Source code for BioSimSpace.Protocol._metadynamics
#####################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2025
#
# 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 metadynamics protocols."""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["Metadynamics"]
import os as _os
import warnings as _warnings
from .. import Types as _Types
from ..Metadynamics import CollectiveVariable as _CollectiveVariable
from ._protocol import Protocol as _Protocol
# Store the collective variable base type.
_colvar_type = _CollectiveVariable._collective_variable.CollectiveVariable
[docs]
class Metadynamics(_Protocol):
"""A class for storing metadynamics protocols."""
[docs]
def __init__(
self,
collective_variable,
timestep=_Types.Time(2, "femtosecond"),
runtime=_Types.Time(1, "nanosecond"),
temperature=_Types.Temperature(300, "kelvin"),
pressure=_Types.Pressure(1, "atmosphere"),
thermostat_time_constant=_Types.Time(1, "picosecond"),
hill_height=_Types.Energy(1, "kj per mol"),
hill_frequency=1000,
report_interval=1000,
restart_interval=1000,
bias_factor=None,
):
"""
Constructor.
Parameters
----------
collective_variable : :class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`, \
[:class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`]
The collective variable (or variables) for the simulation.
timestep : :class:`Time <BioSimSpace.Types.Time>`
The integration timestep.
runtime : :class:`Time <BioSimSpace.Types.Time>`
The running time.
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The temperature.
pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure. Pass pressure=None to use the NVT ensemble.
thermostat_time_constant : :class:`Time <BioSimSpace.Types.Time>`
Time constant for thermostat coupling.
hill_height : :class:`Energy <BioSimSpace.Types.Energy>`
The height of the Gaussian hills.
hill_frequency : int
The frequency at which hills are deposited.
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.)
bias_factor : float
The bias factor for well tempered metadynamics.
"""
# Call the base class constructor.
super().__init__()
# Whether this is a newly created object.
self._is_new_object = True
# Set the collective variable.
self.setCollectiveVariable(collective_variable)
# Set the time step.
self.setTimeStep(timestep)
# Set the runtime.
self.setRunTime(runtime)
# Set the system temperature.
self.setTemperature(temperature)
# Set the report interval.
self.setReportInterval(report_interval)
# Set the restart interval.
self.setRestartInterval(restart_interval)
# Set the system pressure.
if pressure is not None:
self.setPressure(pressure)
else:
self._pressure = None
# Set the thermostat time constant.
self.setThermostatTimeConstant(thermostat_time_constant)
# Set the hill parameters: height, frequency.
self.setHillHeight(hill_height)
self.setHillFrequency(hill_frequency)
# Set the bias factor for well tempered metadynamics.
if bias_factor is not None:
self.setBiasFactor(bias_factor)
else:
self._bias_factor = None
# Flag that the object has been created.
self._is_new_object = False
def __str__(self):
"""Return a human readable string representation of the object."""
if self._is_customised:
return "<BioSimSpace.Protocol.Custom>"
else:
string = "<BioSimSpace.Protocol.Metadynamics: "
string += "collective_variable=%s" % self._collective_variable
string += ", timestep=%s" % self._timestep
string += ", runtime=%s" % self._runtime
string += ", temperature=%s" % self._temperature
if self._pressure is not None:
string += ", pressure=%s" % self._pressure
string += ", hill_height=%s" % self._hill_height
string += ", hill_frequency=%s" % self._hill_frequency
if self._bias_factor is not None:
string += ", bias_factor=%s" % self._bias_factor
string += ", report_interval=%d" % self._report_interval
string += ", restart_interval=%d" % self._restart_interval
string += ">"
return string
def __repr__(self):
"""Return a string showing how to instantiate the object."""
return self.__str__()
def __eq__(self, other):
"""Equality operator."""
if not isinstance(other, Metadynamics):
return False
if self._is_customised or other._is_customised:
return False
return (
self._collective_variable == other._collective_variable
and self._timestep == other._timestep
and self._runtime == other._runtime
and self._temperature == other._temperature
and self._pressure == other._pressure
and self._hill_height == other._hill_height
and self._hill_frequency == other._hill_frequency
and self._bias_factor == other._bias_factor
and self._report_interval == other._report_interval
and self._restart_interval == other._restart_interval
)
[docs]
def getCollectiveVariable(self):
"""
Return the collective variable (or variables).
Returns
-------
collective_variable : [:class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`]
The collective variable (or variables) for the simulation.
"""
return self._collective_variable.copy()
[docs]
def setCollectiveVariable(self, collective_variable):
"""
Set the collective variable (or variables).
Parameters
----------
collective_variable : :class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`, \
[:class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`]
The collective variable (or variables) for the simulation.
