canonical_sampling¶

mc_convergence_checks

Bindings for protocols::canonical_sampling namespace

class pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase¶

Bases: TemperingBase

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::AsyncMPITemperingBase::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, : pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase) → pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase¶: C++: protocols::canonical_sampling::AsyncMPITemperingBase::operator=(const class protocols::canonical_sampling::AsyncMPITemperingBase &) –> class protocols::canonical_sampling::AsyncMPITemperingBase &

static attributes_for_tempering_base(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, : utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::TemperingBase::attributes_for_tempering_base(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, class utility::tag::XMLSchemaDefinition &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

exchange_grid_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶: C++: protocols::canonical_sampling::TemperatureController::exchange_grid_dim() const –> unsigned long

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

callback executed after all Monte Carlo trials

C++: protocols::canonical_sampling::AsyncMPITemperingBase::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

finished_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, trials: int, ntrials: int) → bool¶: C++: protocols::canonical_sampling::AsyncMPITemperingBase::finished_simulation(unsigned long, unsigned long) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → str¶: C++: protocols::canonical_sampling::TemperingBase::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(*args, **kwargs)¶

Overloaded function.

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) -> None

callback executed before any Monte Carlo trials

C++: protocols::canonical_sampling::AsyncMPITemperingBase::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, level: int, temperature: float, cycle: int) -> None

C++: protocols::canonical_sampling::AsyncMPITemperingBase::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long, double, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

level_2_grid_coord(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, level: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::canonical_sampling::TemperatureController::level_2_grid_coord(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → protocols::moves::MonteCarlo¶

Return const access to the MonteCarlo object being controlled.

C++: protocols::canonical_sampling::TemperatureController::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

n_temp_levels(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::n_temp_levels() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nlevels_per_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : int) → int¶: C++: protocols::canonical_sampling::TemperatureController::nlevels_per_dim(unsigned long) const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperingBase::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::TemperingBase::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Register the options used by this mover with the global options: system.

C++: protocols::canonical_sampling::TemperingBase::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo: protocols::moves::MonteCarlo) → None¶

Set the MonteCarlo object to be controlled.

C++: protocols::canonical_sampling::TemperatureController::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) -> float

Return the temperature of the underlying MonteCarlo object.

C++: protocols::canonical_sampling::TemperingBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, level: int) -> float

Return the temperature of the given level.

C++: protocols::canonical_sampling::TemperingBase::temperature(unsigned long) const –> double

temperature_level(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::temperature_level() const –> unsigned long

temperature_move(*args, **kwargs)¶

Overloaded function.

temperature_move(self: pyrosetta.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).

C++: protocols::canonical_sampling::TemperatureController::temperature_move(double) –> double

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, pose: pyrosetta.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.

C++: protocols::canonical_sampling::TemperatureController::temperature_move(class core::pose::Pose &) –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy¶

Bases: ThermodynamicObserver, JobOutputterObserver

add_values_to_job(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : protocols::jd2::Job) → None¶: C++: protocols::canonical_sampling::BiasEnergy::add_values_to_job(const class core::pose::Pose &, class protocols::jd2::Job &) const –> void

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose) → None¶

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.

C++: protocols::canonical_sampling::ThermodynamicObserver::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy) → pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy¶: C++: protocols::canonical_sampling::BiasEnergy::operator=(const class protocols::canonical_sampling::BiasEnergy &) –> class protocols::canonical_sampling::BiasEnergy &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

evaluate(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::canonical_sampling::BiasEnergy::evaluate(const class core::pose::Pose &) const –> double

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::BiasEnergy::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

Each derived class must specify its name. The class name.

C++: protocols::moves::Mover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) → None¶: C++: protocols::canonical_sampling::BiasEnergy::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::BiasEnergy::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::BiasEnergy::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, cycle: int, temp_level: int, temperature: float) → bool¶: C++: protocols::canonical_sampling::BiasEnergy::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, setting: float) → None¶: C++: protocols::canonical_sampling::BiasEnergy::set_temperature(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

swap_replicas(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy) → None¶: C++: protocols::canonical_sampling::BiasEnergy::swap_replicas() –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::BiasEnergy::update(const class core::pose::Pose &) –> void

write_to_string(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, str: str) → None¶: C++: protocols::canonical_sampling::BiasEnergy::write_to_string(std::string &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo¶

Bases: MonteCarlo

bias_energy(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo) → pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy¶: C++: protocols::canonical_sampling::BiasedMonteCarlo::bias_energy() –> class std::shared_ptr<class protocols::canonical_sampling::BiasEnergy>

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose: pyrosetta.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

C++: protocols::canonical_sampling::BiasedMonteCarlo::boltzmann(class core::pose::Pose &, const std::string &, const double, const double) –> bool

change_weight(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, t: pyrosetta.rosetta.core.scoring.ScoreType, setting: float) → None¶

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.

