| | |
- builtins.object
-
- InterpolationType
- MultiTemperatureTrialCounter
- rosetta.protocols.moves.MonteCarlo(builtins.object)
-
- BiasedMonteCarlo
- rosetta.protocols.moves.Mover(builtins.object)
-
- CanonicalSamplingMover
- MetropolisHastingsMover
-
- SidechainMetropolisHastingsMover
- ThermodynamicMover
- ThermodynamicObserver
-
- BiasEnergy
-
- WTEBiasEnergy
- MetricRecorder
- ProgressBarObserver
- TemperatureController
-
- FixedTemperatureController
- TemperingBase
-
- AsyncMPITemperingBase
-
- HamiltonianExchange
- ParallelTempering
- SimulatedTempering
- TrajectoryRecorder
-
- DbTrajectoryRecorder
- PDBTrajectoryRecorder
- SilentTrajectoryRecorder
- TrialCounterObserver
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- DbTrajectoryRecorderCreator
- HamiltonianExchangeCreator
- MetricRecorderCreator
- MetropolisHastingsMoverCreator
- PDBTrajectoryRecorderCreator
- ParallelTemperingCreator
- ProgressBarObserverCreator
- SidechainMetropolisHastingsMoverCreator
- SilentTrajectoryRecorderCreator
- SimulatedTemperingCreator
- TrialCounterObserverCreator
class AsyncMPITemperingBase(TemperingBase) |
| | |
- Method resolution order:
- AsyncMPITemperingBase
- TemperingBase
- TemperatureController
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.AsyncMPITemperingBase) -> NoneType
2. __init__(rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, rosetta.protocols.canonical_sampling.AsyncMPITemperingBase) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase) -> rosetta.protocols.canonical_sampling.AsyncMPITemperingBase
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
callback executed after all Monte Carlo trials
- finished_simulation(...) from builtins.PyCapsule
- finished_simulation(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, trials : int, ntrials : int) -> bool
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(*args, **kwargs)
Overloaded function.
1. initialize_simulation(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, cycle : int) -> NoneType
callback executed before any Monte Carlo trials
2. initialize_simulation(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, level : int, temperature : float, cycle : int) -> NoneType
Methods inherited from TemperingBase:
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.TemperingBase) -> str
- n_temp_levels(...) from builtins.PyCapsule
- n_temp_levels(rosetta.protocols.canonical_sampling.TemperingBase) -> int
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- temperature(...) from builtins.PyCapsule
- temperature(*args, **kwargs)
Overloaded function.
1. temperature(rosetta.protocols.canonical_sampling.TemperingBase) -> float
Return the temperature of the underlying MonteCarlo object.
2. temperature(self : rosetta.protocols.canonical_sampling.TemperingBase, level : int) -> float
Return the temperature of the given level.
- temperature_level(...) from builtins.PyCapsule
- temperature_level(rosetta.protocols.canonical_sampling.TemperingBase) -> int
Methods inherited from TemperatureController:
- exchange_grid_dim(...) from builtins.PyCapsule
- exchange_grid_dim(rosetta.protocols.canonical_sampling.TemperatureController) -> int
- level_2_grid_coord(...) from builtins.PyCapsule
- level_2_grid_coord(self : rosetta.protocols.canonical_sampling.TemperatureController, level : int) -> rosetta.utility.vector1_unsigned_long
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.moves.MonteCarlo
Return const access to the MonteCarlo object being controlled.
- nlevels_per_dim(...) from builtins.PyCapsule
- nlevels_per_dim(self : rosetta.protocols.canonical_sampling.TemperatureController, : int) -> int
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Set the MonteCarlo object to be controlled.
- temperature_move(...) from builtins.PyCapsule
- temperature_move(*args, **kwargs)
Overloaded function.
1. temperature_move(self : rosetta.protocols.canonical_sampling.TemperatureController, score : float) -> float
Execute the temperature move.
This method is called by observe_after_metropolis() and is
expected to return the new temperature (in units of kT, to the extent
that that is meaningful in the context of rosetta).
2. temperature_move(self : rosetta.protocols.canonical_sampling.TemperatureController, pose : rosetta.core.pose.Pose) -> float
Execute a temperature move which depends on the current pose.
The default implementation just calls the pose-independent
temperature_pose() method with the energy of the given pose. However,
the HamiltonianExchange temperature controller needs to evaluate the
alternative Hamiltonian.
Methods inherited from ThermodynamicObserver:
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class BiasEnergy(ThermodynamicObserver) |
| | |
- Method resolution order:
- BiasEnergy
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.BiasEnergy) -> NoneType
2. __init__(self : rosetta.protocols.canonical_sampling.BiasEnergy, stride : int, omega : float, gamma : float) -> NoneType
3. __init__(rosetta.protocols.canonical_sampling.BiasEnergy, rosetta.protocols.canonical_sampling.BiasEnergy) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_values_to_job(...) from builtins.PyCapsule
- add_values_to_job(self : rosetta.protocols.canonical_sampling.BiasEnergy, pose : rosetta.core.pose.Pose, : rosetta.protocols.jd2.Job) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.protocols.canonical_sampling.BiasEnergy) -> rosetta.protocols.canonical_sampling.BiasEnergy
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose) -> float
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : int) -> NoneType
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int, temp_level : int, temperature : float) -> bool
- set_temperature(...) from builtins.PyCapsule
- set_temperature(self : rosetta.protocols.canonical_sampling.BiasEnergy, setting : float) -> NoneType
- swap_replicas(...) from builtins.PyCapsule
- swap_replicas(rosetta.protocols.canonical_sampling.BiasEnergy) -> NoneType
- update(...) from builtins.PyCapsule
- update(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose) -> NoneType
- write_to_string(...) from builtins.PyCapsule
- write_to_string(self : rosetta.protocols.canonical_sampling.BiasEnergy, str : str) -> NoneType
Methods inherited from ThermodynamicObserver:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose) -> NoneType
Callback executed after each move is made.
Even though the argument is a reference to a non-const pose,
this method should not make any changes to the pose. Making changes to
the pose is the role of the ThermodynamicMover class. The role of this
class is to simply observe the poses being generated.
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.moves.Mover) -> str
Each derived class must specify its name. The class name.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class BiasedMonteCarlo(rosetta.protocols.moves.MonteCarlo) |
| | |
- Method resolution order:
- BiasedMonteCarlo
- rosetta.protocols.moves.MonteCarlo
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, init_pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, temperature : float, bias_energy : rosetta.protocols.canonical_sampling.BiasEnergy) -> NoneType
2. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction, temperature : float, bias_energy : rosetta.protocols.canonical_sampling.BiasEnergy) -> NoneType
3. __init__(handle, rosetta.protocols.canonical_sampling.BiasedMonteCarlo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- bias_energy(...) from builtins.PyCapsule
- bias_energy(rosetta.protocols.canonical_sampling.BiasedMonteCarlo) -> rosetta.protocols.canonical_sampling.BiasEnergy
- boltzmann(...) from builtins.PyCapsule
- boltzmann(*args, **kwargs)
Overloaded function.
1. boltzmann(self : rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose : rosetta.core.pose.Pose) -> bool
Applies the Metropolis Criterion on pose based on
the ScoreFunction, temperature, and the last accepted
pose. This method evaluates the change in score, compares
the trial pose to the last accepted pose, and updates the
pose structure and simulation statistics appropriately
example(s):
mc.boltzmann( pose )
See also:
MonteCarlo
MonteCarlo.last_accepted_score
MonteCarlo.lowest_score
2. boltzmann(self : rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose : rosetta.core.pose.Pose, move_type : str) -> bool
Applies the Metropolis Criterion on pose based on
the ScoreFunction, temperature, and the last accepted
pose. This method evaluates the change in score, compares
the trial pose to the last accepted pose, and updates the
pose structure and simulation statistics appropriately
example(s):
mc.boltzmann( pose )
See also:
MonteCarlo
MonteCarlo.last_accepted_score
MonteCarlo.lowest_score
3. boltzmann(self : rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose : rosetta.core.pose.Pose, move_type : str, proposal_density_ratio : float) -> bool
Applies the Metropolis Criterion on pose based on
the ScoreFunction, temperature, and the last accepted
pose. This method evaluates the change in score, compares
the trial pose to the last accepted pose, and updates the
pose structure and simulation statistics appropriately
example(s):
mc.boltzmann( pose )
See also:
MonteCarlo
MonteCarlo.last_accepted_score
MonteCarlo.lowest_score
4. boltzmann(self : rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose : rosetta.core.pose.Pose, move_type : str, proposal_density_ratio : float, inner_score_delta_over_temperature : float) -> bool
Applies the Metropolis Criterion on pose based on
the ScoreFunction, temperature, and the last accepted
pose. This method evaluates the change in score, compares
the trial pose to the last accepted pose, and updates the
pose structure and simulation statistics appropriately
example(s):
mc.boltzmann( pose )
See also:
MonteCarlo
MonteCarlo.last_accepted_score
MonteCarlo.lowest_score
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.BiasedMonteCarlo) -> rosetta.protocols.moves.MonteCarlo
- reset(...) from builtins.PyCapsule
- reset(self : rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose : rosetta.core.pose.Pose) -> NoneType
- score_function(...) from builtins.PyCapsule
- score_function(self : rosetta.protocols.canonical_sampling.BiasedMonteCarlo, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- set_temperature(...) from builtins.PyCapsule
- set_temperature(self : rosetta.protocols.canonical_sampling.BiasedMonteCarlo, temp : float) -> NoneType
Methods inherited from rosetta.protocols.moves.MonteCarlo:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.moves.MonteCarlo) -> str
- change_weight(...) from builtins.PyCapsule
- change_weight(self : rosetta.protocols.moves.MonteCarlo, t : rosetta.core.scoring.ScoreType, setting : float) -> NoneType
Change the weight on a score term in the object's scorefunction. Useful when we don't want to reset the whole scorefunction during an annealing step.
