#####################################################################
# 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 steered molecular dynamics protocols."""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["Steering"]
import math as _math
import os as _os
from .. import Types as _Types
from ..Metadynamics import CollectiveVariable as _CollectiveVariable
from ..Metadynamics import Restraint as _Restraint
from ._protocol import Protocol as _Protocol
# Store the collective variable base type.
_colvar_type = _CollectiveVariable._collective_variable.CollectiveVariable
[docs]
class Steering(_Protocol):
"""A class for storing steered molecular dynamics protocols."""
[docs]
def __init__(
self,
collective_variable,
schedule,
restraints,
verse="both",
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"),
report_interval=1000,
restart_interval=1000,
colvar_file=None,
):
"""
Constructor.
Parameters
----------
collective_variable : :class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`, \
[:class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`]
The collective variable (or variables) used to perform the steering.
schedule : [:class:`Time <BioSimSpace.Types.Time>`]
The time schedule for the steering.
restraints : [:class:`Restraint <BioSimSpace.Metadynamics.Restraint>`] \
[(:class:`Restraint <BioSimSpace.Metadynamics.Restraint>`)]]
The position of the restraint on each collective variable for
each stage of the schedule.
verse : str
Whether the restraint is acting for values of the collective
variable "larger" or "smaller" than the restraint, or acting
on "both" sides (default).
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.
restart_interval : int
The frequency at which restart configurations and trajectory
frames are saved. (In integration steps.)
colvar_file : str
The path to a COLVAR file from a previous simulation. The
information in the file must be consistent with the
'collective_variable' argument.
"""
# 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 verse.
self.setVerse(verse)
# Set the schedule.
self.setSchedule(schedule)
# Set the restraints.
self.setRestraints(restraints)
# 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)
if colvar_file is not None:
self.setColvarFile(colvar_file)
else:
self._colvar_file = 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.Steering: "
string += "collective_variable=%s" % self._collective_variable
string += ", schedule=%s" % self._schedule
string += ", restraints=%s" % self._restraints
string += ", verse=%s" % self._verse
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
if self._colvar_file is not None:
string += ", colvar_file=%r" % self._colvar_file
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, Steering):
return False
if self._is_customised or other._is_customised:
return False
return (
self._collective_variable == other._collective_variable
and self._schedule == other._schedule
and self._restraints == other._restraints
and self._verse == other._verse
and self._timestep == other._timestep
and self._runtime == other._runtime
and self._temperature == other._temperature
and self._pressure == other._pressure
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]
else:
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."
)
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.setRestraints(self._restraints)
[docs]
def getSchedule(self):
"""
Return steering schedule.
Returns
-------
schedule : [int]
The schedule for the steering, i.e. the integration time steps
at which restraints are applied/adjusted.
"""
steps = []
for time in self._schedule:
steps.append(_math.floor(time / self._timestep))
return steps
[docs]
def setSchedule(self, schedule):
"""
Set the steering schedule.
Parameters
----------
schedule : [:class:`Time <BioSimSpace.Types.Tme>`]
The time schedule for the steering.
"""
if isinstance(schedule, (list, tuple)):
if not all(isinstance(x, _Types.Time) for x in schedule):
raise TypeError(
"'schedule' must all be of type " "'BioSimSpace.Types.Time'"
)
else:
raise TypeError(
"'schedule' must be a list of " "'BioSimSpace.Types.Time' types."
)
# Make sure the times are linearly increasing and are less than
# the total run time.
last_time = schedule[0]
for x in range(1, len(schedule)):
if last_time > self._runtime:
raise ValueError("'schedule' values cannot exceed the 'runtime'!")
if schedule[x] > self._runtime:
raise ValueError("'schedule' values cannot exceed the 'runtime'!")
if schedule[x] < last_time:
raise ValueError("The steering 'schedule' must increase in time!")
last_time = schedule[x]
self._schedule = schedule
# If the object has already been created, then check that other member
# data is consistent.
if not self._is_new_object:
self.setRestraints(self._restraints)
[docs]
def getRestraints(self):
"""
Return the restraint on each collective variable for each stage in
the schedule.
Returns
-------
restraints : [:class`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`] \
[(:class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`)]]
The position of the restraint on each collective variable for
each stage of the schedule.
"""
return self._restraints.copy()
[docs]
def setRestraints(self, restraints):
"""
Set the restraints for the steering schedule.