"""
# A single collective variable.
if isinstance(collective_variable, _colvar_type):
self._collective_variable = [collective_variable]
return
if isinstance(collective_variable, (list, tuple)):
if not all(isinstance(x, _colvar_type) for x in collective_variable):
raise TypeError(
"'collective_variable' must all be of type "
"'BioSimSpace.Metadynamics.CollectiveVariable'"
)
else:
raise TypeError(
"'collective_variable' must be of type "
"'BioSimSpace.Metadynamics.CollectiveVariable' "
"or a list of 'BioSimSpace.Metadynamics.CollectiveVariable' types."
)
# Make sure all of the collective variables are consistent. If any have
# a grid set, then so must all other variables.
num_grid = 0
for colvar in collective_variable:
if colvar.getGrid() is not None:
num_grid += 1
if num_grid > 0 and num_grid != len(collective_variable):
raise ValueError(
"If a 'grid' is desired, then all collective "
"variables must define one."
)
self._collective_variable = collective_variable
# If the object has already been created, then check that other member
# data is consistent.
if not self._is_new_object:
self.setHillHeight(self._hill_height)
[docs]
def getTimeStep(self):
"""
Return the time step.
Returns
-------
timestep : :class:`Time <BioSimSpace.Types.Time>`
The integration time step.
"""
return self._timestep
[docs]
def setTimeStep(self, timestep):
"""
Set the time step.
Parameters
----------
timestep : 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 getTemperature(self):
"""
Return temperature.
Returns
-------
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The simulation temperature.
"""
return self._temperature
[docs]
def setTemperature(self, temperature):
"""
Set the temperature.
Parameters
----------
temperature : str, :class:`Temperature <BioSimSpace.Types.Temperature>`
The simulation temperature.
"""
if isinstance(temperature, str):
try:
self._temperature = _Types.Temperature(temperature)
except:
raise ValueError("Unable to parse 'temperature' string.") from None
elif isinstance(temperature, _Types.Temperature):
self._temperature = temperature
else:
raise TypeError(
"'temperature' must be of type 'str' or 'BioSimSpace.Types.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 getHillHeight(self):
"""
Return the height of the Gaussian hills.
Returns
-------
hill_width : :class:`Energy <BioSimSpace.Types.Energy>`
The height of the Gaussian hills.
"""
return self._hill_height
[docs]
def setHillHeight(self, hill_height):
"""
Set the height of the Gaussian hills.
Parameters
----------
hill_height : str, :class:`Energy <BioSimSpace.Types.Energy>`
The hill height.
"""
if isinstance(hill_height, str):
try:
hill_height = _Types.Energy(hill_height)
except:
raise ValueError("Unable to parse 'hill_height' string.") from None
elif not isinstance(hill_height, _Types.Energy):
raise TypeError(
"'hill_height' must be of type 'str' or 'BioSimSpace.Types.Energy'"
)
# Check that heights is greater than zero.
if hill_height.value() <= 0:
raise ValueError("Cannot have 'hill_height' with value <= 0")
self._hill_height = hill_height.kj_per_mol()
[docs]
def getHillFrequency(self):
"""
Return the frequency at which Gaussian hills are deposited.
Returns
-------
hill_frequency : int
The frequency at which hills are deposited.
"""
return self._hill_frequency
[docs]
def setHillFrequency(self, hill_frequency):
"""
Set the frequency at which Gaussian hills are deposited.
Parameters
----------
hill_frequency : int
The frequency at which hills are deposited.
"""
try:
hill_frequency = int(hill_frequency)
except:
raise TypeError("'hill_frequency' must be of type 'int'")
if hill_frequency < 1:
raise ValueError("'hill_frequency' must be >= 1")
self._hill_frequency = hill_frequency
[docs]
def getBiasFactor(self):
"""
Return the bias factor for well tempered metadynamics.
Returns
-------
bias_factor : float
The bias factor for well tempered metadynamics.
"""
return self._bias_factor
[docs]
def setBiasFactor(self, bias_factor=None):
"""
Set the bias factor for well tempered metadynamics.
Call with no arguments to clear the bias factor.
Parameters
----------
bias_factor : float
The bias factor for well tempered metadynamics.
"""
if bias_factor is None:
self._bias_factor = None
return
try:
bias_factor = float(bias_factor)
except:
raise TypeError("'bias_factor' must be of type 'float'")
if bias_factor < 1.0:
raise ValueError("'bias_factor' must be > 1.0")
# OpenMM crashes when the bias factor is exactly one, so add a delta.
delta = 1e-6
if abs(bias_factor - 1.0) < delta:
bias_factor += delta
self._bias_factor = bias_factor
[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