#!/usr/bin/env python3
#
# unicode.py
"""
Functions and constants for converting formulae to unicode.
.. 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
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# This program is distributed in the hope that it will be useful,
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
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# 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.
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# | 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
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#
# stdlib
from typing import Dict, Optional, Sequence, Union
# this package
from ._parser_core import _formula_to_format, _greek_letters, _greek_u
__all__ = ["string_to_unicode", "unicode_subscript", "unicode_superscript"]
_unicode_mapping: Dict[str, str] = {k + '-': v + '-' for k, v in zip(_greek_letters, _greek_u)}
_unicode_mapping['.'] = '⋅'
_unicode_infix_mapping: Dict[str, str] = {'.': '·'}
_unicode_sub: Dict[str, str] = {}
for k, v in enumerate("₀₁₂₃₄₅₆₇₈₉"):
_unicode_sub[str(k)] = v
_unicode_sup: Dict[str, str] = {
'+': '⁺',
'-': '⁻',
}
for k, v in enumerate("⁰¹²³⁴⁵⁶⁷⁸⁹"):
_unicode_sup[str(k)] = v
[docs]def string_to_unicode(
formula: str,
prefixes: Optional[Dict[str, str]] = None,
infixes: Optional[Dict[str, str]] = None,
suffixes: Sequence[str] = ("(s)", "(l)", "(g)", "(aq)"),
) -> str:
"""
Convert the given formula string to a unicode string representation.
:bold-title:`Examples:`
.. code-block:: python
>>> string_to_unicode('NH4+')
'NH₄⁺'
>>> string_to_unicode('Fe(CN)6+2')
'Fe(CN)₆²⁺'
>>> string_to_unicode('Fe(CN)6+2(aq)')
'Fe(CN)₆²⁺(aq)'
>>> string_to_unicode('.NHO-(aq)')
'⋅NHO⁻(aq)'
>>> string_to_unicode('alpha-FeOOH(s)')
'α-FeOOH(s)'
:param formula: Chemical formula, e.g. ``'H2O'``, ``'Fe+3'``, ``'Cl-'``
:param prefixes: Mapping of prefixes to their Unicode equivalents. Default greek letters and ``.``
:no-default prefixes:
:param infixes: Mapping of infixes to their Unicode equivalents.
:param suffixes: Suffixes to keep.
:return: The Unicode representation of the formula.
"""
if prefixes is None:
prefixes = _unicode_mapping
if infixes is None:
infixes = _unicode_infix_mapping
return _formula_to_format(unicode_subscript, unicode_superscript, formula, prefixes, infixes, suffixes)
[docs]def unicode_subscript(val: Union[str, float]) -> str:
"""
Returns the Unicode subscript of the given value.
:param val: The value to superscript
"""
return ''.join(_unicode_sub[str(_)] for _ in str(val))
[docs]def unicode_superscript(val: Union[str, float]) -> str:
"""
Returns the Unicode superscript of the given value.
:param val: The value to subscript
"""
return ''.join(_unicode_sup[str(_)] for _ in str(val))