######################################################################
# 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 equilibration protocols."""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["Equilibration"]
import math as _math
import warnings as _warnings
from .. import Types as _Types
from .. import Units as _Units
from ._position_restraint_mixin import _PositionRestraintMixin
from ._protocol import Protocol as _Protocol
[docs]
class Equilibration(_Protocol, _PositionRestraintMixin):
"""A class for storing equilibration protocols."""
[docs]
def __init__(
self,
timestep=_Types.Time(2, "femtosecond"),
runtime=_Types.Time(0.2, "nanoseconds"),
temperature_start=_Types.Temperature(300, "kelvin"),
temperature_end=_Types.Temperature(300, "kelvin"),
temperature=None,
pressure=None,
thermostat_time_constant=_Types.Time(1, "picosecond"),
report_interval=100,
restart_interval=500,
restraint=None,
force_constant=10 * _Units.Energy.kcal_per_mol / _Units.Area.angstrom2,
):
"""
Constructor.
Parameters
----------
timestep : :class:`Time <BioSimSpace.Types.Time>`
The integration timestep.
runtime : :class:`Time <BioSimSpace.Types.Time>`
The running time.
temperature_start : :class:`Temperature <BioSimSpace.Types.Temperature>`
The starting temperature.
temperature_end : :class:`Temperature <BioSimSpace.Types.Temperature>`
The final temperature.
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The equilibration temperature. This takes precedence of over
the other temperatures, i.e. to run at fixed temperature.
pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure. If this argument is omitted then the simulation
is run using the NVT ensemble.
thermostat_time_constant : :class:`Time <BioSimSpace.Types.Time>`
Time constant for thermostat coupling.
report_interval : int
The frequency at which statistics are recorded. (In integration steps.)
restart_interval : int
The frequency at which restart configurations and trajectory
frames are saved. (In integration steps.)
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.
super().__init__()
# Set the time step.
self.setTimeStep(timestep)
# Set the running time.
self.setRunTime(runtime)
# Constant temperature equilibration.
if temperature is not None:
self.setStartTemperature(temperature)
self.setEndTemperature(temperature)
self._is_const_temp = True
# Heating / cooling simulation.
else:
self._is_const_temp = False
# Set the start temperature.
self.setStartTemperature(temperature_start)
# Set the final temperature.
self.setEndTemperature(temperature_end)
# Constant temperature simulation.
if self._temperature_start == self._temperature_end:
self._is_const_temp = True
# Constant pressure simulation.
if pressure is not None:
self.setPressure(pressure)
else:
self._pressure = None
# Set the thermostat time constant.
self.setThermostatTimeConstant(thermostat_time_constant)
# Set the report interval.
self.setReportInterval(report_interval)
# Set the restart interval.
self.setRestartInterval(restart_interval)
# Set the posistion restraint.
_PositionRestraintMixin.__init__(self, restraint, force_constant)
def _get_parm(self):
"""Return a string representation of the parameters."""
return (
f"timestep={self._timestep}, "
f"runtime={self._runtime}, "
f"temperature_start={self._temperature_start}, "
f"temperature_end={self._temperature_end}, "
f"pressure={self._pressure}, "
f"thermostat_time_constant={self._thermostat_time_constant}, "
f"report_interval={self._report_interval}, "
f"restart_interval={self._restart_interval}, "
+ _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.Equilibration: {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.Equilibration({self._get_parm()})"
def __eq__(self, other):
"""Equality operator."""
if not isinstance(other, Equilibration):
return False
if self._is_customised or other._is_customised:
return False
return (
self._timestep == other._timestep
and self._runtime == other._runtime
and self._temperature_start == other._temperature_start
and self._temperature_end == other._temperature_end
and self._pressure == other._pressure
and self._thermostat_time_constant == other._thermostat_time_constant
and self._report_interval == other._report_interval
and self._restart_interval == other._restart_interval
and _PositionRestraintMixin.__eq__(self, other)
)
[docs]
def getTimeStep(self):
"""
Return the time step.
Returns
-------
time : :class:`Time <BioSimSpace.Types.Time>`
The integration time step.
"""
return self._timestep
[docs]
def setTimeStep(self, timestep):
"""
Set the time step.
Parameters
----------
time : str, :class:`Time <BioSimSpace.Types.Time>`
The integration time step.
"""
if isinstance(timestep, str):
try:
self._timestep = _Types.Time(timestep)
except:
raise ValueError("Unable to parse 'timestep' string.") from None
elif isinstance(timestep, _Types.Time):
self._timestep = timestep
else:
raise TypeError(
"'timestep' must be of type 'str' or 'BioSimSpace.Types.Time'"
)
[docs]
def getRunTime(self):
"""
Return the running time.
Returns
-------
runtime : :class:`Time <BioSimSpace.Types.Time>`
The simulation run time.
"""
return self._runtime
[docs]
def setRunTime(self, runtime):
"""
Set the running time.
Parameters
----------
runtime : str, :class:`Time <BioSimSpace.Types.Time>`
The simulation run time.
"""
if isinstance(runtime, str):
try:
self._runtime = _Types.Time(runtime)
except:
raise ValueError("Unable to parse 'runtime' string.") from None
elif isinstance(runtime, _Types.Time):
self._runtime = runtime
else:
raise TypeError(
"'runtime' must be of type 'str' or 'BioSimSpace.Types.Time'"
)
[docs]
def getStartTemperature(self):
"""
Return the starting temperature.