- check_frequency(...) from builtins.PyCapsule
- check_frequency(rosetta.protocols.moves.MonteCarlo) -> int
- clear_poses(...) from builtins.PyCapsule
- clear_poses(rosetta.protocols.moves.MonteCarlo) -> NoneType
Removes last accepted pose and lowest score pose
example(s):
mc.clear_poses()
See also:
MonteCarlo
MonteCarlo.last_accepted_pose
MonteCarlo.lowest_score_pose
MonteCarlo.recover_low
MonteCarlo.reset
MonteCarlo.set_last_accepted_pose
MonteCarlo.set_lowest_score_pose
- eval_lowest_score_pose(...) from builtins.PyCapsule
- eval_lowest_score_pose(*args, **kwargs)
Overloaded function.
1. eval_lowest_score_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose) -> bool
Compares score of <pose> to the lowest score found.
If lower, sets the current lowest score pose and lowest score.
Use internal pose energies if score_pose is false.
Used to evaluate lowest score without boltzmann. Does not change pose structure.
Does not update simulation statistics or last accepts by default.
example(s):
mc.eval_lowest_score_pose( pose )
See also:
MonteCarlo
MonteCarlo.lowest_score
MonteCarlo.lowest_score_pose
MonteCarlo.recover_low
2. eval_lowest_score_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose, score_pose : bool) -> bool
Compares score of <pose> to the lowest score found.
If lower, sets the current lowest score pose and lowest score.
Use internal pose energies if score_pose is false.
Used to evaluate lowest score without boltzmann. Does not change pose structure.
Does not update simulation statistics or last accepts by default.
example(s):
mc.eval_lowest_score_pose( pose )
See also:
MonteCarlo
MonteCarlo.lowest_score
MonteCarlo.lowest_score_pose
MonteCarlo.recover_low
3. eval_lowest_score_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose, score_pose : bool, update_stats : bool) -> bool
Compares score of <pose> to the lowest score found.
If lower, sets the current lowest score pose and lowest score.
Use internal pose energies if score_pose is false.
Used to evaluate lowest score without boltzmann. Does not change pose structure.
Does not update simulation statistics or last accepts by default.
example(s):
mc.eval_lowest_score_pose( pose )
See also:
MonteCarlo
MonteCarlo.lowest_score
MonteCarlo.lowest_score_pose
MonteCarlo.recover_low
4. eval_lowest_score_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose, score_pose : bool, update_stats : bool, move_type : str) -> bool
Compares score of <pose> to the lowest score found.
If lower, sets the current lowest score pose and lowest score.
Use internal pose energies if score_pose is false.
Used to evaluate lowest score without boltzmann. Does not change pose structure.
Does not update simulation statistics or last accepts by default.
example(s):
mc.eval_lowest_score_pose( pose )
See also:
MonteCarlo
MonteCarlo.lowest_score
MonteCarlo.lowest_score_pose
MonteCarlo.recover_low
- get_update_boinc(...) from builtins.PyCapsule
- get_update_boinc(rosetta.protocols.moves.MonteCarlo) -> bool
- heat_after_cycles(...) from builtins.PyCapsule
- heat_after_cycles(rosetta.protocols.moves.MonteCarlo) -> int
no brief for now
- last_accept(...) from builtins.PyCapsule
- last_accept(rosetta.protocols.moves.MonteCarlo) -> int
Returns the number of trials since last acceptance
example(s):
mc.last_accept()
See also:
MonteCarlo
MonteCarlo.show_counters
MonteCarlo.last_accepted_pose
MonteCarlo.last_accepted_score
- last_accepted_pose(...) from builtins.PyCapsule
- last_accepted_pose(rosetta.protocols.moves.MonteCarlo) -> rosetta.core.pose.Pose
Returns the last accepted pose
example(s):
mc.last_accepted_pose()
See also:
MonteCarlo
MonteCarlo.last_accept
MonteCarlo.last_accepted_score
- last_accepted_score(...) from builtins.PyCapsule
- last_accepted_score(rosetta.protocols.moves.MonteCarlo) -> float
Returns the score value of the last accepted pose
example(s):
mc.last_accepted_score()
See also:
MonteCarlo
MonteCarlo.last_accept
MonteCarlo.last_accepted_pose
MonteCarlo.show_counters
MonteCarlo.show_scores
MonteCarlo.show_state
- lowest_score(...) from builtins.PyCapsule
- lowest_score(rosetta.protocols.moves.MonteCarlo) -> float
Returns the score value of the lowest score pose encountered
example(s):
mc.lowest_score()
See also:
MonteCarlo
MonteCarlo.lowest_score_pose
MonteCarlo.show_counters
MonteCarlo.show_scores
MonteCarlo.show_state
- lowest_score_pose(...) from builtins.PyCapsule
- lowest_score_pose(rosetta.protocols.moves.MonteCarlo) -> rosetta.core.pose.Pose
Returns the lowest score pose encountered
example(s):
mc.lowest_score_pose()
See also:
MonteCarlo
MonteCarlo.last_accepted_pose
MonteCarlo.lowest_score
- mc_accepted(...) from builtins.PyCapsule
- mc_accepted(rosetta.protocols.moves.MonteCarlo) -> rosetta.protocols.moves.MCA
Returns mc_accepted, informative of the last move applied
Note: Returns true for an accept, false otherwise
3 = accepted:score beat low score and last_accepted score
2 = accepted:score beat last_accepted score
1 = thermally accepted: score worse than last_accepted score
0 = not accepted
example(s):
mc.mc_accepted()
See also:
MonteCarlo
MonteCarlo.show_state
- mc_accepted_string(...) from builtins.PyCapsule
- mc_accepted_string(rosetta.protocols.moves.MonteCarlo) -> str
Returns mc_accepted as a human-readable string, informative of the last move applied
- push_back(...) from builtins.PyCapsule
- push_back(self : rosetta.protocols.moves.MonteCarlo, : protocols::moves::MonteCarloExceptionConverge) -> NoneType
no brief for now
- recover_low(...) from builtins.PyCapsule
- recover_low(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose) -> NoneType
Sets the input <pose> and last accepted pose to
the lowest score pose
example(s):
mc.recover_low( pose )
See also:
MonteCarlo
MonteCarlo.last_accept
MonteCarlo.last_accepted_pose
MonteCarlo.last_accepted_score
MonteCarlo.lowest_score
MonteCarlo.lowest_score_pose
- reset_counters(...) from builtins.PyCapsule
- reset_counters(rosetta.protocols.moves.MonteCarlo) -> NoneType
Resets the mover counters
example(s):
mc.reset_counters()
See alse:
MonteCarlo
MonteCarlo.show_counters
- reset_scorefxn(...) from builtins.PyCapsule
- reset_scorefxn(self : rosetta.protocols.moves.MonteCarlo, init_pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Resets the ScoreFunction
- set_autotemp(...) from builtins.PyCapsule
- set_autotemp(self : rosetta.protocols.moves.MonteCarlo, setting : bool, quench_temp : float) -> NoneType
Sets autotemp to quench_temp
example(s):
See also:
MonteCarlo
MonteCarlo.autotemp
MonteCarlo.show_state
- set_heat_after_cycles(...) from builtins.PyCapsule
- set_heat_after_cycles(self : rosetta.protocols.moves.MonteCarlo, setting : int) -> NoneType
no brief for now
- set_last_accepted_pose(...) from builtins.PyCapsule
- set_last_accepted_pose(*args, **kwargs)
Overloaded function.
1. set_last_accepted_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose) -> NoneType
Sets the last accepted pose to the score of <pose>
(does not reset counters)
2. set_last_accepted_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose, score : float) -> NoneType
Sets the last accepted pose and last accepted score
(does not reset counters)
- set_lowest_score_pose(...) from builtins.PyCapsule
- set_lowest_score_pose(*args, **kwargs)
Overloaded function.
1. set_lowest_score_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose) -> NoneType
2. set_lowest_score_pose(self : rosetta.protocols.moves.MonteCarlo, pose : rosetta.core.pose.Pose, score : float) -> NoneType
- set_update_boinc(...) from builtins.PyCapsule
- set_update_boinc(self : rosetta.protocols.moves.MonteCarlo, setting : bool) -> NoneType
no brief for now
- show_counters(...) from builtins.PyCapsule
- show_counters(rosetta.protocols.moves.MonteCarlo) -> NoneType
Displays the number of trials performed, fraction
of trial moves accepted, and the average energy drop per
accepted trial by mover types applied (unknown movers or
perturbations are listed as "unktrials")
example(s):
mc.show_counters()
Output as:
protocols.moves.MonteCarlo: unk trials= X; accepts= Y; energy_drop/trial= Z
See also:
MonteCarlo
MonteCarlo.show_scores
MonteCarlo.show_state
- show_scores(...) from builtins.PyCapsule
- show_scores(rosetta.protocols.moves.MonteCarlo) -> NoneType
Displays the last accepted score and the lowest score
example(s):
mc.show_scores()
Output as:
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: X Y
See also:
MonteCarlo
MonteCarlo.last_accepted_score
MonteCarlo.lowest_score
MonteCarlo.show_counters
MonteCarlo.show_state
- show_state(...) from builtins.PyCapsule
- show_state(rosetta.protocols.moves.MonteCarlo) -> NoneType
Displays the entire MonteCarlo state
temperature, scores, annealing settings,
move statistics, move counters (show_counters)
example(s):
mc.show_state()
Output as:
protocols.moves.MonteCarlo: MC: t l1 l2 las lws la au qu mca
t= temperature
l1= (*score_function_)(*last_accepted_pose_)
l2= (*score_function_)(*lowest_score_pose_)
las= last accepted score
lws= lowest score
la= last_accept_
au= autotemp_
qu= quench_temp_
mca= mc_accepted_
See also:
MonteCarlo
MonteCarlo.show_counters
MonteCarlo.show_scores
MonteCarlo.last_accepted_score
MonteCarlo.lowest_score
MonteCarlo.temperature
- temperature(...) from builtins.PyCapsule
- temperature(rosetta.protocols.moves.MonteCarlo) -> float
Returns the temperature value used in the Metropolis Criterion
example(s):
mc.temperature()
See also:
MonteCarlo
MonteCarlo.set_temperature
MonteCarlo.show_state
- total_score_of_last_considered_pose(...) from builtins.PyCapsule
- total_score_of_last_considered_pose(rosetta.protocols.moves.MonteCarlo) -> float
- total_trials(...) from builtins.PyCapsule
- total_trials(rosetta.protocols.moves.MonteCarlo) -> int
Returns the total number of trials since the last reset
: MonteCarlo.boltzmann(pose) updates the number of trials
example(s):
mc.total_trials()
See also:
MonteCarlo
MonteCarlo.last_accept
MonteCarlo.show_counters
MonteCarlo.show_state
|
class CanonicalSamplingMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- CanonicalSamplingMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, sfxn : rosetta.core.scoring.ScoreFunction, ptr : rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD, ntrial : int) -> NoneType
3. __init__(handle, rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_mover(...) from builtins.PyCapsule
- add_mover(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, m : rosetta.protocols.moves.Mover, weight : float) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, : rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> rosetta.protocols.canonical_sampling.CanonicalSamplingMover
- detailed_balance(...) from builtins.PyCapsule
- detailed_balance(*args, **kwargs)
Overloaded function.
