Add restart flag to equilibration protocols.

python/BioSimSpace/Protocol/_equilibration.py

@@ -50,6 +50,7 @@ def __init__(
         thermostat_time_constant=_Types.Time(1, "picosecond"),
         report_interval=200,
         restart_interval=1000,
+        restart=False,
         restraint=None,
         force_constant=10 * _Units.Energy.kcal_per_mol / _Units.Area.angstrom2,
     ):
@@ -89,6 +90,9 @@ def __init__(
             The frequency at which restart configurations and trajectory
             frames are saved. (In integration steps.)
 
+        restart : bool
+            Whether this is a continuation of a previous simulation.
+
         restraint : str, [int]
             The type of restraint to perform. This should be one of the
             following options:
@@ -155,6 +159,9 @@ def __init__(
         # Set the restart interval.
         self.setRestartInterval(restart_interval)
 
+        # Set the restart flag.
+        self.setRestart(restart)
+
         # Set the posistion restraint.
         _PositionRestraintMixin.__init__(self, restraint, force_constant)
 
@@ -169,7 +176,7 @@ def _get_parm(self):
             f"thermostat_time_constant={self._thermostat_time_constant}, "
             f"report_interval={self._report_interval}, "
             f"restart_interval={self._restart_interval}, "
-            + _PositionRestraintMixin._get_parm(self)
+            f"restart={self._restart}, " + _PositionRestraintMixin._get_parm(self)
         )
 
     def __str__(self):
@@ -204,6 +211,7 @@ def __eq__(self, other):
             and self._thermostat_time_constant == other._thermostat_time_constant
             and self._report_interval == other._report_interval
             and self._restart_interval == other._restart_interval
+            and self._restart == other._restart
             and _PositionRestraintMixin.__eq__(self, other)
         )
 
@@ -484,6 +492,34 @@ def setRestartInterval(self, restart_interval):
 
         self._restart_interval = restart_interval
 
+    def isRestart(self):
+        """
+        Return whether this restart simulation.
+
+        Returns
+        -------
+
+        is_restart : bool
+            Whether this is a restart simulation.
+        """
+        return self._restart
+
+    def setRestart(self, restart):
+        """
+        Set the restart flag.
+
+        Parameters
+        ----------
+
+        restart : bool
+            Whether this is a restart simulation.
+        """
+        if isinstance(restart, bool):
+            self._restart = restart
+        else:
+            _warnings.warn("Non-boolean restart flag. Defaulting to False!")
+            self._restart = False
+
     def isConstantTemp(self):
         """
         Return whether the protocol has a constant temperature.

python/BioSimSpace/Protocol/_free_energy_equilibration.py

@@ -52,6 +52,7 @@ def __init__(
         thermostat_time_constant=_Types.Time(1, "picosecond"),
         report_interval=200,
         restart_interval=1000,
+        restart=False,
         restraint=None,
         force_constant=10 * _Units.Energy.kcal_per_mol / _Units.Area.angstrom2,
         perturbation_type="full",
@@ -106,6 +107,9 @@ def __init__(
             The frequency at which restart configurations and trajectory
             frames are saved. (In integration steps.)
 
+        restart : bool
+            Whether this is a continuation of a previous simulation.
+
         restraint : str, [int]
             The type of restraint to perform. This should be one of the
             following options:
@@ -217,4 +221,5 @@ def _to_regular_protocol(self):
             restart_interval=self.getRestartInterval(),
             restraint=self.getRestraint(),
             force_constant=self.getForceConstant(),
+            restart=self.isRestart(),
         )