C++: protocols::moves::MonteCarlo::change_weight(const enum core::scoring::ScoreType &, const double &) –> void

check_frequency(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → int¶: C++: protocols::moves::MonteCarlo::check_frequency() const –> unsigned long

clear_poses(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

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

C++: protocols::moves::MonteCarlo::clear_poses() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶: C++: protocols::canonical_sampling::BiasedMonteCarlo::clone() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

eval_lowest_score_pose(*args, **kwargs)¶

Overloaded function.

eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool, update_stats: bool) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.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

C++: protocols::moves::MonteCarlo::eval_lowest_score_pose(class core::pose::Pose &, bool, bool, const std::string &) –> bool

get_update_boinc(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → bool¶: C++: protocols::moves::MonteCarlo::get_update_boinc() const –> bool

heat_after_cycles(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → int¶

no brief for now

C++: protocols::moves::MonteCarlo::heat_after_cycles() const –> unsigned long

last_accept(self: pyrosetta.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

C++: protocols::moves::MonteCarlo::last_accept() const –> unsigned long

last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → pyrosetta.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

C++: protocols::moves::MonteCarlo::last_accepted_pose() const –> const class core::pose::Pose &

last_accepted_score(self: pyrosetta.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

C++: protocols::moves::MonteCarlo::last_accepted_score() const –> double

last_score(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → float¶

Returns the score value of the last score

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

C++: protocols::moves::MonteCarlo::last_score() const –> double

lowest_score(self: pyrosetta.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

C++: protocols::moves::MonteCarlo::lowest_score() const –> double

lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → pyrosetta.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

C++: protocols::moves::MonteCarlo::lowest_score_pose() const –> const class core::pose::Pose &

mc_accepted(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → pyrosetta.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

C++: protocols::moves::MonteCarlo::mc_accepted() const –> enum protocols::moves::MCA

mc_accepted_string(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → str¶

Returns mc_accepted as a human-readable string, informative of the last move applied

C++: protocols::moves::MonteCarlo::mc_accepted_string() const –> std::string

push_back(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, : protocols::moves::MonteCarloExceptionConverge) → None¶

no brief for now

C++: protocols::moves::MonteCarlo::push_back(class std::shared_ptr<class protocols::moves::MonteCarloExceptionConverge>) –> void

recover_low(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

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

C++: protocols::moves::MonteCarlo::recover_low(class core::pose::Pose &) –> void

reset(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::BiasedMonteCarlo::reset(const class core::pose::Pose &) –> void

reset_counters(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

Resets the mover counters

example(s):
mc.reset_counters()

See alse:
MonteCarlo MonteCarlo.show_counters

C++: protocols::moves::MonteCarlo::reset_counters() –> void

reset_scorefxn(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, init_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Resets the ScoreFunction

C++: protocols::moves::MonteCarlo::reset_scorefxn(const class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

score_function(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::canonical_sampling::BiasedMonteCarlo::score_function(const class core::scoring::ScoreFunction &) –> void

set_autotemp(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: bool, quench_temp: float) → None¶

Sets autotemp to quench_temp: example(s): See also:

MonteCarlo MonteCarlo.autotemp MonteCarlo.show_state

C++: protocols::moves::MonteCarlo::set_autotemp(const bool, const double) –> void

set_heat_after_cycles(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: int) → None¶

no brief for now

C++: protocols::moves::MonteCarlo::set_heat_after_cycles(unsigned long) –> void

set_last_accepted(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) → None¶: C++: protocols::moves::MonteCarlo::set_last_accepted(double) –> void

set_last_accepted_pose(*args, **kwargs)¶

Overloaded function.

set_last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Sets the last accepted pose to the score of <pose>

(does not reset counters)

C++: protocols::moves::MonteCarlo::set_last_accepted_pose(const class core::pose::Pose &) –> void

set_last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None

Sets the last accepted pose and last accepted score

(does not reset counters)

C++: protocols::moves::MonteCarlo::set_last_accepted_pose(const class core::pose::Pose &, double) –> void

set_last_score(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) → None¶

Set the last score.

C++: protocols::moves::MonteCarlo::set_last_score(double) –> void

set_lowest(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) → None¶: C++: protocols::moves::MonteCarlo::set_lowest(double) –> void

set_lowest_score_pose(*args, **kwargs)¶

Overloaded function.

set_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::moves::MonteCarlo::set_lowest_score_pose(const class core::pose::Pose &) –> void

set_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None

C++: protocols::moves::MonteCarlo::set_lowest_score_pose(const class core::pose::Pose &, double) –> void

set_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo, temp: float) → None¶: C++: protocols::canonical_sampling::BiasedMonteCarlo::set_temperature(const double) –> void

set_total_score_last_considered(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) → None¶: C++: protocols::moves::MonteCarlo::set_total_score_last_considered(double) –> void

set_update_boinc(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: bool) → None¶

no brief for now

C++: protocols::moves::MonteCarlo::set_update_boinc(bool) –> void

show_counters(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

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

C++: protocols::moves::MonteCarlo::show_counters() const –> void

show_scores(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

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

C++: protocols::moves::MonteCarlo::show_scores() const –> void

show_state(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

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

C++: protocols::moves::MonteCarlo::show_state() const –> void

temperature(self: pyrosetta.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

C++: protocols::moves::MonteCarlo::temperature() const –> double

total_score_of_last_considered_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → float¶: C++: protocols::moves::MonteCarlo::total_score_of_last_considered_pose() const –> double

total_trials(self: pyrosetta.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

C++: protocols::moves::MonteCarlo::total_trials() const –> unsigned long

class pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover¶

Bases: Mover

add_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, m: pyrosetta.rosetta.protocols.moves.Mover, weight: float) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, : pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) → pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::operator=(const class protocols::canonical_sampling::CanonicalSamplingMover &) –> class protocols::canonical_sampling::CanonicalSamplingMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

detailed_balance(*args, **kwargs)¶

Overloaded function.

detailed_balance(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse: bool) -> None

C++: protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance(bool) –> void

detailed_balance(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool

C++: protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_ABGEO_string(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loops) → str¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(class core::pose::Pose &, class protocols::loops::Loops &) –> std::string