1. detailed_balance(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse : bool) -> NoneType
2. detailed_balance(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool
- get_ABGEO_string(...) from builtins.PyCapsule
- get_ABGEO_string(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loops) -> str
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> str
- get_temp(...) from builtins.PyCapsule
- get_temp(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> float
- ntrials(...) from builtins.PyCapsule
- ntrials(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, ntrial : int) -> NoneType
- output_only_cluster_transitions(...) from builtins.PyCapsule
- output_only_cluster_transitions(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse : bool) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- set_defaults_from_cmdline(...) from builtins.PyCapsule
- set_defaults_from_cmdline(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> NoneType
- set_interval_data_dump(...) from builtins.PyCapsule
- set_interval_data_dump(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, d_interval : int) -> NoneType
- set_interval_pose_dump(...) from builtins.PyCapsule
- set_interval_pose_dump(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, p_interval : int) -> NoneType
- set_poolrmsd(...) from builtins.PyCapsule
- set_poolrmsd(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, ptr : rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD) -> NoneType
- set_scorefunction(...) from builtins.PyCapsule
- set_scorefunction(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- set_temp(...) from builtins.PyCapsule
- set_temp(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, temperature : float) -> NoneType
- transition_threshold(...) from builtins.PyCapsule
- transition_threshold(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> float
- use_MPI_bcast(...) from builtins.PyCapsule
- use_MPI_bcast(*args, **kwargs)
Overloaded function.
1. use_MPI_bcast(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse : bool) -> NoneType
2. use_MPI_bcast(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool
- use_MPI_sync_pools(...) from builtins.PyCapsule
- use_MPI_sync_pools(*args, **kwargs)
Overloaded function.
1. use_MPI_sync_pools(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse : bool) -> NoneType
2. use_MPI_sync_pools(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool
- use_hierarchical_clustering(...) from builtins.PyCapsule
- use_hierarchical_clustering(*args, **kwargs)
Overloaded function.
1. use_hierarchical_clustering(self : rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse : bool) -> NoneType
2. use_hierarchical_clustering(rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class DbTrajectoryRecorder(TrajectoryRecorder) |
| |
Record a trajectory to an SQL database.
This class builds upon Rosetta's database framework, which means
that there is support for SQLite3, MySQL and PostgreSQL. Database options
must be specified on the command line (i.e. there's no API for this):
|
| |
- Method resolution order:
- DbTrajectoryRecorder
- TrajectoryRecorder
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, job_id : int) -> NoneType
3. __init__(handle, rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) -> rosetta.protocols.moves.Mover
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) -> str
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
- job_id(...) from builtins.PyCapsule
- job_id(*args, **kwargs)
Overloaded function.
1. job_id(rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) -> int
Return the job id that will be used as a foreign key in the
trajectory table that gets generated.
2. job_id(self : rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, id : int) -> NoneType
Set the job id that will be used as a foreign key in the
trajectory table that gets generated.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int, temp_level : int, temperature : float) -> bool
Not implemented, except to complain if accidentally used.
Methods inherited from TrajectoryRecorder:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
- cache_limit(...) from builtins.PyCapsule
- cache_limit(*args, **kwargs)
Overloaded function.
1. cache_limit(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of poses that can be cached.
2. cache_limit(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit : int) -> NoneType
Specify the maximum number of poses that can be cached.
This option can also be specified on the command line using the
-trajectory:cache_limit flag. Note that some recorders don't
use a cache at all, and will therefore ignore this option.
- cumulate_jobs(...) from builtins.PyCapsule
- cumulate_jobs(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different jobs will be written to the
same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_jobs flag.
- cumulate_replicas(...) from builtins.PyCapsule
- cumulate_replicas(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different replicas will be written to
the same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_replicas flag.
- file_name(...) from builtins.PyCapsule
- file_name(*args, **kwargs)
Overloaded function.
1. file_name(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str
Return the file name for the trajectory.
2. file_name(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name : str) -> NoneType
Set the file name for the trajectory.
- model_count(...) from builtins.PyCapsule
- model_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of models that have been saved so far.
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
ThermodynamicObserver::observe_after_metropolis
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset(...) from builtins.PyCapsule
- reset(*args, **kwargs)
Overloaded function.
1. reset(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
Callback executed whenever the simulation is initialized or reset.
2. reset(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
Callback executed whenever the simulation is initialized or reset.
- step_count(...) from builtins.PyCapsule
- step_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of iterations that have occurred so far.
- stride(...) from builtins.PyCapsule
- stride(*args, **kwargs)
Overloaded function.
1. stride(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return how often models should be written to the trajectory.
2. stride(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride : int) -> NoneType
Set how often models should be written to the trajectory.
This option can also be specified on the command line using the
-trajectory:stride flag.
- update_after_boltzmann(...) from builtins.PyCapsule
- update_after_boltzmann(*args, **kwargs)
Overloaded function.
1. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
2. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
ThermodynamicObserver::apply
3. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
ThermodynamicObserver::apply
Methods inherited from ThermodynamicObserver:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> rosetta.protocols.canonical_sampling.ThermodynamicObserver
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class FixedTemperatureController(TemperatureController) |
| |
Maintain a constant temperature.
This is the default temperature controller used by
MetropolisHastingsMover.
|
| |
- Method resolution order:
- FixedTemperatureController
- TemperatureController
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, temp : float) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.FixedTemperatureController) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.FixedTemperatureController, : rosetta.protocols.canonical_sampling.FixedTemperatureController) -> rosetta.protocols.canonical_sampling.FixedTemperatureController
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.FixedTemperatureController) -> rosetta.protocols.moves.Mover
Return a copy of this mover.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.FixedTemperatureController) -> str
- temperature(...) from builtins.PyCapsule
- temperature(*args, **kwargs)
Overloaded function.
1. temperature(rosetta.protocols.canonical_sampling.FixedTemperatureController) -> float
2. temperature(self : rosetta.protocols.canonical_sampling.FixedTemperatureController, : int) -> float
- temperature_move(...) from builtins.PyCapsule
- temperature_move(self : rosetta.protocols.canonical_sampling.FixedTemperatureController, : float) -> float
Return the same constant temperature every time.
Methods inherited from TemperatureController:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.TemperatureController, : rosetta.core.pose.Pose) -> NoneType
No-op implemented only to satisfy the Mover interface.
- exchange_grid_dim(...) from builtins.PyCapsule
- exchange_grid_dim(rosetta.protocols.canonical_sampling.TemperatureController) -> int
- finished_simulation(...) from builtins.PyCapsule
- finished_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, trials : int, ntrials : int) -> bool
Return true if the simulation has been completed.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(*args, **kwargs)
Overloaded function.
1. initialize_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, level : int, temperature : float, cycle : int) -> NoneType
2. initialize_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) -> NoneType
- level_2_grid_coord(...) from builtins.PyCapsule
- level_2_grid_coord(self : rosetta.protocols.canonical_sampling.TemperatureController, level : int) -> rosetta.utility.vector1_unsigned_long
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.moves.MonteCarlo
Return const access to the MonteCarlo object being controlled.
- n_temp_levels(...) from builtins.PyCapsule
- n_temp_levels(rosetta.protocols.canonical_sampling.TemperatureController) -> int
Return the number of temperature levels used by this controller.
temperature_level()
- nlevels_per_dim(...) from builtins.PyCapsule
- nlevels_per_dim(self : rosetta.protocols.canonical_sampling.TemperatureController, : int) -> int
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TemperatureController, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Set the MonteCarlo object to be controlled.
- temperature_level(...) from builtins.PyCapsule
- temperature_level(rosetta.protocols.canonical_sampling.TemperatureController) -> int
Return the current temperature level.
Tempering controllers often work with a handful of discrete
temperature levels. This method makes it possible to work with levels,
which are discrete, rather than temperatures, which are continuous.
n_temp_levels()
temperature()
Methods inherited from ThermodynamicObserver:
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class HamiltonianExchange(AsyncMPITemperingBase) |
| | |
- Method resolution order:
- HamiltonianExchange
- AsyncMPITemperingBase
- TemperingBase
- TemperatureController
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.HamiltonianExchange) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.canonical_sampling.HamiltonianExchange) -> str
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, : rosetta.protocols.canonical_sampling.HamiltonianExchange) -> rosetta.protocols.canonical_sampling.HamiltonianExchange
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.HamiltonianExchange) -> rosetta.protocols.moves.Mover
- exchange_grid_dim(...) from builtins.PyCapsule
- exchange_grid_dim(rosetta.protocols.canonical_sampling.HamiltonianExchange) -> int
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.HamiltonianExchange) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.HamiltonianExchange) -> str
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(*args, **kwargs)
Overloaded function.
1. initialize_simulation(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
callback executed before any Monte Carlo trials
2. initialize_simulation(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, level : int, temperature : float, cycle : int) -> NoneType
- level_2_grid_coord(...) from builtins.PyCapsule
- level_2_grid_coord(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, level : int) -> rosetta.utility.vector1_unsigned_long
- next_exchange_schedule(...) from builtins.PyCapsule
- next_exchange_schedule(rosetta.protocols.canonical_sampling.HamiltonianExchange) -> NoneType
- nlevels_per_dim(...) from builtins.PyCapsule
- nlevels_per_dim(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, : int) -> int
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
- temperature_move(...) from builtins.PyCapsule
- temperature_move(*args, **kwargs)
Overloaded function.
