#!/usr/bin/env python3
#
# parser.py
"""
Functions and parsing formulae.
.. latex:vspace:: -10px
"""
#
# Copyright (c) 2020 Dominic Davis-Foster <dominic@davis-foster.co.uk>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
# Based on Pyteomics (https://github.com/levitsky/pyteomics)
# | Copyright (c) 2011-2015, Anton Goloborodko & Lev Levitsky
# | Licensed under the Apache License, Version 2.0 (the "License");
# | you may not use this file except in compliance with the License.
# | You may obtain a copy of the License at
# |
# | http://www.apache.org/licenses/LICENSE-2.0
# |
# | Unless required by applicable law or agreed to in writing, software
# | distributed under the License is distributed on an "AS IS" BASIS,
# | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# | See the License for the specific language governing permissions and
# | limitations under the License.
# |
# | See also:
# | Goloborodko, A.A.; Levitsky, L.I.; Ivanov, M.V.; and Gorshkov, M.V. (2013)
# | "Pyteomics - a Python Framework for Exploratory Data Analysis and Rapid Software
# | Prototyping in Proteomics", Journal of The American Society for Mass Spectrometry,
# | 24(2), 301–304. DOI: `10.1007/s13361-012-0516-6 <http://dx.doi.org/10.1007/s13361-012-0516-6>`_
# |
# | Levitsky, L.I.; Klein, J.; Ivanov, M.V.; and Gorshkov, M.V. (2018)
# | "Pyteomics 4.0: five years of development of a Python proteomics framework",
# | Journal of Proteome Research.
# | DOI: `10.1021/acs.jproteome.8b00717 <http://dx.doi.org/10.1021/acs.jproteome.8b00717>`_
#
# Also based on ChemPy (https://github.com/bjodah/chempy)
# | Copyright (c) 2015-2018, Björn Dahlgren
# | All rights reserved.
# |
# | Redistribution and use in source and binary forms, with or without modification,
# | are permitted provided that the following conditions are met:
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# | list of conditions and the following disclaimer.
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# | list of conditions and the following disclaimer in the documentation and/or
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# | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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#
# stdlib
import re
from collections import defaultdict
from functools import lru_cache
from string import ascii_lowercase, ascii_uppercase
from typing import Dict, Iterable, List, Mapping, Optional, Sequence, Union
# 3rd party
import pyparsing # nodep
# this package
from chemistry_tools.elements import ELEMENTS
# this package
from ._parser_core import _formula_to_parts, _get_charge, _get_leading_integer
from .latex import _latex_mapping
__all__ = ["string_to_composition", "mass_from_composition"]
_atom = r"([A-Z][a-z+]*)(?:\[(\d+)\])?([+-]?\d+)?"
_atom_re = re.compile(_atom)
_formula_re = re.compile(fr"^({_atom})*$")
#: List of the relative atomic masses of each element, in order.
relative_atomic_masses: List[float] = [element.mass for element in ELEMENTS]
#: List of regular expressions for invalid formulae.
invalid_re: List[str]
#: List of regular expressions for matching elements in formulae.
element_re: List[str]
#: List of regular expressions for matching isotopes in formulae.
isotopes_re: List[str]
# Construct regular expression to match all elements, plus D and T
element_re_dict: Dict[str, List[str]] = {}
for element in (ELEMENTS.symbols + ['D', 'T']):
if len(element) == 1:
if element in element_re_dict:
element_re_dict[element].append('?')
else:
element_re_dict[element] = ['?']
else:
upper, lower = list(element)
if upper in element_re_dict:
element_re_dict[upper].append(lower)
else:
element_re_dict[upper] = [lower]
invalid_uppers = list(ascii_uppercase)
invalid_lowers = {upper: list(ascii_lowercase) for upper in list(ascii_uppercase)}
invalid_re = []
element_re = []
for upper, lowers in element_re_dict.items():
lowers = sorted(lowers)
if lowers == ['?']:
element_re.append(upper)
invalid_uppers.remove(upper)
elif len(lowers) == 1:
element_re.append(f"{upper}{lowers[0]}")
elif '?' in lowers:
lowers.remove('?')