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) → str¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_temp(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) → float¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::get_temp() –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

ntrials(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, ntrial: int) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::ntrials(int) –> void

output_only_cluster_transitions(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse: bool) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::output_only_cluster_transitions(bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_defaults_from_cmdline(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::set_defaults_from_cmdline() –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_interval_data_dump(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, d_interval: int) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::set_interval_data_dump(int) –> void

set_interval_pose_dump(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, p_interval: int) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::set_interval_pose_dump(int) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_poolrmsd(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, ptr: pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::set_poolrmsd(class std::shared_ptr<class protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD>) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_temp(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, temperature: float) → None¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::set_temp(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

transition_threshold(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) → float¶: C++: protocols::canonical_sampling::CanonicalSamplingMover::transition_threshold() const –> double

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

use_MPI_bcast(*args, **kwargs)¶

Overloaded function.

use_MPI_bcast(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse: bool) -> None

C++: protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_bcast(bool) –> void

use_MPI_bcast(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool

C++: protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_bcast() const –> bool

use_MPI_sync_pools(*args, **kwargs)¶

Overloaded function.

use_MPI_sync_pools(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse: bool) -> None

C++: protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools(bool) –> void

use_MPI_sync_pools(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool

C++: protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools() const –> bool

use_hierarchical_clustering(*args, **kwargs)¶

Overloaded function.

use_hierarchical_clustering(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover, truefalse: bool) -> None

C++: protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering(bool) –> void

use_hierarchical_clustering(self: pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover) -> bool

C++: protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering() const –> bool

class pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder¶

Bases: 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):

class Frame¶

Bases: pybind11_object

Helper struct used store cached poses.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder.Frame, : pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder.Frame) → pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder.Frame¶: C++: protocols::canonical_sampling::DbTrajectoryRecorder::Frame::operator=(const struct protocols::canonical_sampling::DbTrajectoryRecorder::Frame &) –> struct protocols::canonical_sampling::DbTrajectoryRecorder::Frame &

property iteration¶

property pose¶

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver¶: C++: protocols::canonical_sampling::ThermodynamicObserver::operator=(const class protocols::canonical_sampling::ThermodynamicObserver &) –> class protocols::canonical_sampling::ThermodynamicObserver &

static attributes_for_trajectory_recorder(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::canonical_sampling::TrajectoryRecorder::attributes_for_trajectory_recorder(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

cache_limit(*args, **kwargs)¶

Overloaded function.

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return the number of poses that can be cached.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit() –> unsigned long

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit(unsigned long) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::DbTrajectoryRecorder::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cumulate_jobs(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs() const –> bool

cumulate_replicas(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas() const –> bool

file_name(*args, **kwargs)¶

Overloaded function.

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str

Return the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name() const –> const std::string &

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name: str) -> None

Set the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name(const std::string &) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::DbTrajectoryRecorder::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::DbTrajectoryRecorder::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder) → str¶: C++: protocols::canonical_sampling::DbTrajectoryRecorder::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶: C++: protocols::canonical_sampling::DbTrajectoryRecorder::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

job_id(*args, **kwargs)¶

Overloaded function.

job_id(self: pyrosetta.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.

C++: protocols::canonical_sampling::DbTrajectoryRecorder::job_id() const –> unsigned long

job_id(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, id: int) -> None

Set the job id that will be used as a foreign key in the: trajectory table that gets generated.

C++: protocols::canonical_sampling::DbTrajectoryRecorder::job_id(unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

model_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of models that have been saved so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::model_count() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

ThermodynamicObserver::observe_after_metropolis

C++: protocols::canonical_sampling::TrajectoryRecorder::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Configure this mover from a RosettaScripts tag.

C++: protocols::canonical_sampling::TrajectoryRecorder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Associate relevant options with the TemperedDocking class.

C++: protocols::canonical_sampling::TrajectoryRecorder::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None
reset(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

Callback executed whenever the simulation is initialized or reset.

C++: protocols::canonical_sampling::TrajectoryRecorder::reset(const class protocols::moves::MonteCarlo &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int, temp_level: int, temperature: float) → bool¶

Not implemented, except to complain if accidentally used.

C++: protocols::canonical_sampling::DbTrajectoryRecorder::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

step_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of iterations that have occurred so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::step_count() const –> unsigned long

stride(*args, **kwargs)¶

Overloaded function.

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return how often models should be written to the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride() const –> unsigned long

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride(unsigned long) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_after_boltzmann(*args, **kwargs)¶

Overloaded function.

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) -> None
update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class protocols::moves::MonteCarlo &) –> void

class pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator¶

Bases: MoverCreator

RosettaScripts factory for DbTrajectoryRecorder.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator, : pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator) → pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator¶: C++: protocols::canonical_sampling::DbTrajectoryRecorderCreator::operator=(const class protocols::canonical_sampling::DbTrajectoryRecorderCreator &) –> class protocols::canonical_sampling::DbTrajectoryRecorderCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::DbTrajectoryRecorderCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator) → str¶: C++: protocols::canonical_sampling::DbTrajectoryRecorderCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::canonical_sampling::DbTrajectoryRecorderCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController¶

Bases: TemperatureController

Maintain a constant temperature.

This is the default temperature controller used by MetropolisHastingsMover.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : pyrosetta.rosetta.core.pose.Pose) → None¶

No-op implemented only to satisfy the Mover interface.

