Source code for buildamol.extensions.bio.glycans.iupac
"""
Functions to work with the IUPAC glycan nomenclature.
"""
[docs]
class IUPACParser:
"""
A parser for condensed IUPAC glycan nomenclature strings. This class will generate
a list of connecting glycan segments from a string from which a Molecule can be built.
"""
def __init__(self):
self._string = ""
self.reset()
@property
def _current(self):
return self._string[-self._idx]
@property
def _next(self):
return self._string[-self._idx - 1]
@property
def _can_shift(self):
return self._idx < len(self._string)
@property
def _is_at_bracket(self):
return self._current in ("(", ")")
@property
def _is_at_open_square_bracket(self):
return self._current == "]"
@property
def _is_at_close_square_bracket(self):
return self._current == "["
@property
def _can_store(self):
return (
not self._is_still_parsing
and len(self._latest_residue) >= 1
and len(self._latest_linkage) >= 3
and len(self._second_latest_residue) >= 1
)
@property
def _is_still_parsing(self):
if not self._can_shift:
return False
return self._current not in ("(", ")", "[", "]")
[docs]
def parse(self, string):
"""
Parse a string of IUPAC glycan nomenclature into a list of glycan segments.
Parameters
----------
string : str
The IUPAC glycan nomenclature string.
Returns
-------
list
A list of tuples where each segment is a tuple of (residue1, residue2, linkage).
"""
self._string = self._prep_greek_letters(string)
self.reset()
self._parse()
self._glycan = self._adjust_betas(self._glycan)
return self._glycan
[docs]
def reset(self):
"""
Reset the parser.
"""
self._glycan = []
self._idx = 1
self._residue_counts = {}
self._past_residue_before_square_bracket = []
self._past_conformations_before_square_bracket = []
self._latest_residue = ""
self._latest_conformation = ""
self._latest_linkage = ""
self._second_latest_residue = ""
self._second_latest_conformation = ""
# self._latest_residue_before_square_bracket = ""
# self._latest_conformation_before_square_bracket = ""
@property
def _latest_residue_before_square_bracket(self):
return self._past_residue_before_square_bracket[-1]
@property
def _latest_conformation_before_square_bracket(self):
return self._past_conformations_before_square_bracket[-1]
def _push_residue_before_square_bracket(self, residue):
self._past_residue_before_square_bracket.append(residue)
def _push_conformation_before_square_bracket(self, conformation):
self._past_conformations_before_square_bracket.append(conformation)
def _pop_residue_before_square_bracket(self):
return self._past_residue_before_square_bracket.pop()
def _pop_conformation_before_square_bracket(self):
return self._past_conformations_before_square_bracket.pop()
def _shift(self):
self._idx += 1
def _shift_residue(self):
self._second_latest_residue = self._latest_residue
self._latest_residue = ""
self._second_latest_conformation = self._latest_conformation
self._latest_conformation = ""
def _parse(self):
self._crop_end()
while self._can_shift:
if self._can_store:
self._store()
continue
if self._is_at_bracket:
self._shift_residue()
self._latest_linkage = self._parse_linkage()
self._shift()
continue
if self._is_at_open_square_bracket:
_latest_residue_before_square_bracket = self._fit_residue(
self._latest_residue, increase_count=False
)
self._latest_residue = _latest_residue_before_square_bracket
self._push_residue_before_square_bracket(self._latest_residue)
self._push_conformation_before_square_bracket(self._latest_conformation)
# self._latest_conformation_before_square_bracket = (
# self._latest_conformation
# )
self._shift()
continue
if self._is_at_close_square_bracket:
self._latest_residue = self._pop_residue_before_square_bracket()
self._latest_conformation = (
self._pop_conformation_before_square_bracket()
)
# self._latest_residue = self._latest_residue_before_square_bracket
# self._latest_conformation = (
# self._latest_conformation_before_square_bracket
# )
self._second_latest_residue = ""
self._second_latest_conformation = ""
self._shift()
continue
self._latest_residue += self._current
self._shift()
self._latest_residue += self._current
self._store()
def _store(self):
second = self._second_latest_residue
if "@" not in second:
second = self._fit_residue(second)
self._second_latest_residue = second
latest = self._latest_residue
if not "@" in latest:
latest = self._fit_residue(latest)
self._latest_residue = latest
branch = (second, latest, self._reformat_link(self._latest_linkage))
self._glycan.append(branch)
self._latest_linkage = ""
def _fit_residue(self, r, increase_count=True):
if "@" in r:
return r
r = r[::-1]
if r in self._residue_counts:
if increase_count:
self._residue_counts[r] += 1
r += "@" + str(self._residue_counts[r])
else:
self._residue_counts[r] = 1
r += "@1"
return r
def _parse_linkage(self):
self._shift()
linkage = ""
while self._can_shift and not self._is_at_bracket:
linkage += self._current
self._shift()
self._latest_conformation = linkage[-1]
linkage = linkage[:-1]
return linkage
def _crop_end(self):
if self._string[-1] == "-":
while self._next != "(":
self._shift()
self._latest_conformation = self._current
self._shift()
self._string = self._string[: -self._idx]
self._idx = 1
else:
self._latest_conformation = (
"a" # assume alpha conformation if not specified
)
def _reformat_link(self, link):
if "-" not in link:
return link[::-1]
link = link[::-1].replace("-", "")
link = link + self._second_latest_conformation + self._latest_conformation
return link
def _prep_greek_letters(self, string):
string = string.replace("α", "a").replace("β", "b")
return string
def _adjust_betas(self, segments):
for i in range(len(segments)):
a, b, link = segments[i]
if link[2] == "b" and not a.startswith("b-"):
a = "b-" + a
if link[3] == "b" and not b.startswith("b-"):
b = "b-" + b
segments[i] = (a, b, link)
return segments
def __call__(self, *args, **kwds):
return self.parse(*args, **kwds)
if __name__ == "__main__":
parser = IUPACParser()
segments = parser("Gal(b1-4)[Gal(b2-2)Glc(b1-6)]GlcNAc")