1. temperature_move(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, score : float) -> float
not possible for HamExchange -- exit with ERROR if called
2. temperature_move(self : rosetta.protocols.canonical_sampling.HamiltonianExchange, pose : rosetta.core.pose.Pose) -> float
execute the temperatur move ( called by observer_after_metropolis )
returns the current temperatur in kT.
Methods inherited from AsyncMPITemperingBase:
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
callback executed after all Monte Carlo trials
- finished_simulation(...) from builtins.PyCapsule
- finished_simulation(self : rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, trials : int, ntrials : int) -> bool
Methods inherited from TemperingBase:
- n_temp_levels(...) from builtins.PyCapsule
- n_temp_levels(rosetta.protocols.canonical_sampling.TemperingBase) -> int
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- temperature(...) from builtins.PyCapsule
- temperature(*args, **kwargs)
Overloaded function.
1. temperature(rosetta.protocols.canonical_sampling.TemperingBase) -> float
Return the temperature of the underlying MonteCarlo object.
2. temperature(self : rosetta.protocols.canonical_sampling.TemperingBase, level : int) -> float
Return the temperature of the given level.
- temperature_level(...) from builtins.PyCapsule
- temperature_level(rosetta.protocols.canonical_sampling.TemperingBase) -> int
Methods inherited from TemperatureController:
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.moves.MonteCarlo
Return const access to the MonteCarlo object being controlled.
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
new input.
Methods inherited from ThermodynamicObserver:
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class MetricRecorder(ThermodynamicObserver) |
| |
Periodically output miscellaneous information.
This class is capable of writing out a variety of data related to
the trajectory. This includes the job name, the replica, the temperature,
and the score. Any number of torsion angles can also be added to the
report using add_torsion(). Methods are also provided for specifying an
output filename. Most of the IO work is done by update_after_boltzmann().
|
| |
- Method resolution order:
- MetricRecorder
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.MetricRecorder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_torsion(...) from builtins.PyCapsule
- add_torsion(*args, **kwargs)
Overloaded function.
1. add_torsion(self : rosetta.protocols.canonical_sampling.MetricRecorder, torsion_id : rosetta.core.id.TorsionID) -> NoneType
Include the given torsion in the output.
2. add_torsion(self : rosetta.protocols.canonical_sampling.MetricRecorder, torsion_id : rosetta.core.id.TorsionID, name : str) -> NoneType
Include the given torsion in the output.
3. add_torsion(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose, rsd : str, type : str, torsion : int) -> NoneType
Include the given torsion in the output.
4. add_torsion(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose, rsd : str, type : str, torsion : int, name : str) -> NoneType
Include the given torsion in the output.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose) -> NoneType
Just invoke update_after_boltzmann() with a const pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.MetricRecorder, : rosetta.protocols.canonical_sampling.MetricRecorder) -> rosetta.protocols.canonical_sampling.MetricRecorder
Assignment operator.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.MetricRecorder) -> rosetta.protocols.moves.Mover
Return a copy of this mover.
- cumulate_jobs(...) from builtins.PyCapsule
- cumulate_jobs(*args, **kwargs)
Overloaded function.
1. cumulate_jobs(rosetta.protocols.canonical_sampling.MetricRecorder) -> bool
Return true if every job is being reported to the same file.
2. cumulate_jobs(self : rosetta.protocols.canonical_sampling.MetricRecorder, cumulate_jobs : bool) -> NoneType
Indicate whether or not every job should be reported to the same
file.
- cumulate_replicas(...) from builtins.PyCapsule
- cumulate_replicas(*args, **kwargs)
Overloaded function.
1. cumulate_replicas(rosetta.protocols.canonical_sampling.MetricRecorder) -> bool
Return true if every replica is being reported to the same file.
2. cumulate_replicas(self : rosetta.protocols.canonical_sampling.MetricRecorder, cumulate_replicas : bool) -> NoneType
Indicate whether or not every replica should be reported to the
same file.
- file_name(...) from builtins.PyCapsule
- file_name(*args, **kwargs)
Overloaded function.
1. file_name(rosetta.protocols.canonical_sampling.MetricRecorder) -> str
Return the name of the file being written to.
2. file_name(self : rosetta.protocols.canonical_sampling.MetricRecorder, file_name : str) -> NoneType
Set the name of the file being written to.
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.MetricRecorder) -> rosetta.protocols.moves.Mover
Return a newly instantiated mover.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.MetricRecorder) -> str
Return the name of this mover.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.MetricRecorder, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- prepend_output_name(...) from builtins.PyCapsule
- prepend_output_name(*args, **kwargs)
Overloaded function.
1. prepend_output_name(rosetta.protocols.canonical_sampling.MetricRecorder) -> bool
Return true if the job name should be prepended onto the output
filename.
2. prepend_output_name(self : rosetta.protocols.canonical_sampling.MetricRecorder, prepend_output_name : bool) -> NoneType
Indicate whether or not the job name should be prepended onto the
output filename.
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.MetricRecorder) -> bool
Return true. This mover needs to be reinitialized for each job.
- reset(...) from builtins.PyCapsule
- reset(*args, **kwargs)
Overloaded function.
1. reset(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose) -> NoneType
Truncate the output file and rewrite the output header.
This method may not actually truncate the output file. It
really just closes and reopens the file, and I'm not sure whether or not
it picks a new name when it does the reopening.
2. reset(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
Truncate the output file and rewrite the output header.
This method may not actually truncate the output file. It
really just closes and reopens the file, and I'm not sure whether or not
it picks a new name when it does the reopening.
- stride(...) from builtins.PyCapsule
- stride(*args, **kwargs)
Overloaded function.
1. stride(rosetta.protocols.canonical_sampling.MetricRecorder) -> int
Return the frequency with which data is written.
2. stride(self : rosetta.protocols.canonical_sampling.MetricRecorder, stride : int) -> NoneType
Set the frequency with which data is written.
- update_after_boltzmann(...) from builtins.PyCapsule
- update_after_boltzmann(*args, **kwargs)
Overloaded function.
1. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose) -> NoneType
Write information like temperature, score, and torsion angles to a
file.
2. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.MetricRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
Write information like temperature, score, and torsion angles to a
file.
Methods inherited from ThermodynamicObserver:
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class MetropolisHastingsMover(rosetta.protocols.moves.Mover) |
| |
Manage the main loop of a canonical Monte Carlo simulation.
To make the simulation flexible, most aspects of the algorithm
have been delegated to other classes. Use the add_mover() methods to
control which moves are used during the simulation. Use the
set_tempering() method to control how the temperature changes during the
simulation. This can be used to setup simulated annealing or parallel
tempering runs. Management of the score function is delegated to the
underlying MonteCarlo object, so use set_monte_carlo() to specify a score
function. Use add_observer() to keep track of statistics and to record the
trajectory.
|
| |
- Method resolution order:
- MetropolisHastingsMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_backrub_mover(...) from builtins.PyCapsule
- add_backrub_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float) -> NoneType
Convenience method to add a backrub move to the simulation.
- add_kic_mover(...) from builtins.PyCapsule
- add_kic_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float, loop : rosetta.protocols.loops.Loop) -> NoneType
Convenience method to add a kinematic closure move to the
simulation.
- add_mover(...) from builtins.PyCapsule
- add_mover(*args, **kwargs)
Overloaded function.
1. add_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover : rosetta.protocols.canonical_sampling.ThermodynamicMover, weight : float, subtag : rosetta.utility.tag.Tag) -> NoneType
Add the given mover to the simulation.
2. add_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover : rosetta.protocols.canonical_sampling.ThermodynamicMover, weight : float) -> NoneType
Add the given mover to the simulation.
- add_observer(...) from builtins.PyCapsule
- add_observer(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, observer : rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> NoneType
Add the given observer to this simulation.
- add_shear_mover(...) from builtins.PyCapsule
- add_shear_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float) -> NoneType
Convenience method to add a shear move to the simulation.
- add_sidechain_mc_mover(...) from builtins.PyCapsule
- add_sidechain_mc_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float, prob_uniform : float, prob_withinrot : float, preserve_cbeta : bool, ntrials : int) -> NoneType
Convenience method to add a Monte Carlo sidechain move to the
simulation. This move uses an internal Monte Carlo loop to generate a
whole new set of sidechain conformations.
- add_sidechain_mover(...) from builtins.PyCapsule
- add_sidechain_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float, prob_uniform : float, prob_withinrot : float, preserve_cbeta : bool) -> NoneType
Convenience method to add a sidechain move to the simulation.
- add_small_mover(...) from builtins.PyCapsule
- add_small_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float) -> NoneType
Convenience method to add a small move to the simulation.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, pose : rosetta.core.pose.Pose) -> NoneType
Run the Metropolis-Hastings simulation.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.MetropolisHastingsMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.moves.Mover
Return a copy of this mover.
- current_trial(...) from builtins.PyCapsule
- current_trial(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> int
Return the iteration currently being processed by the simulation.
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.moves.Mover
Return a newly instantiated mover.
- get_last_checkpoint(...) from builtins.PyCapsule
- get_last_checkpoint(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> str
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> str
Return the name of this mover.
- last_accepted(...) from builtins.PyCapsule
- last_accepted(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> bool
Return true if the last attempted move was accepted.
- last_move(...) from builtins.PyCapsule
- last_move(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.ThermodynamicMover
Return the most recently used ThermodynamicMover.
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.moves.MonteCarlo
Return the MonteCarlo object being used by this simulation.
- ntrials(...) from builtins.PyCapsule
- ntrials(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> int
Return the number of iterations used by this simulation.
- output_file_name(...) from builtins.PyCapsule
- output_file_name(*args, **kwargs)
Overloaded function.
1. output_file_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix : str) -> str
Return a file name that is consistent with the given options.
If is true, the same filename will be returned
for different jobs, so that the jobs all get cumulated in the same file.