C++: protocols::canonical_sampling::TemperatureController::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController, : pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController) → pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController¶: C++: protocols::canonical_sampling::FixedTemperatureController::operator=(const class protocols::canonical_sampling::FixedTemperatureController &) –> class protocols::canonical_sampling::FixedTemperatureController &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a copy of this mover.

C++: protocols::canonical_sampling::FixedTemperatureController::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

exchange_grid_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶: C++: protocols::canonical_sampling::TemperatureController::exchange_grid_dim() const –> unsigned long

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

finished_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, trials: int, ntrials: int) → bool¶

Return true if the simulation has been completed.

C++: protocols::canonical_sampling::TemperatureController::finished_simulation(unsigned long, unsigned long) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController) → str¶: C++: protocols::canonical_sampling::FixedTemperatureController::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(*args, **kwargs)¶

Overloaded function.

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, level: int, temperature: float, cycle: int) -> None

C++: protocols::canonical_sampling::TemperatureController::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long, double, unsigned long) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) -> None

C++: protocols::canonical_sampling::TemperatureController::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

level_2_grid_coord(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, level: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::canonical_sampling::TemperatureController::level_2_grid_coord(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → protocols::moves::MonteCarlo¶

Return const access to the MonteCarlo object being controlled.

C++: protocols::canonical_sampling::TemperatureController::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

n_temp_levels(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶

Return the number of temperature levels used by this controller.

temperature_level()

C++: protocols::canonical_sampling::TemperatureController::n_temp_levels() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nlevels_per_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : int) → int¶: C++: protocols::canonical_sampling::TemperatureController::nlevels_per_dim(unsigned long) const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperatureController::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo: protocols::moves::MonteCarlo) → None¶

Set the MonteCarlo object to be controlled.

C++: protocols::canonical_sampling::TemperatureController::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController) -> float

C++: protocols::canonical_sampling::FixedTemperatureController::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController, : int) -> float

C++: protocols::canonical_sampling::FixedTemperatureController::temperature(unsigned long) const –> double

temperature_level(self: pyrosetta.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()

C++: protocols::canonical_sampling::TemperatureController::temperature_level() const –> unsigned long

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController, : float) → float¶

Return the same constant temperature every time.

C++: protocols::canonical_sampling::FixedTemperatureController::temperature_move(double) –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange¶

Bases: AsyncMPITemperingBase

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::HamiltonianExchange::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, : pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange) → pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange¶: C++: protocols::canonical_sampling::HamiltonianExchange::operator=(const class protocols::canonical_sampling::HamiltonianExchange &) –> class protocols::canonical_sampling::HamiltonianExchange &

static attributes_for_tempering_base(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, : utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::TemperingBase::attributes_for_tempering_base(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, class utility::tag::XMLSchemaDefinition &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::HamiltonianExchange::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

exchange_grid_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange) → int¶: C++: protocols::canonical_sampling::HamiltonianExchange::exchange_grid_dim() const –> unsigned long

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

callback executed after all Monte Carlo trials

C++: protocols::canonical_sampling::AsyncMPITemperingBase::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

finished_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase, trials: int, ntrials: int) → bool¶: C++: protocols::canonical_sampling::AsyncMPITemperingBase::finished_simulation(unsigned long, unsigned long) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::HamiltonianExchange::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange) → str¶: C++: protocols::canonical_sampling::HamiltonianExchange::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(*args, **kwargs)¶

Overloaded function.

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) -> None

callback executed before any Monte Carlo trials

C++: protocols::canonical_sampling::HamiltonianExchange::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, level: int, temperature: float, cycle: int) -> None

C++: protocols::canonical_sampling::HamiltonianExchange::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long, double, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

level_2_grid_coord(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, level: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::canonical_sampling::HamiltonianExchange::level_2_grid_coord(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → protocols::moves::MonteCarlo¶

Return const access to the MonteCarlo object being controlled.

C++: protocols::canonical_sampling::TemperatureController::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

static mover_name() → str¶: C++: protocols::canonical_sampling::HamiltonianExchange::mover_name() –> std::string

n_temp_levels(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::n_temp_levels() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

next_exchange_schedule(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange) → None¶: C++: protocols::canonical_sampling::HamiltonianExchange::next_exchange_schedule() –> void

nlevels_per_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, : int) → int¶: C++: protocols::canonical_sampling::HamiltonianExchange::nlevels_per_dim(unsigned long) const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperingBase::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::HamiltonianExchange::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::HamiltonianExchange::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶: C++: protocols::canonical_sampling::HamiltonianExchange::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, monte_carlo: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶: C++: protocols::canonical_sampling::HamiltonianExchange::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, : pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::canonical_sampling::HamiltonianExchange::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) -> float

Return the temperature of the underlying MonteCarlo object.

C++: protocols::canonical_sampling::TemperingBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, level: int) -> float

Return the temperature of the given level.

C++: protocols::canonical_sampling::TemperingBase::temperature(unsigned long) const –> double

temperature_level(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::temperature_level() const –> unsigned long

temperature_move(*args, **kwargs)¶

Overloaded function.

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, score: float) -> float

not possible for HamExchange – exit with ERROR if called

C++: protocols::canonical_sampling::HamiltonianExchange::temperature_move(double) –> double

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange, pose: pyrosetta.rosetta.core.pose.Pose) -> float

execute the temperatur move ( called by observer_after_metropolis ): returns the current temperatur in kT.