invalid_uppers.remove(upper)
for lower in lowers:
invalid_lowers[upper].remove(lower)
element_re.append(f"(({upper}[{''.join(lowers)}]?)(?![{''.join(invalid_lowers[upper])}]))(?![a-z])")
invalid_re.append(f"{upper}[{''.join(lowers)}][{''.join(invalid_lowers[upper])}]+")
invalid_re.append(f"{upper}[{''.join(invalid_lowers[upper])}]+")
else:
invalid_uppers.remove(upper)
for lower in lowers:
invalid_lowers[upper].remove(lower)
element_re.append(f"({upper}[{''.join(lowers)}]?)(?![a-z])")
invalid_re.append(f"{upper}[{''.join(lowers)}][{''.join(invalid_lowers[upper])}]+")
invalid_re.append(f"{upper}[{''.join(invalid_lowers[upper])}]+")
# print(invalid_uppers, invalid_lowers)
element_re.sort()
# Isotopes either as [C12], C[12] or [12C]
isotopes_re = []
for elem in element_re:
isotopes_re.append(rf"\b{elem}\[[0-9]+\]")
isotopes_re.append(rf"\[{elem}[0-9]+\]")
isotopes_re.append(rf"\[[0-9]+{elem}\]")
@lru_cache()
def _get_formula_parser() -> pyparsing.Forward:
"""
Create a forward pyparsing parser for chemical formulae.
BNF for simple chemical formula (no nesting)
integer :: '0'..'9'+
element :: 'A'..'Z' 'a'..'z'*
term :: element [integer]
formula :: term+
BNF for nested chemical formula
integer :: '0'..'9'+
element :: 'A'..'Z' 'a'..'z'*
term :: (element | '(' formula ')') [integer]
formula :: term+
Notes
-----
Based on http://stackoverflow.com/a/18555142/790973
Copyright 2013 Paul McGuire (http://stackoverflow.com/users/165216/paul-mcguire)
Licensed under CC-BY-SA 3.0.
"""
Forward, Group, OneOrMore = pyparsing.Forward, pyparsing.Group, pyparsing.OneOrMore
Suppress, Word, nums = pyparsing.Suppress, pyparsing.Word, pyparsing.nums
LPAR, RPAR = map(Suppress, "()")
integer = Word(nums)
# add parse action to convert integers to ints, to support doing addition
# and multiplication at parse time
integer.setParseAction(lambda t: int(t[0]))
element = pyparsing.Regex('|'.join(isotopes_re + element_re) + '$')