Parameters
----------
restraint : [:class`Restraint <BioSimSpace.Metadynamics.Restraint>`] \
[(:class:`Restraint <BioSimSpace.Metadynamics.Restraint>`)]]
The position of the restraint on each collective variable for
each stage of the schedule.
"""
# Validate type.
if not isinstance(restraints, (list, tuple)):
raise TypeError(
"'restraints' must be a list of "
"'BioSimSpace.CollectiveVariable.Restraint' types."
)
# Make sure we are self-consistent with the schedule.
if len(restraints) != len(self._schedule):
raise ValueError(
f"'len(restraints) != len(schedule), i.e. {len(restraints)} != {len(self._schedule)}"
)
# Convert all single entries to lists and validate types.
new_restraints = []
num_cvs = len(self._collective_variable)
for restraint in restraints:
# Convert tuple to list.
if isinstance(restraint, tuple):
restraint = list(restraint)
# Convert any non-list type to a list.
if not isinstance(restraint, list):
restraint = [restraint]
# Validate that there is a restraint for each collective variable
# for each stage in the schedule.
if len(restraint) != num_cvs:
raise ValueError(
"Must have a restraint for each collective "
"variable for each stage of the schedule."
)
# Validate type.
if not all(isinstance(x, _Restraint) for x in restraint):
raise TypeError(
"'restraint' must all be of type "
"'BioSimSpace.Metadynamics.Restraint'"
)
# Validate that restraints are harmonic.
if not all(r.getSlope() == 0 for r in restraint):
raise ValueError("'restraints' can only contain harmonic restraints!")
# Validate that the value of the restraint matches the type of each
# collective variable for each stage in the schedule.
if not all(
type(r.getValue()) in self._collective_variable[x]._types
for x, r in enumerate(restraint)
):
raise ValueError(
"The type of value for each restraint must match the "
"type of the collective variable to which it corresponds."
)
# Append to the new list.
new_restraints.append(restraint)
self._restraints = new_restraints
[docs]
def getVerse(self):
"""
Returns whether the restraint is acting for values of the collective
variable "larger" or "smaller" than the restraint, or acting on "both"
sides (default).
Returns
-------
verse : str
Whether the restraint is acting for values of the collective
variable "larger" or "smaller" than the restraint, or acting
on "both" sides (default).
"""
return self._verse
[docs]
def setVerse(self, verse):
"""
Set whether the restraint is acting for values of the collective
variable "larger" or "smaller" than the restraint, or acting on "both"
sides (default).
Parameters
----------
verse : str, [str]
Whether the restraint is acting for values of the collective
variable "larger" or "smaller" than the restraint, or acting
on "both" sides (default).
"""
# Convert string to list.
if isinstance(verse, str):
# Use the same verse for all collective variables.
verse = [verse] * len(self.getCollectiveVariable())
if isinstance(verse, (list, tuple)):
if not all(isinstance(x, str) for x in verse):
raise TypeError(
"'verse' must be of type 'str' or a list of 'str' types."
)
elif len(verse) != len(self.getCollectiveVariable()):
raise ValueError(
"'verse' must be of same length as 'collective_variable'"
)
else:
raise TypeError("'verse' must be of type 'str' or a list of 'str' types.")
new_verse = []
allowed = ["both", "larger", "smaller"]
for v in verse:
# Convert to lower case and strip whitespace.
v = v.lower().replace(" ", "")
if v not in allowed:
raise ValueError(f"'verse' must be one of: {allowed}")
else:
new_verse.append(v)
self._verse = new_verse
[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'"
)
# If the object has already been created, then check that other member
# data is consistent.
if not self._is_new_object:
self.setSchedule(self._schedule)
[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'"
)
# If the object has already been created, then check that other member
# data is consistent.
if not self._is_new_object:
self.setSchedule(self._schedule)
[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 '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 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 getColvarFile(self):
"""
Return the path to the COLVAR file.
Returns
-------
colvar_file : str
The path to the COLVAR file.
"""
return self._colvar_file
[docs]
def setColvarFile(self, colvar_file):
"""
Set the location of an existing COLVAR file.
Parameters
----------
colvar_file : str
The path to an existing COLVAR file.
"""
if not isinstance(colvar_file, str):
raise ValueError("'colvar_file' must be of type 'str'")
if not _os.path.isfile(colvar_file):
raise ValueError("'colvar_file' doesn't exist: %s" % colvar_file)
self._colvar_file = colvar_file