Returns
-------
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The starting temperature.
"""
return self._temperature_start
[docs]
def setStartTemperature(self, temperature):
"""
Set the starting temperature.
Parameters
----------
temperature : str, :class:`Temperature <BioSimSpace.Types.Temperature>`
The starting temperature.
"""
if isinstance(temperature, str):
try:
temperature = _Types.Temperature(temperature)
except:
raise ValueError("Unable to parse 'temperature' string.") from None
elif not isinstance(temperature, _Types.Temperature):
raise TypeError(
"'temperature' must be of type 'str' or 'BioSimSpace.Types.Temperature'"
)
if _math.isclose(temperature.kelvin().value(), 0, rel_tol=1e-6):
temperature._value = 0.01
self._temperature_start = temperature
[docs]
def getEndTemperature(self):
"""
Return the final temperature.
Returns
-------
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The final temperature.
"""
return self._temperature_end
[docs]
def setEndTemperature(self, temperature):
"""
Set the final temperature.
Parameters
----------
temperature : str, :class:`Temperature <BioSimSpace.Types.Temperature>`
The final temperature.
"""
if isinstance(temperature, str):
try:
temperature = _Types.Temperature(temperature)
except:
raise ValueError("Unable to parse 'temperature' string.") from None
elif not isinstance(temperature, _Types.Temperature):
raise TypeError(
"'temperature' must be of type 'str' or 'BioSimSpace.Types.Temperature'"
)
if _math.isclose(temperature.kelvin().value(), 0, rel_tol=1e-6):
temperature._value = 0.01
self._temperature_end = temperature
[docs]
def getPressure(self):
"""
Return the pressure.
Returns
-------
pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure.
"""
return self._pressure
[docs]
def setPressure(self, pressure):
"""
Set the pressure.
Parameters
----------
pressure : str, :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure.
"""
if isinstance(pressure, str):
try:
self._pressure = _Types.Pressure(pressure)
except:
raise ValueError("Unable to parse 'pressure' string.") from None
elif isinstance(pressure, _Types.Pressure):
self._pressure = pressure
else:
raise TypeError(
"'pressure' must be of type 'str' or 'BioSimSpace.Types.Pressure'"
)
[docs]
def getThermostatTimeConstant(self):
"""
Return the time constant for the thermostat.
Returns
-------
runtime : :class:`Time <BioSimSpace.Types.Time>`
The time constant for the thermostat.
"""
return self._thermostat_time_constant
[docs]
def setThermostatTimeConstant(self, thermostat_time_constant):
"""
Set the time constant for the thermostat.
Parameters
----------
thermostat_time_constant : str, :class:`Time <BioSimSpace.Types.Time>`
The time constant for the thermostat.
"""
if isinstance(thermostat_time_constant, str):
try:
self._thermostat_time_constant = _Types.Time(thermostat_time_constant)
except:
raise ValueError(
"Unable to parse 'thermostat_time_constant' string."
) from None
elif isinstance(thermostat_time_constant, _Types.Time):
self._thermostat_time_constant = thermostat_time_constant
else:
raise TypeError(
"'thermostat_time_constant' must be of type 'str' or 'BioSimSpace.Types.Time'"
)
[docs]
def getReportInterval(self):
"""
Return the interval between reporting statistics. (In integration steps.).
Returns
-------
report_interval : int
The number of integration steps between reporting statistics.
"""
return self._report_interval
[docs]
def setReportInterval(self, report_interval):
"""
Set the interval at which statistics are reported. (In integration steps.).
Parameters
----------
report_interval : int
The number of integration steps between reporting statistics.
"""
if not type(report_interval) is int:
raise TypeError("'report_interval' must be of type 'int'")
if report_interval <= 0:
_warnings.warn("'report_interval' must be positive. Using default (100).")
report_interval = 100
self._report_interval = report_interval
[docs]
def getRestartInterval(self):
"""
Return the interval between saving restart confiugrations, and/or
trajectory frames. (In integration steps.).
Returns
-------
restart_interval : int
The number of integration steps between saving restart
configurations and/or trajectory frames.
"""
return self._restart_interval
[docs]
def setRestartInterval(self, restart_interval):
"""
Set the interval between saving restart confiugrations, and/or
trajectory frames. (In integration steps.).
Parameters
----------
restart_interval : int
The number of integration steps between saving restart
configurations and/or trajectory frames.
"""
if not type(restart_interval) is int:
raise TypeError("'restart_interval' must be of type 'int'")
if restart_interval <= 0:
_warnings.warn("'restart_interval' must be positive. Using default (500).")
restart_interval = 500
self._restart_interval = restart_interval
[docs]
def isConstantTemp(self):
"""
Return whether the protocol has a constant temperature.
Returns
-------
is_const_temp : bool
Whether the temperature is fixed.
"""
return self._temperature_start == self._temperature_end
[docs]
@classmethod
def restraints(cls):
"""
Return a list of the supported restraint keywords.
Returns
-------
restraints : [str]
A list of the supported restraint keywords.
"""
return cls._restraints.copy()