#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# latex.py
"""
Functions and constants for converting formulae to LaTeX
"""
#
# 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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# | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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# | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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#
# this package
from ._parser_core import _formula_to_format, _greek_letters
_latex_mapping = {k + '-': '\\' + k + '-' for k in _greek_letters}
_latex_mapping['epsilon-'] = '\\varepsilon-'
_latex_mapping['omicron-'] = 'o-'
_latex_mapping['.'] = '^\\bullet '
_latex_infix_mapping = {'.': '\\cdot '}
[docs]def string_to_latex(formula, prefixes=None, infixes=None, **kwargs):
r"""
Convert formula string to latex representation
Parameters
----------
formula: str
Chemical formula, e.g. 'H2O', 'Fe+3', 'Cl-'
prefixes: dict
Prefix transofmrations, default: greek letters and .
infixes: dict
Infix transformations, default: .
suffixes: iterable of str
What suffixes not to interpret, default: (s), (l), (g), (aq)
Examples
--------
>>> string_to_latex('NH4+')
'NH_{4}^{+}'
>>> string_to_latex('Fe(CN)6+2')
'Fe(CN)_{6}^{2+}'
>>> string_to_latex('Fe(CN)6+2(aq)')
'Fe(CN)_{6}^{2+}(aq)'
>>> string_to_latex('.NHO-(aq)')
'^\\bullet NHO^{-}(aq)'
>>> string_to_latex('alpha-FeOOH(s)')
'\\alpha-FeOOH(s)'
"""
if prefixes is None:
prefixes = _latex_mapping
if infixes is None:
infixes = _latex_infix_mapping
return _formula_to_format(
lambda x: '_{%s}' % x, lambda x: f'^{{{x}}}',
formula, prefixes, infixes, **kwargs)