C++: protocols::canonical_sampling::HamiltonianExchange::temperature_move(class core::pose::Pose &) –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator¶

Bases: MoverCreator

RosettaScripts factory for HamiltonianExchange.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator, : pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator) → pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator¶: C++: protocols::canonical_sampling::HamiltonianExchangeCreator::operator=(const class protocols::canonical_sampling::HamiltonianExchangeCreator &) –> class protocols::canonical_sampling::HamiltonianExchangeCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::HamiltonianExchangeCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator) → str¶: C++: protocols::canonical_sampling::HamiltonianExchangeCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::HamiltonianExchangeCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.InterpolationType¶

Bases: pybind11_object

Members:

linear

exponential

exponential = <InterpolationType.exponential: 1>¶

linear = <InterpolationType.linear: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder¶

Bases: 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().

add_torsion(*args, **kwargs)¶

Overloaded function.

add_torsion(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, torsion_id: pyrosetta.rosetta.core.id.TorsionID) -> None
add_torsion(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, torsion_id: pyrosetta.rosetta.core.id.TorsionID, name: str) -> None

Include the given torsion in the output.

C++: protocols::canonical_sampling::MetricRecorder::add_torsion(const class core::id::TorsionID &, const std::string &) –> void

add_torsion(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose, rsd: str, type: str, torsion: int) -> None
add_torsion(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose, rsd: str, type: str, torsion: int, name: str) -> None

Include the given torsion in the output.

C++: protocols::canonical_sampling::MetricRecorder::add_torsion(const class core::pose::Pose &, const std::string &, const std::string &, unsigned long, const std::string &) –> void

add_torsion(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, torsion: pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec) -> None

C++: protocols::canonical_sampling::MetricRecorder::add_torsion(const struct protocols::canonical_sampling::TorsionSpec &) –> void

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Just invoke update_after_boltzmann() with a const pose.

C++: protocols::canonical_sampling::MetricRecorder::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver¶: C++: protocols::canonical_sampling::ThermodynamicObserver::operator=(const class protocols::canonical_sampling::ThermodynamicObserver &) –> class protocols::canonical_sampling::ThermodynamicObserver &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a copy of this mover.

C++: protocols::canonical_sampling::MetricRecorder::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cumulate_jobs(*args, **kwargs)¶

Overloaded function.

cumulate_jobs(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) -> bool

Return true if every job is being reported to the same file.

C++: protocols::canonical_sampling::MetricRecorder::cumulate_jobs() const –> bool

cumulate_jobs(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, cumulate_jobs: bool) -> None

Indicate whether or not every job should be reported to the same: file.

C++: protocols::canonical_sampling::MetricRecorder::cumulate_jobs(bool) –> void

cumulate_replicas(*args, **kwargs)¶

Overloaded function.

cumulate_replicas(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) -> bool

Return true if every replica is being reported to the same file.

C++: protocols::canonical_sampling::MetricRecorder::cumulate_replicas() const –> bool

cumulate_replicas(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, cumulate_replicas: bool) -> None

Indicate whether or not every replica should be reported to the: same file.

C++: protocols::canonical_sampling::MetricRecorder::cumulate_replicas(bool) –> void

file_name(*args, **kwargs)¶

Overloaded function.

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) -> str

Return the name of the file being written to.

C++: protocols::canonical_sampling::MetricRecorder::file_name() const –> const std::string &

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, file_name: str) -> None

Set the name of the file being written to.

C++: protocols::canonical_sampling::MetricRecorder::file_name(const std::string &) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::MetricRecorder::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a newly instantiated mover.

C++: protocols::canonical_sampling::MetricRecorder::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) → str¶: C++: protocols::canonical_sampling::MetricRecorder::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶: C++: protocols::canonical_sampling::MetricRecorder::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::canonical_sampling::MetricRecorder::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::MetricRecorder::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Use a RosettaScripts tag to configure this mover.

C++: protocols::canonical_sampling::MetricRecorder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

prepend_output_name(*args, **kwargs)¶

Overloaded function.

prepend_output_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) -> bool

Return true if the job name should be prepended onto the output: filename.

C++: protocols::canonical_sampling::MetricRecorder::prepend_output_name() const –> bool

prepend_output_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, prepend_output_name: bool) -> None

Indicate whether or not the job name should be prepended onto the: output filename.

C++: protocols::canonical_sampling::MetricRecorder::prepend_output_name(bool) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::MetricRecorder::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) → bool¶

Return true. This mover needs to be reinitialized for each job.

C++: protocols::canonical_sampling::MetricRecorder::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose) -> None
reset(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

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.

C++: protocols::canonical_sampling::MetricRecorder::reset(const class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

stride(*args, **kwargs)¶

Overloaded function.

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder) -> int

Return the frequency with which data is written.

C++: protocols::canonical_sampling::MetricRecorder::stride() const –> unsigned long

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, stride: int) -> None

Set the frequency with which data is written.

C++: protocols::canonical_sampling::MetricRecorder::stride(unsigned long) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_after_boltzmann(*args, **kwargs)¶

Overloaded function.

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose) -> None
update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

Write information like temperature, score, and torsion angles to a: file.