Likewise, if is true, the same filename will be
returned for all replicas. If either of these options are set, MPI must
be enabled.
2. output_file_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix : str, cumulate_jobs : bool) -> str
Return a file name that is consistent with the given options.
If is true, the same filename will be returned
for different jobs, so that the jobs all get cumulated in the same file.
Likewise, if is true, the same filename will be
returned for all replicas. If either of these options are set, MPI must
be enabled.
3. output_file_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix : str, cumulate_jobs : bool, cumulate_replicas : bool) -> str
Return a file name that is consistent with the given options.
If is true, the same filename will be returned
for different jobs, so that the jobs all get cumulated in the same file.
Likewise, if is true, the same filename will be
returned for all replicas. If either of these options are set, MPI must
be enabled.
- output_name(...) from builtins.PyCapsule
- output_name(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> str
Return the file name used by some of the observers to output data.
- random_mover(...) from builtins.PyCapsule
- random_mover(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.ThermodynamicMover
Return a randomly chosen mover to use in the next iteration.
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> bool
Return false. This mover does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> bool
Return false. This mover does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Provide a MonteCarlo object to use for this simulation.
- set_ntrials(...) from builtins.PyCapsule
- set_ntrials(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, ntrials : int) -> NoneType
Set the number of iterations to use for this simulation.
- set_output_name(...) from builtins.PyCapsule
- set_output_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, output_name : str) -> NoneType
Set the file name used by some of the observers to output data.
- set_tempering(...) from builtins.PyCapsule
- set_tempering(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : rosetta.protocols.canonical_sampling.TemperatureController) -> NoneType
Provide a TemperatureController to use for this simulation.
- tempering(...) from builtins.PyCapsule
- tempering(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.TemperatureController
Return the TemperatureController being used by this simulation.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class MultiTemperatureTrialCounter(builtins.object) |
| |
Keep track of trial statistics for any number of replicas.
This class helps MetropolisHastingsMover keep track of move
statistics. At the end of a simulation, operator[]() can be used to access
the TrialCounter objects kept for each temperature level. Alternatively,
the show() and write_to_file() methods can also be used to directly output
acceptance rates to a stream or file.
|
| |
Methods defined here:
- __getitem__(...) from builtins.PyCapsule
- __getitem__(*args, **kwargs)
Overloaded function.
1. __getitem__(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : int) -> rosetta.protocols.moves.TrialCounter
Return const access to the TrialCounter for the given temperature
level.
2. __getitem__(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : int) -> rosetta.protocols.moves.TrialCounter
Return non-const access to the TrialCounter for the given
temperature level.
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) -> NoneType
2. __init__(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : rosetta.protocols.canonical_sampling.TemperatureController) -> NoneType
3. __init__(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) -> rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter
- count_accepted(...) from builtins.PyCapsule
- count_accepted(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : str) -> NoneType
Note that a move of the given type was accepted.
- count_energy_drop(...) from builtins.PyCapsule
- count_energy_drop(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : str, : float) -> NoneType
Note that a move of the given type led to the given energy drop.
- count_trial(...) from builtins.PyCapsule
- count_trial(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : str) -> NoneType
Note that a move of the given type was attempted.
- reset(...) from builtins.PyCapsule
- reset(rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) -> NoneType
Set all counters for all temperatures to zero.
- set_temperature_observer(...) from builtins.PyCapsule
- set_temperature_observer(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : rosetta.protocols.canonical_sampling.TemperatureController) -> NoneType
Set the temperature controller.
- show(...) from builtins.PyCapsule
- show(rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) -> NoneType
Write acceptance rates for each move at each temperature to this
module's tracer.
- write_to_file(...) from builtins.PyCapsule
- write_to_file(self : rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, file : str, tag : str) -> NoneType
Write acceptance rates for each move at each temperature to the
given file.
|
class PDBTrajectoryRecorder(TrajectoryRecorder) |
| |
Record a trajectory to the PDB file format.
|
| |
- Method resolution order:
- PDBTrajectoryRecorder
- TrajectoryRecorder
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder) -> rosetta.protocols.moves.Mover
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder) -> str
- reset(...) from builtins.PyCapsule
- reset(*args, **kwargs)
Overloaded function.
1. reset(self : rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
2. reset(self : rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
Methods inherited from TrajectoryRecorder:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
- cache_limit(...) from builtins.PyCapsule
- cache_limit(*args, **kwargs)
Overloaded function.
1. cache_limit(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of poses that can be cached.
2. cache_limit(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit : int) -> NoneType
Specify the maximum number of poses that can be cached.
This option can also be specified on the command line using the
-trajectory:cache_limit flag. Note that some recorders don't
use a cache at all, and will therefore ignore this option.
- cumulate_jobs(...) from builtins.PyCapsule
- cumulate_jobs(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different jobs will be written to the
same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_jobs flag.
- cumulate_replicas(...) from builtins.PyCapsule
- cumulate_replicas(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different replicas will be written to
the same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_replicas flag.
- file_name(...) from builtins.PyCapsule
- file_name(*args, **kwargs)
Overloaded function.
1. file_name(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str
Return the file name for the trajectory.
2. file_name(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name : str) -> NoneType
Set the file name for the trajectory.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
ThermodynamicObserver::initialize_simulation
- model_count(...) from builtins.PyCapsule
- model_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of models that have been saved so far.
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
ThermodynamicObserver::observe_after_metropolis
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- step_count(...) from builtins.PyCapsule
- step_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of iterations that have occurred so far.
- stride(...) from builtins.PyCapsule
- stride(*args, **kwargs)
Overloaded function.
1. stride(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return how often models should be written to the trajectory.
2. stride(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride : int) -> NoneType
Set how often models should be written to the trajectory.
This option can also be specified on the command line using the
-trajectory:stride flag.
- update_after_boltzmann(...) from builtins.PyCapsule
- update_after_boltzmann(*args, **kwargs)
Overloaded function.
1. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
2. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
ThermodynamicObserver::apply
3. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
ThermodynamicObserver::apply
Methods inherited from ThermodynamicObserver:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> rosetta.protocols.canonical_sampling.ThermodynamicObserver
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class ParallelTempering(TemperingBase) |
| |
The only way to set the temperature range used for simulated
annealing is to use the command line. The relevant options are:
|
| |
- Method resolution order:
- ParallelTempering
- TemperingBase
- TemperatureController
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.ParallelTempering) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.ParallelTempering, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ParallelTempering, : rosetta.protocols.canonical_sampling.ParallelTempering) -> rosetta.protocols.canonical_sampling.ParallelTempering
Assignment operator.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.ParallelTempering) -> rosetta.protocols.moves.Mover
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ParallelTempering, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.ParallelTempering) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.ParallelTempering) -> str
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.ParallelTempering, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- temperature_move(...) from builtins.PyCapsule
- temperature_move(self : rosetta.protocols.canonical_sampling.ParallelTempering, score : float) -> float
Methods inherited from TemperingBase:
- n_temp_levels(...) from builtins.PyCapsule
- n_temp_levels(rosetta.protocols.canonical_sampling.TemperingBase) -> int
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- temperature(...) from builtins.PyCapsule
- temperature(*args, **kwargs)
Overloaded function.
1. temperature(rosetta.protocols.canonical_sampling.TemperingBase) -> float
Return the temperature of the underlying MonteCarlo object.
2. temperature(self : rosetta.protocols.canonical_sampling.TemperingBase, level : int) -> float
Return the temperature of the given level.
- temperature_level(...) from builtins.PyCapsule
- temperature_level(rosetta.protocols.canonical_sampling.TemperingBase) -> int
Methods inherited from TemperatureController:
- exchange_grid_dim(...) from builtins.PyCapsule
- exchange_grid_dim(rosetta.protocols.canonical_sampling.TemperatureController) -> int
- finished_simulation(...) from builtins.PyCapsule
- finished_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, trials : int, ntrials : int) -> bool
Return true if the simulation has been completed.
- level_2_grid_coord(...) from builtins.PyCapsule
- level_2_grid_coord(self : rosetta.protocols.canonical_sampling.TemperatureController, level : int) -> rosetta.utility.vector1_unsigned_long
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.moves.MonteCarlo
Return const access to the MonteCarlo object being controlled.
- nlevels_per_dim(...) from builtins.PyCapsule
- nlevels_per_dim(self : rosetta.protocols.canonical_sampling.TemperatureController, : int) -> int
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Set the MonteCarlo object to be controlled.
Methods inherited from ThermodynamicObserver:
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class ProgressBarObserver(ThermodynamicObserver) |
| |
Print an progress bar that updated on each iteration.
The progress bar is currently written to stdout, which of course
is not a tracer. I'm not really sure if this is a good idea or not. I
think it'd be cool to detect whether or not rosetta is attached to a TTY
and change how the progress bar is drawn depending. For example, when
writing to files it's nicer to not write carriage return '' characters.
|
| |
- Method resolution order:
- ProgressBarObserver
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.ProgressBarObserver) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ProgressBarObserver, : rosetta.protocols.canonical_sampling.ProgressBarObserver) -> rosetta.protocols.canonical_sampling.ProgressBarObserver
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.ProgressBarObserver) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.ProgressBarObserver) -> str
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.ProgressBarObserver, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ProgressBarObserver) -> bool
Return false, as a valid pose is not required for printing a
progress bar.
Methods inherited from ThermodynamicObserver:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose) -> NoneType
Callback executed after each move is made.
Even though the argument is a reference to a non-const pose,
this method should not make any changes to the pose. Making changes to
the pose is the role of the ThermodynamicMover class. The role of this
class is to simply observe the poses being generated.
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) -> NoneType
Callback executed before any Monte Carlo trials are attempted.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class SidechainMetropolisHastingsMover(MetropolisHastingsMover) |
| |
Run a sidechain-only canonical Monte Carlo simulation.
The Monte Carlo algorithm present in apply() has been optimized
for the case where only the sidechains can moves. This makes it possible
speed up score function evaluation by either precalculating and/or caching
residue pair energies. In this specific case, however, I'm not exactly
sure how the algorithm is doing its optimization.
