######################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2024
#
# Authors: Lester Hedges <lester.hedges@gmail.com>
#
# BioSimSpace is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# BioSimSpace 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 General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with BioSimSpace. If not, see <http://www.gnu.org/licenses/>.
#####################################################################
"""A charge type."""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["Charge"]
from sire.legacy import Units as _SireUnits
from ._type import Type as _Type
[docs]
class Charge(_Type):
"""A charge type."""
# A list of the supported Sire unit names.
_sire_units = ["e_charge", "coulomb"]
# Dictionary of allowed units.
_supported_units = {
"ELECTRON CHARGE": _SireUnits.e_charge,
"COULOMB": _SireUnits.coulomb,
}
# Map unit abbreviations to the full name.
_abbreviations = {"E": "ELECTRON CHARGE", "C": "COULOMB"}
# Print formatting.
_print_format = {"ELECTRON CHARGE": "|e|", "COULOMB": "C"}
# Documentation strings.
_doc_strings = {
"ELECTRON CHARGE": "A charge in electron charge.",
"COULOMB": "A charge in Coulomb.",
}
# Null type unit for avoiding issue printing configargparse help.
_default_unit = "ELECTRON CHARGE"
# The dimension mask.
_dimensions = tuple(list(_supported_units.values())[0].dimensions())
[docs]
def __init__(self, *args):
"""
Constructor.
``*args`` can be a value and unit, or a string representation
of the charge, e.g. "0.2 e".
Parameters
----------
value : float
The value.
unit : str
The unit.
string : str
A string representation of the charge.
Examples
--------
Create an object representing a charge of 27.8 electron charge
print the charge in Coulomb.
>>> import BioSimSpace as BSS
>>> charge = BSS.Types.Charge(27.8, "e")
>>> print(charge.coulomb())
The same as above, except passing a string representation of the
charge to the constructor.
>>> import BioSimSpace as BSS
>>> charge = BSS.Types.Charge("3.1 atm")
>>> print(charge.coulomb())
The string matching is extremeley flexible, so all of the following
would be valid arguments: "27.8 e", "27.8 electron charge",
"2.78e1 e".
"""
# Call the base class constructor.
super().__init__(*args)
[docs]
def electron_charge(self):
"""
Return the charge in electron charge.
Returns
-------
charge : :class:`Charge <BioSimSpace.Types.Charge>`
The charge in electron charge.
"""
return Charge(
(self._value * self._supported_units[self._unit]).to(_SireUnits.e_charge),
"ELECTRON CHARGE",
)
[docs]
def coulomb(self):
"""
Return the charge in Coulomb.
Returns
-------
charge : :class:`Charge <BioSimSpace.Types.Charge>`
The charge in Coulomb.
"""
return Charge(
(self._value * self._supported_units[self._unit]).to(_SireUnits.coulomb),
"COULOMB",
)
def _to_default_unit(self, mag=None):
"""
Internal method to return an object of the same type in the default unit.
Parameters
----------
mag : float
The value (optional).
Returns
-------
charge : :class:`Charge <BioSimSpace.Types.Charge>`
The charge in the default unit of electron charge.
"""
if mag is None:
return self.electron_charge()
else:
return Charge(mag, "ELECTRON CHARGE")
def _convert_to(self, unit):
"""
Return the charge in a different unit.
Parameters
----------
unit : str
The unit to convert to.
Returns
-------
charge : :class:`Charge <BioSimSpace.Types.Charge>`
The charge in the specified unit.
"""
if unit == "ELECTRON CHARGE":
return self.electron_charge()
elif unit == "COULOMB":
return self.coulomb()
else:
raise ValueError(
"Supported units are: '%s'" % list(self._supported_units.keys())
)
@classmethod
def _validate_unit(cls, unit):
"""Validate that the unit are supported."""
# Strip whitespace and convert to upper case.
unit = unit.replace(" ", "").upper()
# Replace all instances of ELECTRON with E.
unit = unit.replace("ELECTRON", "E")
# Replace all instances of ELECT with E.
unit = unit.replace("ELECT", "E")
# Replace all instances of ELEC with E.
unit = unit.replace("ELEC", "E")
# Strip all instances of CHARGE.
unit = unit.replace("CHARGE", "")
# Strip all instances of -.
unit = unit.replace("-", "")
# Strip all instances of S.
unit = unit.replace("S", "")
# Replace all instance of COULOMB with C.
unit = unit.replace("COULOMB", "C")
# Replace all instance of COUL with C.
unit = unit.replace("COUL", "C")
# Check that the unit is supported.
if unit in cls._abbreviations:
return cls._abbreviations[unit]
else:
raise ValueError(
"Supported units are: '%s'" % list(cls._supported_units.keys())
)
@staticmethod
def _to_sire_format(unit):
"""
Reformat the unit string so it adheres to the Sire unit formatting.
Parameters
----------
unit : str
A string representation of the unit.
Returns
-------
sire_unit : str
The unit string in Sire compatible format.
"""
unit = unit.replace("coulombs", "coulomb")
unit = unit.replace("electroncharge", "e_charge")
unit = unit.replace("echarge", "e_charge")
# Convert powers. (Just 2nd and third for now.)
unit = unit.replace("coloumb2", "(coulomb*coulomb)")
unit = unit.replace("coloumb3", "(coulomb*coulomb*coulomb)")
unit = unit.replace("coloumb-1", "(1/coulomb)")
unit = unit.replace("coloumb-2", "(1/(coulomb*coulomb))")
unit = unit.replace("coloumb3", "(1/(coulomb*coulomb*coulomb))")
unit = unit.replace("e_charge2", "(e_charge*e_charge)")
unit = unit.replace("e_charge3", "(e_charge*e_charge*e_charge)")
unit = unit.replace("e_charge-1", "(1/e_charge)")
unit = unit.replace("e_charge-2", "(1/(e_charge*e_charge))")
unit = unit.replace("e_charge-3", "(1/(e_charge*e_charge*e_charge))")
return unit