Modification SuperClass = constants.SuperClass def tryint(i): try: return int(i) except ValueError: return -1
("Kdo", "W"), ("GalA", "L"), ("IdoA", "I"), ("Rha", "H"), ("Fuc", "F"), ("Xyl", "X"), ("Rib", "B"), ("Ara", "R"), ("GlcA", "U"), ("All", 'O'), ("Api", 'P'), ("Fru", "E") )) #: A mapping from symbol to common monosaccharide name monosaccharides_from = invert_dict(dict(monosaccharides_to)) #: A mapping from common substituent names to symbol substituents_to = { 'amino': 'Q', 'ethanolominephosphate': 'PE', 'inositol': "IN", 'methyl': "ME", 'n_acetyl': 'N', 'o_acetyl': 'T', 'phosphate': 'P', 'phosphocholine': "PC", 'pyruvate': 'PYR', 'sulfate': 'S', 'sulfide': 'SH', '2-aminoethylphosphonic acid': 'EP'