"""A parser for reaction formulae."""
# The MIT License (MIT)
#
# Copyright (c) 2018 Institute for Molecular Systems Biology, ETH Zurich.
# Copyright (c) 2018 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
from typing import Any, List, Tuple
import pyparsing
[docs]
POSSIBLE_REACTION_ARROWS = (
# Three-character arrows.
"<=>",
"<->",
"-->",
"<--",
# Two-character arrows.
"=>",
"<=",
"->",
"<-",
# Single character unicode arrows.
"=",
"⇌",
"⇀",
"⇋",
"↽",
)
def _parsed_compound(c_list: List[Any]) -> Tuple[float, str]:
"""Convert a list of ."""
if len(c_list) == 2:
return c_list[0], c_list[1]
elif len(c_list) == 1:
return 1.0, c_list[0]
else:
raise ValueError(f"Error while parsing this compound field: {str(c_list)}")
def _make_reaction_side_parser() -> pyparsing.Forward:
"""Build a parser for one side of a reaction.
Coefficients are usually integral, but they can be floats or fractions too.
Returns
-------
parser : pyparsing.Forward
"""
#
int_coeff = pyparsing.Word(pyparsing.nums)
float_coeff = pyparsing.Word(pyparsing.nums + "." + pyparsing.nums)
frac_coeff = int_coeff + "/" + int_coeff
int_coeff.setParseAction(lambda i: int(i[0]))
float_coeff.setParseAction(lambda t: float(t[0]))
frac_coeff.setParseAction(lambda f: float(f[0]) / float(f[2]))
coeff = pyparsing.Or([int_coeff, float_coeff, frac_coeff])
optional_coeff = pyparsing.Optional(coeff)
compound_separator = pyparsing.Literal("+").suppress()
compound_name_component = pyparsing.Word(
pyparsing.alphanums + "()", pyparsing.alphanums + "-+,()'_"
)
compound_name = pyparsing.Forward()
compound_name << (
compound_name_component + pyparsing.ZeroOrMore(compound_name_component)
)
compound_name.setParseAction(lambda s: " ".join(s))
compound_with_coeff = pyparsing.Forward()
compound_with_coeff << ((optional_coeff + compound_name) | compound_name)
compound_with_coeff.setParseAction(_parsed_compound)
compound_with_coeff.setResultsName("compound")
compound_with_separator = pyparsing.Forward()
compound_with_separator << (compound_with_coeff + compound_separator)
reaction_side = pyparsing.Forward()
reaction_side << (
pyparsing.ZeroOrMore(compound_with_separator) + compound_with_coeff
)
reaction_side.setParseAction(lambda _list: [_list])
reaction_side.setResultsName("reaction_side")
return reaction_side
[docs]
def make_reaction_parser() -> pyparsing.Forward:
"""Build pyparsing-based recursive descent parser for chemical reactions.
Returns
-------
parser : pyparsing.Forward
"""
reaction_side = _make_reaction_side_parser()
side_separators = [pyparsing.Literal(s) for s in POSSIBLE_REACTION_ARROWS]
side_separator = pyparsing.Or(side_separators)
reaction = pyparsing.Forward()
reaction << (reaction_side + side_separator + reaction_side)
return reaction