"""
These are name mappings for glycan residues between their PDB identifiers and IUPAC names.
"""
__pdb_id_to_iupac_name_mapping__ = {
"TNO": "TalN",
"KDO": "Kdo",
"KDM": "Kdn",
"KDN": "b-Kdn",
"NDG": "GlcNAc",
"NGZ": "GlcNAc",
"NAG": "b-GlcNAc",
"MUB": "MurNAc",
"AMU": "b-MurNAc",
"PSE": "Pse",
"Z0F": "Ido",
"ZCD": "Ido",
"4N2": "b-Ido",
"AL1": "AltN",
"6AN": "6dAltNAc",
"ADA": "GalA",
"GTK": "b-GalA",
"GTR": "b-GalA",
"TLO": "TalNAc",
"66O": "6dGul",
"4LG": "4eLeg",
"A0N": "AllN",
"QUN": "QuiNAc",
"Z9W": "QuiNAc",
"4LC": "MurNGc",
"AFD": "All",
"Z2D": "All",
"ALL": "b-All",
"WOO": "b-All",
"BM3": "ManNAc",
"BM7": "b-ManNAc",
"GLA": "Gal",
"GXL": "Gal",
"GAL": "b-Gal",
"GIV": "b-Gal",
"GZL": "b-Gal",
"DHA": "Dha",
"Z3U": "Dig",
"HSY": "Xyl",
"XYS": "Xyl",
"LXC": "b-Xyl",
"XYP": "b-Xyl",
"XYZ": "b-Xyl",
"T6T": "Tag",
"LXB": "b-GulNAc",
"TYV": "Tyv",
"95Z": "ManN",
"ABE": "Abe",
"GCU": "GlcA",
"BDP": "b-GlcA",
"MUR": "b-Mur",
"1S4": "b-Mur",
"A2G": "GalNAc",
"YYQ": "GalNAc",
"NGA": "b-GalNAc",
"IIO": "IdoN",
"PZU": "Par",
"4GL": "Gul",
"GUP": "Gul",
"GL0": "b-Gul",
"Z8H": "b-Gul",
"GUN": "GulN",
"PA1": "GlcN",
"GCS": "b-GlcN",
"GLC": "Glc",
"BGC": "b-Glc",
"Z8T": "b-Glc",
"IDR": "IdoA",
"LEG": "Leg",
"289": "DDmanHep",
"A5C": "Tal",
"SDY": "b-Tal",
"ZEE": "b-Tal",
"MAN": "Man",
"BMA": "b-Man",
"DDA": "Oli",
"RAE": "Oli",
"Z5J": "b-Oli",
"ACI": "Aci",
"LGU": "GulA",
"SHD": "Alt",
"Z6H": "Alt",
"3MK": "b-Alt",
"SIA": "Neu5Ac",
"SLB": "b-Neu5Ac",
"GMH": "LDmanHep",
"NEX": "Neu",
"Z9N": "Fru",
"BDF": "b-Fru",
"FRU": "b-Fru",
"LFR": "b-Fru",
"COL": "Col",
"MAV": "ManA",
"BEM": "b-ManA",
"6TT": "6dTal",
"BAC": "Bac",
"B6D": "Bac",
"X6X": "GalN",
"1GN": "b-GalN",
"RIB": "Rib",
"YYM": "Rib",
"Z6J": "Rib",
"0MK": "b-Rib",
"32O": "b-Rib",
"BDR": "b-Rib",
"RIP": "b-Rib",
"API": "Api",
"XXM": "b-Api",
"64K": "Ara",
"AHR": "Ara",
"ARA": "Ara",
"BXY": "Ara",
"ARB": "b-Ara",
"BXX": "b-Ara",
"FUB": "b-Ara",
"SEJ": "b-Ara",
"FCA": "Fuc",
"FUC": "Fuc",
"FCB": "b-Fuc",
"FUL": "b-Fuc",
"GYE": "b-Fuc",
"ATN": "AltNAc",
"AUA": "AllA",
"NAA": "b-AllNAc",
"6TN": "6dTalNAc",
"SOE": "Sor",
"UEA": "b-Sor",
"G6D": "Qui",
"YYK": "b-Qui",
"X1X": "TalA",
"X0X": "b-TalA",
"PSV": "Psi",
"SF6": "Psi",
"SF9": "b-Psi",
"TTV": "b-Psi",
"RAM": "Rha",
"XXR": "Rha",
"RM4": "b-Rha",
"6AT": "6dAlt",
"NGC": "Neu5Gc",
"NGE": "b-Neu5Gc",
"LDY": "Lyx",
"Z4W": "b-Lyx",
"HSQ": "IdoNAc",
"LXZ": "IdoNAc",
"UNF": "FucNAc",
"49T": "b-FucNAc",
"ATA": "AltA",
}
# just in case someone external has already incorporated this
__pdb_id_to_name_mapping__ = __pdb_id_to_iupac_name_mapping__
"""
WARNING: This is deprecated, use `__pdb_id_to_iupac_name_mapping__` instead.
"""
__iupac_name_to_pdb_id_mapping__ = {
value: key for key, value in __pdb_id_to_iupac_name_mapping__.items()
}
__beta_compounds_pdb_ids__ = set(
[
key
for key, value in __pdb_id_to_iupac_name_mapping__.items()
if value.startswith("b-")
]
)
"""
A set of PDB ids for monosaccharides that are beta-configured.
"""
[docs]
def id_to_name(id: str) -> str:
"""
Translate a monosaccharide PDB id to a name
Parameters
----------
id: str
The PDB id of the monosaccharide
Returns
-------
str
The name of the monosaccharide.
If the id is not found, it is returned as is.
"""
return __pdb_id_to_iupac_name_mapping__.get(id, id)
[docs]
def is_beta(id: str) -> bool:
"""
Check if a monosaccharide PDB id is beta-configured.
Parameters
----------
id: str
The PDB id of the monosaccharide
Returns
-------
bool
True if the monosaccharide is beta-configured, False otherwise.
"""
return id in __beta_compounds_pdb_ids__
