def drop_positions(residue):
if _resolve_special_base_type(residue) is None:
modifications = OrderedMultiMap()
for k, v in residue.modifications.items():
modifications[-1] = v
residue.modifications = modifications
for p, link in list(residue.substituent_links.items()):
link.break_link(refund=True)
link.parent_position = -1
link.apply()
def to_iupac_lite(residue):
"""
Encode a subset of traits of a :class:`Monosaccharide`-like object
using a limited subset of the IUPAC three letter code. The information
present is sufficient to reconstruct a :class:`MonosaccharideResidue` instance
reflecting the base type and its native substituents and modificats.
.. note::
This function is not suitable for use on whole |Glycan| objects. Instead,
see :meth:`GlycanComposition.from_glycan` and :meth:`GlycanComposition.serialize`
Parameters
----------
residue: Monosaccharide
The object to be encoded
Returns
-------
str
See Also
--------
:func:`from_iupac_lite`
"""
if isinstance(residue, (SubstituentResidue, MolecularComposition)):
return residue.to_iupac_lite()
template = "{modification}{base_type}{substituent}"
modification = ""
base_type = _resolve_special_base_type(residue)
if base_type is None:
if residue.stem[0] is not Stem.Unknown:
base_type = residue.stem[0].name.title()
else:
base_type = residue.superclass.name.title()
# Omit unknown coordinates on modifications and substituents
modification = extract_modifications(residue.modifications, base_type).replace("-1-", "")
substituent = resolve_substituent(residue).replace("-1", "")
return template.format(
modification=modification,
base_type=base_type,
substituent=substituent
)
def from_monosaccharide(cls, monosaccharide, configuration=False, stem=True, ring=False):
"""Construct an instance of :class:`MonosaccharideResidue` from an instance
of |Monosaccharide|. This function attempts to preserve derivatization if possible.
This function will create a *deep copy* of `monosaccharide`.
Parameters
----------
monosaccharide : Monosaccharide
The monosaccharide to be converted
configuration : bool, optional
Whether or not to preserve |Configuration|. Defaults to |False|
stem : bool, optional
Whether or not to preserve |Stem|. Defaults to |True|
ring : bool, optional
Whether or not to preserve |RingType|. Defaults to |False|
Returns
-------
MonosaccharideResidue
"""
residue = monosaccharide.clone(monosaccharide_type=cls)
premass = residue.mass()
deriv = has_derivatization(monosaccharide)
strip_derivatization(residue)
if _resolve_special_base_type(monosaccharide) is None:
if not configuration:
residue.configuration = (Configuration.x,)
if not stem:
residue.stem = (Stem.x,)
if not ring:
residue.ring_start = residue.ring_end = None
if deriv:
derivatize(residue, deriv)
if residue.mass() != premass and not deriv:
residue.composition += water_composition
return residue
def drop_configuration(residue):
if _resolve_special_base_type(residue) is None:
residue.configuration = (None,)
def drop_stem(residue):
if _resolve_special_base_type(residue) is None:
residue.stem = (None,)