Although this class inherits from MetropolisHastingsMover, it
doesn't support all of its parent's interface. In particular, since the
algorithm is customized for a particular sidechain move, movers added via
add_mover() or its related methods are ignored. However, observers added
via add_observer() can still be used to report on the state of the
simulation.
|
| |
- Method resolution order:
- SidechainMetropolisHastingsMover
- MetropolisHastingsMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, stride : int) -> NoneType
3. __init__(handle, rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, pose : rosetta.core.pose.Pose) -> NoneType
Run the sidechain-only simulation.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, : rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) -> str
- output_count(...) from builtins.PyCapsule
- output_count(self : rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, ct : int) -> int
Return non-zero if the observers should be invoked on this
iteration.
set_stride()
- pass_metropolis(...) from builtins.PyCapsule
- pass_metropolis(self : rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, delta_energy : float, last_proposal_density_ratio : float) -> bool
Return true if a move should be accepted, given
and
- set_stride(...) from builtins.PyCapsule
- set_stride(self : rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, setting : int) -> NoneType
Set the frequency with which the observers should be invoked.
output_count()
Methods inherited from MetropolisHastingsMover:
- add_backrub_mover(...) from builtins.PyCapsule
- add_backrub_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float) -> NoneType
Convenience method to add a backrub move to the simulation.
- add_kic_mover(...) from builtins.PyCapsule
- add_kic_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float, loop : rosetta.protocols.loops.Loop) -> NoneType
Convenience method to add a kinematic closure move to the
simulation.
- add_mover(...) from builtins.PyCapsule
- add_mover(*args, **kwargs)
Overloaded function.
1. add_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover : rosetta.protocols.canonical_sampling.ThermodynamicMover, weight : float, subtag : rosetta.utility.tag.Tag) -> NoneType
Add the given mover to the simulation.
2. add_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover : rosetta.protocols.canonical_sampling.ThermodynamicMover, weight : float) -> NoneType
Add the given mover to the simulation.
- add_observer(...) from builtins.PyCapsule
- add_observer(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, observer : rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> NoneType
Add the given observer to this simulation.
- add_shear_mover(...) from builtins.PyCapsule
- add_shear_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float) -> NoneType
Convenience method to add a shear move to the simulation.
- add_sidechain_mc_mover(...) from builtins.PyCapsule
- add_sidechain_mc_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float, prob_uniform : float, prob_withinrot : float, preserve_cbeta : bool, ntrials : int) -> NoneType
Convenience method to add a Monte Carlo sidechain move to the
simulation. This move uses an internal Monte Carlo loop to generate a
whole new set of sidechain conformations.
- add_sidechain_mover(...) from builtins.PyCapsule
- add_sidechain_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float, prob_uniform : float, prob_withinrot : float, preserve_cbeta : bool) -> NoneType
Convenience method to add a sidechain move to the simulation.
- add_small_mover(...) from builtins.PyCapsule
- add_small_mover(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight : float) -> NoneType
Convenience method to add a small move to the simulation.
- current_trial(...) from builtins.PyCapsule
- current_trial(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> int
Return the iteration currently being processed by the simulation.
- get_last_checkpoint(...) from builtins.PyCapsule
- get_last_checkpoint(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> str
- last_accepted(...) from builtins.PyCapsule
- last_accepted(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> bool
Return true if the last attempted move was accepted.
- last_move(...) from builtins.PyCapsule
- last_move(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.ThermodynamicMover
Return the most recently used ThermodynamicMover.
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.moves.MonteCarlo
Return the MonteCarlo object being used by this simulation.
- ntrials(...) from builtins.PyCapsule
- ntrials(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> int
Return the number of iterations used by this simulation.
- output_file_name(...) from builtins.PyCapsule
- output_file_name(*args, **kwargs)
Overloaded function.
1. output_file_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix : str) -> str
Return a file name that is consistent with the given options.
If is true, the same filename will be returned
for different jobs, so that the jobs all get cumulated in the same file.
Likewise, if is true, the same filename will be
returned for all replicas. If either of these options are set, MPI must
be enabled.
2. output_file_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix : str, cumulate_jobs : bool) -> str
Return a file name that is consistent with the given options.
If is true, the same filename will be returned
for different jobs, so that the jobs all get cumulated in the same file.
Likewise, if is true, the same filename will be
returned for all replicas. If either of these options are set, MPI must
be enabled.
3. output_file_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix : str, cumulate_jobs : bool, cumulate_replicas : bool) -> str
Return a file name that is consistent with the given options.
If is true, the same filename will be returned
for different jobs, so that the jobs all get cumulated in the same file.
Likewise, if is true, the same filename will be
returned for all replicas. If either of these options are set, MPI must
be enabled.
- output_name(...) from builtins.PyCapsule
- output_name(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> str
Return the file name used by some of the observers to output data.
- random_mover(...) from builtins.PyCapsule
- random_mover(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.ThermodynamicMover
Return a randomly chosen mover to use in the next iteration.
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> bool
Return false. This mover does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> bool
Return false. This mover does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Provide a MonteCarlo object to use for this simulation.
- set_ntrials(...) from builtins.PyCapsule
- set_ntrials(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, ntrials : int) -> NoneType
Set the number of iterations to use for this simulation.
- set_output_name(...) from builtins.PyCapsule
- set_output_name(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, output_name : str) -> NoneType
Set the file name used by some of the observers to output data.
- set_tempering(...) from builtins.PyCapsule
- set_tempering(self : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : rosetta.protocols.canonical_sampling.TemperatureController) -> NoneType
Provide a TemperatureController to use for this simulation.
- tempering(...) from builtins.PyCapsule
- tempering(rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> rosetta.protocols.canonical_sampling.TemperatureController
Return the TemperatureController being used by this simulation.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class SilentTrajectoryRecorder(TrajectoryRecorder) |
| |
Record a trajectory to the rosetta-specific silent file format.
|
| |
- Method resolution order:
- SilentTrajectoryRecorder
- TrajectoryRecorder
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder) -> str
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int, temp_level : int, temperature : float) -> bool
Methods inherited from TrajectoryRecorder:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
- cache_limit(...) from builtins.PyCapsule
- cache_limit(*args, **kwargs)
Overloaded function.
1. cache_limit(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of poses that can be cached.
2. cache_limit(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit : int) -> NoneType
Specify the maximum number of poses that can be cached.
This option can also be specified on the command line using the
-trajectory:cache_limit flag. Note that some recorders don't
use a cache at all, and will therefore ignore this option.
- cumulate_jobs(...) from builtins.PyCapsule
- cumulate_jobs(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different jobs will be written to the
same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_jobs flag.
- cumulate_replicas(...) from builtins.PyCapsule
- cumulate_replicas(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different replicas will be written to
the same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_replicas flag.
- file_name(...) from builtins.PyCapsule
- file_name(*args, **kwargs)
Overloaded function.
1. file_name(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str
Return the file name for the trajectory.
2. file_name(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name : str) -> NoneType
Set the file name for the trajectory.
- model_count(...) from builtins.PyCapsule
- model_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of models that have been saved so far.
- reset(...) from builtins.PyCapsule
- reset(*args, **kwargs)
Overloaded function.
1. reset(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
Callback executed whenever the simulation is initialized or reset.
2. reset(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
Callback executed whenever the simulation is initialized or reset.
- step_count(...) from builtins.PyCapsule
- step_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of iterations that have occurred so far.
- stride(...) from builtins.PyCapsule
- stride(*args, **kwargs)
Overloaded function.
1. stride(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return how often models should be written to the trajectory.
2. stride(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride : int) -> NoneType
Set how often models should be written to the trajectory.
This option can also be specified on the command line using the
-trajectory:stride flag.
- update_after_boltzmann(...) from builtins.PyCapsule
- update_after_boltzmann(*args, **kwargs)
Overloaded function.
1. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
2. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
ThermodynamicObserver::apply
3. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
ThermodynamicObserver::apply
Methods inherited from ThermodynamicObserver:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> rosetta.protocols.canonical_sampling.ThermodynamicObserver
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class SimulatedTempering(TemperingBase) |
| |
The only way to set the temperature range used for simulated
annealing is to use the command line. The relevant options are:
|
| |
- Method resolution order:
- SimulatedTempering
- TemperingBase
- TemperatureController
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.SimulatedTempering) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.SimulatedTempering, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.SimulatedTempering, : rosetta.protocols.canonical_sampling.SimulatedTempering) -> rosetta.protocols.canonical_sampling.SimulatedTempering
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.SimulatedTempering) -> rosetta.protocols.moves.Mover
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(*args, **kwargs)
Overloaded function.
1. finalize_simulation(self : rosetta.protocols.canonical_sampling.SimulatedTempering, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
callback executed after all Monte Carlo trials
2. finalize_simulation(self : rosetta.protocols.canonical_sampling.SimulatedTempering, output_name : str) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.canonical_sampling.SimulatedTempering) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.SimulatedTempering) -> str
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.SimulatedTempering, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
callback executed before any Monte Carlo trials
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- temperature_move(...) from builtins.PyCapsule
- temperature_move(self : rosetta.protocols.canonical_sampling.SimulatedTempering, score : float) -> float
execute the temperatur move ( called by observer_after_metropolis )
returns the current temperatur in kT.
Methods inherited from TemperingBase:
- n_temp_levels(...) from builtins.PyCapsule
- n_temp_levels(rosetta.protocols.canonical_sampling.TemperingBase) -> int
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- temperature(...) from builtins.PyCapsule
- temperature(*args, **kwargs)
Overloaded function.
1. temperature(rosetta.protocols.canonical_sampling.TemperingBase) -> float
Return the temperature of the underlying MonteCarlo object.
2. temperature(self : rosetta.protocols.canonical_sampling.TemperingBase, level : int) -> float
Return the temperature of the given level.
- temperature_level(...) from builtins.PyCapsule
- temperature_level(rosetta.protocols.canonical_sampling.TemperingBase) -> int
Methods inherited from TemperatureController:
- exchange_grid_dim(...) from builtins.PyCapsule
- exchange_grid_dim(rosetta.protocols.canonical_sampling.TemperatureController) -> int
- finished_simulation(...) from builtins.PyCapsule
- finished_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, trials : int, ntrials : int) -> bool
Return true if the simulation has been completed.