# element = pyparsing.Regex(
# r"A[cglmrstu]|B[aehikr]?|C[adeflmorsu]?|D[bsy]|E[rsu]|F[emr]?|G[ade]"
# r"|H[efgos]?|I[nr]?|Kr?|L[airu]|M[dgnot]|N[abdeiop]?|Os?|P[abdmortu]?"
# r"|R[abefghnu]|S[bcegimnr]?|T[abcehilm]|Uu[bhopqst]|U|V|W|Xe|Yb?|Z[nr]")
# forward declare 'formula' so it can be used in definition of 'term'
formula = Forward()
_term_subgroup = (element | Group(LPAR + formula + RPAR)("subgroup"))
term = Group(_term_subgroup + pyparsing.Optional(integer, default=1)("mult"))
# add parse actions for parse-time processing
# parse action to multiply out subgroups
def multiplyContents(tokens): # noqa: MAN001,MAN002
t = tokens[0]
# if these tokens contain a subgroup, then use multiplier to
# extend counts of all elements in the subgroup
if t.subgroup:
mult = t.mult
for term in t.subgroup:
term[1] *= mult
return t.subgroup
term.setParseAction(multiplyContents)
# add parse action to sum up multiple references to the same element
def sum_by_element(tokens) -> Optional[pyparsing.ParseResults]: # noqa: MAN001
elementsList = [t[0] for t in tokens]
# construct set to see if there are duplicates
duplicates = len(elementsList) > len(set(elementsList))
# if there are duplicate element names, sum up by element and
# return a new nested pyparsing.ParseResults
if duplicates:
ctr: Dict = defaultdict(int)
for t in tokens:
ctr[t[0]] += t[1]
return pyparsing.ParseResults([pyparsing.ParseResults([k, v]) for k, v in ctr.items()])
return None
# define contents of a formula as one or more terms
formula << OneOrMore(term) # pylint: disable=expression-not-assigned
formula.setParseAction(sum_by_element)
return formula
# def _parse_stoich(stoich) -> Dict[int, Any]:
# if stoich == 'e': # special case, the electron is not an element
# return {}
# symbols = ELEMENTS.symbols + ['D', 'T']
# if re.findall('|'.join(invalid_re), stoich):
# raise ValueError(f"Unrecognised formula: {stoich}")
# return {symbols.index(k) + 1: n for k, n in _get_formula_parser().parseString(stoich)}
[docs]def string_to_composition(
formula: str,
prefixes: Optional[Iterable[str]] = None,
suffixes: Sequence[str] = ("(s)", "(l)", "(g)", "(aq)"),
) -> Dict[int, int]:
"""
Parse composition of formula representing a chemical formula.
:bold-title:`Examples:`
.. code-block:: python
>>> string_to_composition('NH4+') == {0: 1, "H": 4, "N": 1}
True
>>> string_to_composition('.NHO-(aq)') == {0: -1, "H": 1, "N": 1, "O": 1}
True
>>> string_to_composition('Na2CO3.7H2O') == {"Na": 2, "C": 1, "O": 10, "H": 14}
True
.. latex:vspace:: -10px
:param formula: Chemical formula, e.g. ``'H2O'``, ``'Fe+3'``, ``'Cl-'``
:param prefixes: Prefixes to ignore, e.g. ``('.', 'alpha-')``
:param suffixes: Suffixes to ignore.
:return: The composition, as a dictionary mapping atomic number -> multiplicity.
"Atomic number" 0 represents net charge.
"""
if prefixes is None:
prefixes = _latex_mapping.keys()
stoich_tok, chg_tok = _formula_to_parts(formula, prefixes, suffixes)[:2]
tot_comp = {}
parts = stoich_tok.split('.')
for idx, stoich in enumerate(parts):
if idx == 0:
m = 1
else:
m, stoich = _get_leading_integer(stoich)
# comp = _parse_stoich(stoich)
if stoich == 'e': # special case, the electron is not an element
pass
else:
try:
if re.findall('|'.join(invalid_re), stoich):
raise ValueError(f"Unrecognised formula: {formula}")
comp = _get_formula_parser().parse_string(stoich)
except pyparsing.ParseException:
raise ValueError(f"Unrecognised formula: {formula}")
# for k, v in comp.items():
k: int
v: int
for k, v in comp:
if k not in tot_comp:
tot_comp[k] = m * v
else:
tot_comp[k] += m * v
if chg_tok is not None:
tot_comp[0] = _get_charge(chg_tok)
return tot_comp
[docs]def mass_from_composition(composition: Mapping[Union[str, int], int], charge: int = 0) -> float:
"""
Calculates molecular mass, in atomic mass units, from atomic weights.
.. latex:vspace:: -5px
.. note:: Atomic number 0 denotes charge or "net electron defficiency"
.. latex:vspace:: -15px
:bold-title:`Example:`
.. code-block:: python
>>> f'{mass_from_composition({0: -1, "H": 1, 8: 1}):.2f}'
'17.01'
:param composition: Mapping of :class:`str` or :class:`int` (element symbol or atomic number) to int (coefficient)
:param charge: The charge of the composition.
"""
if charge and 0 in composition:
if charge != composition[0]:
raise ValueError(
"'charge' can only be specified once, "
"either as a keyword argument or as the '0' key of 'composition'"
)
mass = 0.0
for k, v in composition.items():
if k == 0: # electron
mass -= v * 5.489e-4
elif isinstance(k, str):
mass += v * ELEMENTS[k].mass
elif isinstance(k, int):
mass += v * ELEMENTS[k].mass
return mass