######################################################################
# 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/>.
#####################################################################
"""Functionality for configuring restraints on collective variables."""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["Restraint"]
from ..Types._type import Type as _Type
[docs]
class Restraint:
[docs]
def __init__(self, value, force_constant=100.0, slope=0.0):
"""
Constructor.
Set a restraint on the value of a collective variable.
The expression for the bias is:
.. math::
k/2 (x - a)^2 + m (x - a)
The default restraint is purely harmonic.
Parameters
----------
value : int, float, :class:`Type <BioSimSpace.Types>`
The value of the restraint. Use 'int' or 'float' for dimensionless
collective variables.
force_constant : float
The force constant (k) for the harmonic term of the restraint.
slope : float
The slope (m) for the linar term of the restraint.
"""
self.setValue(value)
self.setForceConstant(force_constant)
self.setSlope(slope)
def __str__(self):
"""Return a human readable string representation of the object."""
return (
"<BioSimSpace.Metadynamics.Restraint: value=%s, force_constant=%s, slope=%s>"
% (self._value, self._force_constant, self._slope)
)
def __repr__(self):
"""Return a human readable string representation of the object."""
return self.__str__()
def __eq__(self, other):
"""Equality operator."""
return (
self._value == other._value
and self._force_constant == other._force_constant
and self._slope == other._slope
)
[docs]
def setValue(self, value):
"""
Set the value of the bound.
Parameters
----------
value : int, float, :class:`Type <BioSimSpace.Types>`
The value of the bound.
"""
if not isinstance(value, (float, _Type)) and not type(value) is int:
raise TypeError(
"'value' must be of type 'int', 'float', or 'BioSimSpace.Types._type.Type'"
)
self._value = value
[docs]
def getValue(self):
"""
Get the value of the bound.
Returns
-------
value : int, float, :class:`Type <BioSimSpace.Types>`
The value of the bound.
"""
return self._value
[docs]
def setForceConstant(self, force_constant):
"""
Set the force constant (k) for the harmonic term of the restraint.
Parameters
----------
force_constant : float
The force constant for the harmonic term of the restraint.
"""
try:
self._force_constant = float(force_constant)
except:
raise TypeError("'force_constant' must be of type 'float'")
[docs]
def getForceConstant(self):
"""
Get the force constant (k) for the harmonic term of the restraint.
Returns
-------
force_constant : float
The force constant for the harmonic term of the restraint.
"""
return self._force_constant
[docs]
def setSlope(self, slope):
"""
Set the slope (m) for the linear term of the restraint.
Parameters
----------
slope : float
The slope for the linear term of the restraint.
"""
try:
self._slope = float(slope)
except:
raise TypeError("'slope' must be of type 'float'")
[docs]
def getSlope(self):
"""
Get the slope (m) for the linear term of the restraint.
Returns
-------
slope : float
The slope for the linear term of the restraint.
"""
return self._slope