Remediate other doctest exceptions
@@ -269,7 +269,7 @@ class ThermodynamicsError(Exception):
>>> raise ThermodynamicsError(ThermodynamicsError.MULTIPLE_BAROSTATS)
Traceback (most recent call last):
...
- ThermodynamicsError: System has multiple barostats.
+ openmmtools.states.ThermodynamicsError: System has multiple barostats.
"""
@@ -329,7 +329,7 @@ class SamplerStateError(Exception):
>>> raise SamplerStateError(SamplerStateError.INCONSISTENT_VELOCITIES)
Traceback (most recent call last):
...
- SamplerStateError: Velocities have different length than positions.
+ openmmtools.states.SamplerStateError: Velocities have different length than positions.
"""
@@ -430,7 +430,7 @@ class ThermodynamicState(object):
... pressure=1.0*unit.atmosphere)
Traceback (most recent call last):
...
- ThermodynamicsError: Non-periodic systems cannot have a barostat.
+ openmmtools.states.ThermodynamicsError: Non-periodic systems cannot have a barostat.
When temperature and/or pressure are not specified (i.e. they are
None) ThermodynamicState tries to infer them from a thermostat or
@@ -439,7 +439,7 @@ class ThermodynamicState(object):
>>> state = ThermodynamicState(system=waterbox)
Traceback (most recent call last):
...
- ThermodynamicsError: System does not have a thermostat specifying the temperature.
+ openmmtools.states.ThermodynamicsError: System does not have a thermostat specifying the temperature.
>>> thermostat = openmm.AndersenThermostat(200.0*unit.kelvin, 1.0/unit.picosecond)
>>> force_id = waterbox.addForce(thermostat)
>>> state = ThermodynamicState(system=waterbox)
@@ -538,7 +538,7 @@ class ThermodynamicState(object):
>>> state.system = alanine.system
Traceback (most recent call last):
...
- ThermodynamicsError: System does not have a thermostat specifying the temperature.
+ openmmtools.states.ThermodynamicsError: System does not have a thermostat specifying the temperature.
We can fix both thermostat and barostat while setting the system.
>>> state.set_system(alanine.system, fix_state=True)
@@ -812,7 +812,7 @@ class ThermodynamicState(object):
>>> state.reduced_potential(incompatible_sampler_state)
Traceback (most recent call last):
...
- ThermodynamicsError: The sampler state has a different number of particles.
+ openmmtools.states.ThermodynamicsError: The sampler state has a different number of particles.
In case a cached SamplerState containing the potential energy
and the volume of the context is not available, the method
