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'