Source code for BioSimSpace.Protocol._minimisation
######################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2023
#
# 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 minimisation protocols."""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["Minimisation"]
import warnings as _warnings
from .. import Units as _Units
from ._position_restraint_mixin import _PositionRestraintMixin
from ._protocol import Protocol as _Protocol
[docs]
class Minimisation(_Protocol, _PositionRestraintMixin):
"""A class for storing minimisation protocols."""
[docs]
def __init__(
self,
steps=10000,
restraint=None,
force_constant=10 * _Units.Energy.kcal_per_mol / _Units.Area.angstrom2,
):
"""
Constructor.
Parameters
----------
steps : int
The maximum number of steps to perform.
restraint : str, [int]
The type of restraint to perform. This should be one of the
following options:
"backbone"
Protein backbone atoms. The matching is done by a name
template, so is unreliable on conversion between
molecular file formats.
"heavy"
All non-hydrogen atoms that aren't part of water
molecules or free ions.
"all"
All atoms that aren't part of water molecules or free
ions.
Alternatively, the user can pass a list of atom indices for
more fine-grained control. If None, then no restraints are used.
force_constant : :class:`GeneralUnit <BioSimSpace.Types._GeneralUnit>`, float
The force constant for the restraint potential. If a 'float' is
passed, then default units of 'kcal_per_mol / angstrom**2' will
be used.
"""
# Call the base class constructor.
_Protocol.__init__(self)
_PositionRestraintMixin.__init__(self, restraint, force_constant)
# Set the number of steps.
self.setSteps(steps)
def _get_parm(self):
"""Return a string representation of the parameters."""
return f"steps={self._steps}, " + _PositionRestraintMixin._get_parm(self)
def __str__(self):
"""Return a human readable string representation of the object."""
if self._is_customised:
return "<BioSimSpace.Protocol.Custom>"
else:
return f"<BioSimSpace.Protocol.Minimisation: {self._get_parm()}>"
def __repr__(self):
"""Return a string showing how to instantiate the object."""
if self._is_customised:
return "BioSimSpace.Protocol.Custom"
else:
return f"BioSimSpace.Protocol.Minimisation({self._get_parm()})"
[docs]
def getSteps(self):
"""
Return the maximum number of steps.
Returns
-------
steps : int
The maximum number of minimisation steps.
"""
return self._steps
[docs]
def setSteps(self, steps):
"""
Set the maximum number of steps.
Parameters
----------
steps : int
The maximum number of minimisation steps.
"""
if not type(steps) is int:
raise TypeError("'steps' must be of type 'int'")
if steps <= 0:
_warnings.warn(
"Number of steps must be greater than zero. Using default (10000)."
)
self._steps = 10000
else:
self._steps = steps