C++: protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(const class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

class pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator¶

Bases: MoverCreator

RosettaScripts factory for MetricRecorder.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator, : pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator) → pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator¶: C++: protocols::canonical_sampling::MetricRecorderCreator::operator=(const class protocols::canonical_sampling::MetricRecorderCreator &) –> class protocols::canonical_sampling::MetricRecorderCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::MetricRecorderCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator) → str¶: C++: protocols::canonical_sampling::MetricRecorderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::MetricRecorderCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover¶

Bases: 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.

add_backrub_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float) → None¶

Convenience method to add a backrub move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_backrub_mover(double) –> void

static add_ct_name(: str) → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::add_ct_name(std::string) –> std::string

add_kic_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float, loop: pyrosetta.rosetta.protocols.loops.Loop) → None¶

Convenience method to add a kinematic closure move to the: simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_kic_mover(double, const class protocols::loops::Loop &) –> void

add_mover(*args, **kwargs)¶

Overloaded function.

add_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, weight: float, subtag: pyrosetta.rosetta.utility.tag.Tag) -> None

Add the given mover to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_mover(class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicMover>, double, const class std::shared_ptr<const class utility::tag::Tag> &) –> void

add_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, weight: float) -> None

Add the given mover to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_mover(class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicMover>, double) –> void

add_observer(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, observer: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → None¶

Add the given observer to this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_observer(class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicObserver>) –> void

add_shear_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float) → None¶

Convenience method to add a shear move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover(double) –> void

add_sidechain_mc_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float, prob_uniform: float, prob_withinrot: float, preserve_cbeta: bool, ntrials: int) → None¶

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.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mc_mover(double, double, double, bool, unsigned long) –> void

add_sidechain_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float, prob_uniform: float, prob_withinrot: float, preserve_cbeta: bool) → None¶

Convenience method to add a sidechain move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mover(double, double, double, bool) –> void

add_small_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float) → None¶

Convenience method to add a small move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover(double) –> void

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Run the Metropolis-Hastings simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::operator=(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> class protocols::canonical_sampling::MetropolisHastingsMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a copy of this mover.

C++: protocols::canonical_sampling::MetropolisHastingsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

current_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → int¶

Return the iteration currently being processed by the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::current_trial() const –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a newly instantiated mover.

C++: protocols::canonical_sampling::MetropolisHastingsMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_checkpoint(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::get_last_checkpoint() const –> std::string

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_accepted(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → bool¶

Return true if the last attempted move was accepted.

C++: protocols::canonical_sampling::MetropolisHastingsMover::last_accepted() const –> bool

last_move(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover¶

Return the most recently used ThermodynamicMover.

C++: protocols::canonical_sampling::MetropolisHastingsMover::last_move() const –> const class protocols::canonical_sampling::ThermodynamicMover &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶

Return the MonteCarlo object being used by this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

static mover_name() → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::mover_name() –> std::string

static mover_or_add_group_name() → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::mover_or_add_group_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

ntrials(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → int¶

Return the number of iterations used by this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::ntrials() const –> unsigned long

output_file_name(*args, **kwargs)¶

Overloaded function.

output_file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix: str) -> str
output_file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix: str, cumulate_jobs: bool) -> str
output_file_name(self: pyrosetta.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.

C++: protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(const std::string &, bool, bool) const –> std::string

output_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → str¶

Return the file name used by some of the observers to output data.

C++: protocols::canonical_sampling::MetropolisHastingsMover::output_name() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Use a RosettaScripts tag to configure this mover.

C++: protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

random_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover¶

Return a randomly chosen mover to use in the next iteration.

C++: protocols::canonical_sampling::MetropolisHastingsMover::random_mover() const –> class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicMover>

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → bool¶

Return false. This mover does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::MetropolisHastingsMover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → bool¶

Return false. This mover does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::MetropolisHastingsMover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, monte_carlo: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

Provide a MonteCarlo object to use for this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_ntrials(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, ntrials: int) → None¶

Set the number of iterations to use for this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_ntrials(unsigned long) –> void

set_output_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, output_name: str) → None¶

Set the file name used by some of the observers to output data.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_output_name(const std::string &) –> void

set_tempering(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → None¶

Provide a TemperatureController to use for this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_tempering(class std::shared_ptr<class protocols::canonical_sampling::TemperatureController>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

tempering(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController¶

Return the TemperatureController being used by this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::tempering() const –> class std::shared_ptr<const class protocols::canonical_sampling::TemperatureController>

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator¶

Bases: MoverCreator

RosettaScripts factory for MetropolisHastingsMover.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator, : pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator) → pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator¶: C++: protocols::canonical_sampling::MetropolisHastingsMoverCreator::operator=(const class protocols::canonical_sampling::MetropolisHastingsMoverCreator &) –> class protocols::canonical_sampling::MetropolisHastingsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶

Static alias for keyname(). Not sure why this is needed.

C++: protocols::canonical_sampling::MetropolisHastingsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator) → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::MetropolisHastingsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter¶

Bases: pybind11_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.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) → pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter¶: C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::operator=(const class protocols::canonical_sampling::MultiTemperatureTrialCounter &) –> class protocols::canonical_sampling::MultiTemperatureTrialCounter &

count_accepted(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : str) → None¶

Note that a move of the given type was accepted.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::count_accepted(const std::string &) –> void

count_energy_drop(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : str, : float) → None¶

Note that a move of the given type led to the given energy drop.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::count_energy_drop(const std::string &, double) –> void

count_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : str) → None¶

Note that a move of the given type was attempted.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::count_trial(const std::string &) –> void

reset(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) → None¶

Set all counters for all temperatures to zero.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::reset() –> void

set_temperature_observer(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → None¶

Set the temperature controller.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::set_temperature_observer(const class protocols::canonical_sampling::TemperatureController *) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, : pyrosetta.rosetta.std.ostream) -> None

Write acceptance rates for each move at each temperature to the: given stream.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::show(std::ostream &) const –> void

show(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter) -> None

Write acceptance rates for each move at each temperature to this: module’s tracer.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::show() const –> void

write_to_file(self: pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter, file: str, tag: str) → None¶

Write acceptance rates for each move at each temperature to the: given file.

