#!/usr/bin/env python3
#
# species.py
#
# 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 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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# Also 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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# |
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# | See the License for the specific language governing permissions and
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# |
# | 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 molmass (https://github.com/cgohlke/molmass)
# | Copyright (c) 1990-2020, Christoph Gohlke
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# | Licensed under the BSD 3-Clause License
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# | modification, are permitted provided that the following conditions are met:
# |
# | 1. Redistributions of source code must retain the above copyright notice,
# | this list of conditions and the following disclaimer.
# |
# | 2. Redistributions in binary form must reproduce the above copyright notice,
# | this list of conditions and the following disclaimer in the documentation
# | and/or other materials provided with the distribution.
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# | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# | POSSIBILITY OF SUCH DAMAGE.
# |
# 3rd party
from cawdrey import frozendict
# this package
from .formula import Formula
[docs]class Species(Formula):
"""
Formula with phase information (e.g. solid, liquid, gas, or aqueous)
Species extends :class:`Formula` with the new attribute :attr:`phase`
Attributes
----------
phase: Either "s", "l", "g", or "aq". ``None`` represents an unknown phase.
"""
_phases = frozendict(s="Solid", l="Liquid", g="Gas", aq="Aqueous")
def __init__(self, composition=None, charge=0, phase=None):
"""
:param composition: A :py:class:`Formula` or :py:class:`Species` object with the elemental composition of a substance,
or a :class:`python:dict` representing the same.
If ``None`` an empty object is created
:type composition: :py:class:`Formula`, optional
:param charge:
:type charge: int, optional
:param phase: Either "s", "l", "g", or "aq". ``None`` represents an unknown phase.
:type phase: str or None
"""
super().__init__(composition, charge)
self.phase = phase
[docs] @classmethod
def from_kwargs(cls, *, charge=0, phase=None, **kwargs):
"""
Create a new :class:`Species` object from keyword arguments representing the elements in the compound
:param charge:
:type charge: int, optional
:rtype: :class:`Formula`
"""
return cls(kwargs, charge=charge, phase=phase)
[docs] @classmethod
def from_string(
cls, formula, phase=None, charge=0):
"""
Create a new :class:`Species` object by parsing a string
Analogous to :meth:`Formula.from_string` but with the addition that
the phase is determined from the formula.
Parameters
----------
formula: str
e.g. 'H2O', 'NaCl(s)', 'CO2(aq)', 'CO2(g)'
phase: Either "s", "l", "g", or "aq". ``None`` represents an unknown phase.
Examples
--------
>>> water = Species.from_string('H2O')
>>> water.phase
None
>>> NaCl = Species.from_string('NaCl(s)')
>>> NaCl.phase
s
>>> Hg_l = Species.from_string('Hg(l)')
>>> Hg_l.phase
l
>>> CO2g = Species.from_string('CO2(g)')
>>> CO2g.phase
g
>>> CO2aq = Species.from_string('CO2(aq)')
>>> CO2aq.phase
aq
"""
if phase is None:
for p in cls._phases:
if formula.endswith(f"({p})"):
phase = p
break
f = super().from_string(formula, charge)
f.phase = phase
return f
[docs] def copy(self):
return self.__class__(self, charge=self.charge, phase=self.phase)
def __eq__(self, other):
if isinstance(other, Species):
if super().__eq__(other):
return self.phase == other.phase
else:
return super().__eq__(other)
def _repr_elements(self):
elements = super()._repr_elements()
if self.phase:
elements.append(f"phase={self.phase}")
return elements
@property
def hill_formula(self):
"""
:return:
:rtype: str
"""
hill = super().hill_formula
if self.phase:
return f"{hill}({self.phase})"
else:
return hill
@property
def empirical_formula(self):
"""
:return:
:rtype: str
"""
hill = super().empirical_formula
if self.phase:
return f"{hill}({self.phase})"
else:
return hill