- level_2_grid_coord(...) from builtins.PyCapsule
- level_2_grid_coord(self : rosetta.protocols.canonical_sampling.TemperatureController, level : int) -> rosetta.utility.vector1_unsigned_long
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.moves.MonteCarlo
Return const access to the MonteCarlo object being controlled.
- nlevels_per_dim(...) from builtins.PyCapsule
- nlevels_per_dim(self : rosetta.protocols.canonical_sampling.TemperatureController, : int) -> int
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Set the MonteCarlo object to be controlled.
Methods inherited from ThermodynamicObserver:
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class TemperatureController(ThermodynamicObserver) |
| |
Base class for controlling the temperature of a simulation.
Many schemes to improve the performance of condensed phase Monte
Carlo simulations depends on changing the temperature of the system.
Common examples include simulated annealing and parallel tempering. This
class provides an interface for writing these algorithms. The most
important method is temperature_move(), which is responsible for actually
changing the temperature of the MonteCarlo object used for the underlying
simulation. Methods like temperature_level() are also provided for
managing a discrete number of different temperature levels, which is a
common feature of these algorithms.
The TemperingBase class serves a similar role to this one, but is geared
towards controllers that actually intend to change the temperature. This
class also is parent to FixedTemperatureController, which is the default
controller used by MetropolisHastingsMover.
|
| |
- Method resolution order:
- TemperatureController
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.TemperatureController) -> NoneType
2. __init__(rosetta.protocols.canonical_sampling.TemperatureController, rosetta.protocols.canonical_sampling.TemperatureController) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.TemperatureController, : rosetta.core.pose.Pose) -> NoneType
No-op implemented only to satisfy the Mover interface.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.TemperatureController, : rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.canonical_sampling.TemperatureController
- exchange_grid_dim(...) from builtins.PyCapsule
- exchange_grid_dim(rosetta.protocols.canonical_sampling.TemperatureController) -> int
- finished_simulation(...) from builtins.PyCapsule
- finished_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, trials : int, ntrials : int) -> bool
Return true if the simulation has been completed.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.TemperatureController) -> str
Return the name of this class.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(*args, **kwargs)
Overloaded function.
1. initialize_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, level : int, temperature : float, cycle : int) -> NoneType
2. initialize_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) -> NoneType
- level_2_grid_coord(...) from builtins.PyCapsule
- level_2_grid_coord(self : rosetta.protocols.canonical_sampling.TemperatureController, level : int) -> rosetta.utility.vector1_unsigned_long
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.moves.MonteCarlo
Return const access to the MonteCarlo object being controlled.
- n_temp_levels(...) from builtins.PyCapsule
- n_temp_levels(rosetta.protocols.canonical_sampling.TemperatureController) -> int
Return the number of temperature levels used by this controller.
temperature_level()
- nlevels_per_dim(...) from builtins.PyCapsule
- nlevels_per_dim(self : rosetta.protocols.canonical_sampling.TemperatureController, : int) -> int
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TemperatureController, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Set the MonteCarlo object to be controlled.
- temperature(...) from builtins.PyCapsule
- temperature(*args, **kwargs)
Overloaded function.
1. temperature(rosetta.protocols.canonical_sampling.TemperatureController) -> float
Return the current temperature.
2. temperature(self : rosetta.protocols.canonical_sampling.TemperatureController, level : int) -> float
Set the current temperature to match given level.
- temperature_level(...) from builtins.PyCapsule
- temperature_level(rosetta.protocols.canonical_sampling.TemperatureController) -> int
Return the current temperature level.
Tempering controllers often work with a handful of discrete
temperature levels. This method makes it possible to work with levels,
which are discrete, rather than temperatures, which are continuous.
n_temp_levels()
temperature()
- temperature_move(...) from builtins.PyCapsule
- temperature_move(*args, **kwargs)
Overloaded function.
1. temperature_move(self : rosetta.protocols.canonical_sampling.TemperatureController, score : float) -> float
Execute the temperature move.
This method is called by observe_after_metropolis() and is
expected to return the new temperature (in units of kT, to the extent
that that is meaningful in the context of rosetta).
2. temperature_move(self : rosetta.protocols.canonical_sampling.TemperatureController, pose : rosetta.core.pose.Pose) -> float
Execute a temperature move which depends on the current pose.
The default implementation just calls the pose-independent
temperature_pose() method with the energy of the given pose. However,
the HamiltonianExchange temperature controller needs to evaluate the
alternative Hamiltonian.
Methods inherited from ThermodynamicObserver:
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class TemperingBase(TemperatureController) |
| |
Base class for tempering Monte Carlo optimizations.
Many important Monte Carlo optimization techniques, like simulated
annealing and parallel tempering, depend on a changing temperature
schedule. TemperatureController provides the essential interface for
providing this functionality. This class provides a lot of useful
protected member functions, especially with regard to input (i.e.
command-line or file) and output (i.e. tracer or silent file).
That said, my first impression is that this class really limits what you
can do in terms of output. The emphasis seems to be on silent files, so it
would be hard to instead use (for example) database output. In general,
putting IO code in a base class seems like a bad idea. Better to do that
kind of stuff with object composition, so different IO formats can easily
be swapped in and out. Perhaps this would be a good target for a small
refactoring project.
|
| |
- Method resolution order:
- TemperingBase
- TemperatureController
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.TemperingBase) -> NoneType
2. __init__(rosetta.protocols.canonical_sampling.TemperingBase, rosetta.protocols.canonical_sampling.TemperingBase) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.TemperingBase, : rosetta.core.pose.Pose) -> NoneType
No-op implemented only to satisfy the Mover interface.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.TemperingBase, : rosetta.protocols.canonical_sampling.TemperingBase) -> rosetta.protocols.canonical_sampling.TemperingBase
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.TemperingBase, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.TemperingBase) -> str
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(*args, **kwargs)
Overloaded function.
1. initialize_simulation(self : rosetta.protocols.canonical_sampling.TemperingBase, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, cycle : int) -> NoneType
2. initialize_simulation(self : rosetta.protocols.canonical_sampling.TemperingBase, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, level : int, temperature : float, cycle : int) -> NoneType
- n_temp_levels(...) from builtins.PyCapsule
- n_temp_levels(rosetta.protocols.canonical_sampling.TemperingBase) -> int
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- temperature(...) from builtins.PyCapsule
- temperature(*args, **kwargs)
Overloaded function.
1. temperature(rosetta.protocols.canonical_sampling.TemperingBase) -> float
Return the temperature of the underlying MonteCarlo object.
2. temperature(self : rosetta.protocols.canonical_sampling.TemperingBase, level : int) -> float
Return the temperature of the given level.
- temperature_level(...) from builtins.PyCapsule
- temperature_level(rosetta.protocols.canonical_sampling.TemperingBase) -> int
Methods inherited from TemperatureController:
- exchange_grid_dim(...) from builtins.PyCapsule
- exchange_grid_dim(rosetta.protocols.canonical_sampling.TemperatureController) -> int
- finished_simulation(...) from builtins.PyCapsule
- finished_simulation(self : rosetta.protocols.canonical_sampling.TemperatureController, trials : int, ntrials : int) -> bool
Return true if the simulation has been completed.
- level_2_grid_coord(...) from builtins.PyCapsule
- level_2_grid_coord(self : rosetta.protocols.canonical_sampling.TemperatureController, level : int) -> rosetta.utility.vector1_unsigned_long
- monte_carlo(...) from builtins.PyCapsule
- monte_carlo(rosetta.protocols.canonical_sampling.TemperatureController) -> rosetta.protocols.moves.MonteCarlo
Return const access to the MonteCarlo object being controlled.
- nlevels_per_dim(...) from builtins.PyCapsule
- nlevels_per_dim(self : rosetta.protocols.canonical_sampling.TemperatureController, : int) -> int
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
each job.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.canonical_sampling.TemperatureController) -> bool
Return false. This class does not need to be reinitialized for
new input.
- set_monte_carlo(...) from builtins.PyCapsule
- set_monte_carlo(self : rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo : rosetta.protocols.moves.MonteCarlo) -> NoneType
Set the MonteCarlo object to be controlled.
- temperature_move(...) from builtins.PyCapsule
- temperature_move(*args, **kwargs)
Overloaded function.
1. temperature_move(self : rosetta.protocols.canonical_sampling.TemperatureController, score : float) -> float
Execute the temperature move.
This method is called by observe_after_metropolis() and is
expected to return the new temperature (in units of kT, to the extent
that that is meaningful in the context of rosetta).
2. temperature_move(self : rosetta.protocols.canonical_sampling.TemperatureController, pose : rosetta.core.pose.Pose) -> float
Execute a temperature move which depends on the current pose.
The default implementation just calls the pose-independent
temperature_pose() method with the energy of the given pose. However,
the HamiltonianExchange temperature controller needs to evaluate the
alternative Hamiltonian.
Methods inherited from ThermodynamicObserver:
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class ThermodynamicMover(rosetta.protocols.moves.Mover) |
| |
Base class for moves that can obey detailed balance.
In order to sample a thermodynamic state using a Monte Carlo
simulation, the moves must obey detailed balance. This base class provides
a framework for writing moves that can obey this condition. One
interesting method is set_preserve_detailed_balance(), which indicates
whether or not detailed balance needs to be obeyed. This flag makes it
possible to implement fancy (but biased) features for use in contexts where
rigorous thermodynamic sampling isn't needed. If the move requires a
non-unity proposal ratio to obey detailed balance, it can reimplement
last_proposal_density_ratio(). Support for movers that make multiple trial
moves under the hood is provided by is_multi_trial() and its related
methods. A number of callbacks, including initialize_simulation(),
observe_after_metropolis(), and finalize_simulation(), are also defined to
let the mover react to certain milestones in the simulation.
|
| |
- Method resolution order:
- ThermodynamicMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> NoneType
2. __init__(rosetta.protocols.canonical_sampling.ThermodynamicMover, rosetta.protocols.canonical_sampling.ThermodynamicMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, : rosetta.protocols.canonical_sampling.ThermodynamicMover) -> rosetta.protocols.canonical_sampling.ThermodynamicMover
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, cycle : int) -> NoneType
Callback executed before any Monte Carlo trials are attempted.