C++: protocols::canonical_sampling::MultiTemperatureTrialCounter::write_to_file(const std::string &, const std::string &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder¶

Bases: TrajectoryRecorder

Record a trajectory to the PDB file format.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver¶: C++: protocols::canonical_sampling::ThermodynamicObserver::operator=(const class protocols::canonical_sampling::ThermodynamicObserver &) –> class protocols::canonical_sampling::ThermodynamicObserver &

static attributes_for_trajectory_recorder(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::canonical_sampling::TrajectoryRecorder::attributes_for_trajectory_recorder(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

cache_limit(*args, **kwargs)¶

Overloaded function.

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return the number of poses that can be cached.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit() –> unsigned long

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit(unsigned long) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorder::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cumulate_jobs(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs() const –> bool

cumulate_replicas(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas() const –> bool

file_name(*args, **kwargs)¶

Overloaded function.

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str

Return the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name() const –> const std::string &

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name: str) -> None

Set the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name(const std::string &) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorder::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorder::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder) → str¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorder::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

ThermodynamicObserver::initialize_simulation

C++: protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

model_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of models that have been saved so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::model_count() const –> unsigned long

static mover_name() → str¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorder::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

ThermodynamicObserver::observe_after_metropolis

C++: protocols::canonical_sampling::TrajectoryRecorder::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorder::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Associate relevant options with the TemperedDocking class.

C++: protocols::canonical_sampling::TrajectoryRecorder::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None
reset(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> None

C++: protocols::canonical_sampling::PDBTrajectoryRecorder::reset(const class protocols::moves::MonteCarlo &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

step_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of iterations that have occurred so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::step_count() const –> unsigned long

stride(*args, **kwargs)¶

Overloaded function.

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return how often models should be written to the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride() const –> unsigned long

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride(unsigned long) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_after_boltzmann(*args, **kwargs)¶

Overloaded function.

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) -> None
update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class protocols::moves::MonteCarlo &) –> void

class pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator¶

Bases: MoverCreator

RosettaScripts factory for PDBTrajectoryRecorder.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator, : pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator) → pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorderCreator::operator=(const class protocols::canonical_sampling::PDBTrajectoryRecorderCreator &) –> class protocols::canonical_sampling::PDBTrajectoryRecorderCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorderCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator) → str¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::PDBTrajectoryRecorderCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering¶

Bases: TemperingBase

The only way to set the temperature range used for simulated annealing is to use the command line. The relevant options are:

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::ParallelTempering::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering, : pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering) → pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering¶

Assignment operator.

C++: protocols::canonical_sampling::ParallelTempering::operator=(const class protocols::canonical_sampling::ParallelTempering &) –> class protocols::canonical_sampling::ParallelTempering &

static attributes_for_tempering_base(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, : utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::TemperingBase::attributes_for_tempering_base(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, class utility::tag::XMLSchemaDefinition &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::ParallelTempering::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

exchange_grid_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶: C++: protocols::canonical_sampling::TemperatureController::exchange_grid_dim() const –> unsigned long

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::ParallelTempering::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

finished_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, trials: int, ntrials: int) → bool¶

Return true if the simulation has been completed.

C++: protocols::canonical_sampling::TemperatureController::finished_simulation(unsigned long, unsigned long) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::ParallelTempering::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering) → str¶: C++: protocols::canonical_sampling::ParallelTempering::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle: int) → None¶: C++: protocols::canonical_sampling::ParallelTempering::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

level_2_grid_coord(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, level: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::canonical_sampling::TemperatureController::level_2_grid_coord(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → protocols::moves::MonteCarlo¶

Return const access to the MonteCarlo object being controlled.

C++: protocols::canonical_sampling::TemperatureController::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

static mover_name() → str¶: C++: protocols::canonical_sampling::ParallelTempering::mover_name() –> std::string

n_temp_levels(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::n_temp_levels() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nlevels_per_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : int) → int¶: C++: protocols::canonical_sampling::TemperatureController::nlevels_per_dim(unsigned long) const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperingBase::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::ParallelTempering::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::ParallelTempering::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶: C++: protocols::canonical_sampling::ParallelTempering::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo: protocols::moves::MonteCarlo) → None¶

Set the MonteCarlo object to be controlled.

C++: protocols::canonical_sampling::TemperatureController::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) -> float

Return the temperature of the underlying MonteCarlo object.

C++: protocols::canonical_sampling::TemperingBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, level: int) -> float

Return the temperature of the given level.

C++: protocols::canonical_sampling::TemperingBase::temperature(unsigned long) const –> double

temperature_level(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::temperature_level() const –> unsigned long

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering, score: float) → float¶: C++: protocols::canonical_sampling::ParallelTempering::temperature_move(double) –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator¶

Bases: MoverCreator

RosettaScripts factory for ParallelTempering.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator, : pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator) → pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator¶: C++: protocols::canonical_sampling::ParallelTemperingCreator::operator=(const class protocols::canonical_sampling::ParallelTemperingCreator &) –> class protocols::canonical_sampling::ParallelTemperingCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::ParallelTemperingCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator) → str¶: C++: protocols::canonical_sampling::ParallelTemperingCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::ParallelTemperingCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver¶

Bases: 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.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose) → None¶

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.