- is_multi_trial(...) from builtins.PyCapsule
- is_multi_trial(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> bool
Return true if the move performs multiple trials on each apply.
last_inner_score_delta_over_temperature()
metropolis_hastings_mover()
set_metropolis_hastings_mover()
- last_inner_score_delta_over_temperature(...) from builtins.PyCapsule
- last_inner_score_delta_over_temperature(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> float
If this is a multi-trial move, return the change in internal
score/temperature caused by the last call to apply().
is_multi_trial()
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> float
Return the proposal density ratio for last apply method.
- metropolis_hastings_mover(...) from builtins.PyCapsule
- metropolis_hastings_mover(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t
If this is a multi-trial move, return the MetropolisHastingsMover
being used internally.
is_multi_trial()
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after the Metropolis criterion is evaluated.
- preserve_detailed_balance(...) from builtins.PyCapsule
- preserve_detailed_balance(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> bool
Return true if detailed balance is being preserved (i.e. no branch
angle optimization).
- set_metropolis_hastings_mover(...) from builtins.PyCapsule
- set_metropolis_hastings_mover(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover : rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) -> NoneType
If this is a multi-trial move, set the MetropolisHastingsMover to
be used internally.
is_multi_trial()
- set_preserve_detailed_balance(...) from builtins.PyCapsule
- set_preserve_detailed_balance(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, preserve_detailed_balance : bool) -> NoneType
Set to true if detailed balance should be preserved (i.e. no
branch angle optimization). This will be set to true for all movers used
by MetropolisHastingsMover.
- torsion_id_ranges(...) from builtins.PyCapsule
- torsion_id_ranges(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_core_id_TorsionID_Range
Return a list specifying which torsions may be perturbed by
apply(), and the in what range each perturbation may be.
This method should probably not be pure virtual, and in fact
should probably not even exist. I searched most of the codebase, and
could only find it being used in one pilot app. It is also a somewhat
difficult method to write, which means that most of the implementations
are either untested or no-ops. It might be better to remove the method
altogether and implement it on a class-by-class basis as necessary.
Methods inherited from rosetta.protocols.moves.Mover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.moves.Mover, : rosetta.core.pose.Pose) -> NoneType
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.moves.Mover) -> str
Each derived class must specify its name. The class name.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class ThermodynamicObserver(rosetta.protocols.moves.Mover) |
| |
Base class for reporting and recording data from a simulation.
|
| |
- Method resolution order:
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> NoneType
2. __init__(rosetta.protocols.canonical_sampling.ThermodynamicObserver, rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose) -> NoneType
Callback executed after each move is made.
Even though the argument is a reference to a non-const pose,
this method should not make any changes to the pose. Making changes to
the pose is the role of the ThermodynamicMover class. The role of this
class is to simply observe the poses being generated.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> rosetta.protocols.canonical_sampling.ThermodynamicObserver
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) -> NoneType
Callback executed before any Monte Carlo trials are attempted.
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after the Metropolis criterion is evaluated.
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.moves.Mover) -> str
Each derived class must specify its name. The class name.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class TrajectoryRecorder(ThermodynamicObserver) |
| |
Base class for recording a simulation trajectory.
This class seems a little too geared towards file IO, which will
make it awkward to create the database trajectory subclass that I want.
But I'll get it to work one way or another.
|
| |
- Method resolution order:
- TrajectoryRecorder
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> NoneType
2. __init__(rosetta.protocols.canonical_sampling.TrajectoryRecorder, rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
- cache_limit(...) from builtins.PyCapsule
- cache_limit(*args, **kwargs)
Overloaded function.
1. cache_limit(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of poses that can be cached.
2. cache_limit(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit : int) -> NoneType
Specify the maximum number of poses that can be cached.
This option can also be specified on the command line using the
-trajectory:cache_limit flag. Note that some recorders don't
use a cache at all, and will therefore ignore this option.
- cumulate_jobs(...) from builtins.PyCapsule
- cumulate_jobs(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different jobs will be written to the
same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_jobs flag.
- cumulate_replicas(...) from builtins.PyCapsule
- cumulate_replicas(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> bool
Return true if poses from different replicas will be written to
the same trajectory file.
I suspect this is only meant to be used in the context of jd2.
This option can only be set from the command line using the
-trajectory:cumulate_replicas flag.
- file_name(...) from builtins.PyCapsule
- file_name(*args, **kwargs)
Overloaded function.
1. file_name(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str
Return the file name for the trajectory.
2. file_name(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name : str) -> NoneType
Set the file name for the trajectory.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str
Return the name of this mover.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
ThermodynamicObserver::initialize_simulation
- model_count(...) from builtins.PyCapsule
- model_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of models that have been saved so far.
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
ThermodynamicObserver::observe_after_metropolis
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset(...) from builtins.PyCapsule
- reset(*args, **kwargs)
Overloaded function.
1. reset(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
Callback executed whenever the simulation is initialized or reset.
2. reset(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
Callback executed whenever the simulation is initialized or reset.
- step_count(...) from builtins.PyCapsule
- step_count(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return the number of iterations that have occurred so far.
- stride(...) from builtins.PyCapsule
- stride(*args, **kwargs)
Overloaded function.
1. stride(rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int
Return how often models should be written to the trajectory.
2. stride(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride : int) -> NoneType
Set how often models should be written to the trajectory.
This option can also be specified on the command line using the
-trajectory:stride flag.
- update_after_boltzmann(...) from builtins.PyCapsule
- update_after_boltzmann(*args, **kwargs)
Overloaded function.
1. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose) -> NoneType
ThermodynamicObserver::apply
2. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
ThermodynamicObserver::apply
3. update_after_boltzmann(self : rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType
ThermodynamicObserver::apply
Methods inherited from ThermodynamicObserver:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> rosetta.protocols.canonical_sampling.ThermodynamicObserver
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class TrialCounterObserver(ThermodynamicObserver) |
| |
Record the acceptance rate for every type of move attempted.
Most of the work is done by observe_after_metropolis(). Separate
statistics are recorded for moves made at different temperature levels.
|
| |
- Method resolution order:
- TrialCounterObserver
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.canonical_sampling.TrialCounterObserver) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.TrialCounterObserver, : rosetta.protocols.canonical_sampling.TrialCounterObserver) -> rosetta.protocols.canonical_sampling.TrialCounterObserver
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.canonical_sampling.TrialCounterObserver) -> rosetta.protocols.moves.Mover
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.TrialCounterObserver, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.TrialCounterObserver) -> str
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.TrialCounterObserver, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int) -> NoneType
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.TrialCounterObserver, metropolis_hastings_mover : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.TrialCounterObserver) -> bool
Return false, as a valid pose is not required for counting trials.
Methods inherited from ThermodynamicObserver:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose) -> NoneType
Callback executed after each move is made.
Even though the argument is a reference to a non-const pose,
this method should not make any changes to the pose. Making changes to
the pose is the role of the ThermodynamicMover class. The role of this
class is to simply observe the poses being generated.
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int, : int, : float) -> bool
Attempt to restart the last simulation that was recorded by this
observer.
For example, consider an observer that records trajectories.
This method should open the file that was going to be written, read out
the last pose in that trajectory, and assign it to the given pose
reference so that the current trajectory can start from the same place.
Other observers may help setup other parts of the simulation.
This is not a particularly robust system, because it may require several
unrelated observers working in concert to properly reconstitute the
simulation. In fact, the restart feature in MetropolisHastingsMover is
currently commented out, so this method is never actually invoked. I
would advise reimplementing this method to utility_exit_with_message() in
any subclasses you write, so that you don't waste time writing an unused
method but so you don't confuse anyone if this feature gets revived in
the future.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class WTEBiasEnergy(BiasEnergy) |
| | |
- Method resolution order:
- WTEBiasEnergy
- BiasEnergy
- ThermodynamicObserver
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, stride : int, omega : float, gamma : float) -> NoneType
2. __init__(handle) -> NoneType
3. __init__(handle, rosetta.protocols.canonical_sampling.WTEBiasEnergy) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.canonical_sampling.WTEBiasEnergy, : rosetta.protocols.canonical_sampling.WTEBiasEnergy) -> rosetta.protocols.canonical_sampling.WTEBiasEnergy
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.canonical_sampling.WTEBiasEnergy) -> str
Methods inherited from BiasEnergy:
- add_values_to_job(...) from builtins.PyCapsule
- add_values_to_job(self : rosetta.protocols.canonical_sampling.BiasEnergy, pose : rosetta.core.pose.Pose, : rosetta.protocols.jd2.Job) -> NoneType
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose) -> float
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : int) -> NoneType
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> NoneType
- restart_simulation(...) from builtins.PyCapsule
- restart_simulation(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose, : rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle : int, temp_level : int, temperature : float) -> bool
- set_temperature(...) from builtins.PyCapsule
- set_temperature(self : rosetta.protocols.canonical_sampling.BiasEnergy, setting : float) -> NoneType
- swap_replicas(...) from builtins.PyCapsule
- swap_replicas(rosetta.protocols.canonical_sampling.BiasEnergy) -> NoneType
- update(...) from builtins.PyCapsule
- update(self : rosetta.protocols.canonical_sampling.BiasEnergy, : rosetta.core.pose.Pose) -> NoneType
- write_to_string(...) from builtins.PyCapsule
- write_to_string(self : rosetta.protocols.canonical_sampling.BiasEnergy, str : str) -> NoneType
Methods inherited from ThermodynamicObserver:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.canonical_sampling.ThermodynamicObserver, : rosetta.core.pose.Pose) -> NoneType
Callback executed after each move is made.
Even though the argument is a reference to a non-const pose,
this method should not make any changes to the pose. Making changes to
the pose is the role of the ThermodynamicMover class. The role of this
class is to simply observe the poses being generated.
- requires_pose(...) from builtins.PyCapsule
- requires_pose(rosetta.protocols.canonical_sampling.ThermodynamicObserver) -> bool
Return false if this observer does not require a valid pose.
TrialCounterObserver is an example of such an observer.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
| |