C++: protocols::canonical_sampling::ThermodynamicObserver::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver, : pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver) → pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver¶: C++: protocols::canonical_sampling::ProgressBarObserver::operator=(const class protocols::canonical_sampling::ProgressBarObserver &) –> class protocols::canonical_sampling::ProgressBarObserver &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::ProgressBarObserver::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver) → str¶: C++: protocols::canonical_sampling::ProgressBarObserver::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicObserver::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::ProgressBarObserver::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver) → bool¶

Return false, as a valid pose is not required for printing a: progress bar.

C++: protocols::canonical_sampling::ProgressBarObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator¶

Bases: MoverCreator

RosettaScripts factory for ProgressBarObserver.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator, : pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator) → pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator¶: C++: protocols::canonical_sampling::ProgressBarObserverCreator::operator=(const class protocols::canonical_sampling::ProgressBarObserverCreator &) –> class protocols::canonical_sampling::ProgressBarObserverCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::ProgressBarObserverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator) → str¶: C++: protocols::canonical_sampling::ProgressBarObserverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::canonical_sampling::ProgressBarObserverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover¶

Bases: 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.

add_backrub_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float) → None¶

Convenience method to add a backrub move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_backrub_mover(double) –> void

static add_ct_name(: str) → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::add_ct_name(std::string) –> std::string

add_kic_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float, loop: pyrosetta.rosetta.protocols.loops.Loop) → None¶

Convenience method to add a kinematic closure move to the: simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_kic_mover(double, const class protocols::loops::Loop &) –> void

add_mover(*args, **kwargs)¶

Overloaded function.

add_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, weight: float, subtag: pyrosetta.rosetta.utility.tag.Tag) -> None

Add the given mover to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_mover(class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicMover>, double, const class std::shared_ptr<const class utility::tag::Tag> &) –> void

add_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, mover: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, weight: float) -> None

Add the given mover to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_mover(class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicMover>, double) –> void

add_observer(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, observer: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → None¶

Add the given observer to this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_observer(class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicObserver>) –> void

add_shear_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float) → None¶

Convenience method to add a shear move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover(double) –> void

add_sidechain_mc_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float, prob_uniform: float, prob_withinrot: float, preserve_cbeta: bool, ntrials: int) → None¶

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.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mc_mover(double, double, double, bool, unsigned long) –> void

add_sidechain_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float, prob_uniform: float, prob_withinrot: float, preserve_cbeta: bool) → None¶

Convenience method to add a sidechain move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mover(double, double, double, bool) –> void

add_small_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, weight: float) → None¶

Convenience method to add a small move to the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover(double) –> void

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Run the sidechain-only simulation.

C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, : pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::operator=(const class protocols::canonical_sampling::SidechainMetropolisHastingsMover &) –> class protocols::canonical_sampling::SidechainMetropolisHastingsMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

current_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → int¶

Return the iteration currently being processed by the simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::current_trial() const –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_checkpoint(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::get_last_checkpoint() const –> std::string

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover) → str¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_accepted(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → bool¶

Return true if the last attempted move was accepted.

C++: protocols::canonical_sampling::MetropolisHastingsMover::last_accepted() const –> bool

last_move(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover¶

Return the most recently used ThermodynamicMover.

C++: protocols::canonical_sampling::MetropolisHastingsMover::last_move() const –> const class protocols::canonical_sampling::ThermodynamicMover &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶

Return the MonteCarlo object being used by this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

static mover_name() → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::mover_name() –> std::string

static mover_or_add_group_name() → str¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::mover_or_add_group_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

ntrials(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → int¶

Return the number of iterations used by this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::ntrials() const –> unsigned long

output_count(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, ct: int) → int¶

Return non-zero if the observers should be invoked on this

iteration.

set_stride()

C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::output_count(unsigned long) const –> unsigned long

output_file_name(*args, **kwargs)¶

Overloaded function.

output_file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix: str) -> str
output_file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, suffix: str, cumulate_jobs: bool) -> str
output_file_name(self: pyrosetta.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.

C++: protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(const std::string &, bool, bool) const –> std::string

output_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → str¶

Return the file name used by some of the observers to output data.

C++: protocols::canonical_sampling::MetropolisHastingsMover::output_name() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pass_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, delta_energy: float, last_proposal_density_ratio: float) → bool¶

Return true if a move should be accepted, given: and

C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(double, double) const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::MetropolisHastingsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

random_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover¶

Return a randomly chosen mover to use in the next iteration.

C++: protocols::canonical_sampling::MetropolisHastingsMover::random_mover() const –> class std::shared_ptr<class protocols::canonical_sampling::ThermodynamicMover>

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → bool¶

Return false. This mover does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::MetropolisHastingsMover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → bool¶

Return false. This mover does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::MetropolisHastingsMover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, monte_carlo: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

Provide a MonteCarlo object to use for this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_ntrials(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, ntrials: int) → None¶

Set the number of iterations to use for this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_ntrials(unsigned long) –> void

set_output_name(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, output_name: str) → None¶

Set the file name used by some of the observers to output data.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_output_name(const std::string &) –> void

set_stride(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover, setting: int) → None¶

Set the frequency with which the observers should be invoked.

output_count()

C++: protocols::canonical_sampling::SidechainMetropolisHastingsMover::set_stride(unsigned long) –> void

set_tempering(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, : pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → None¶

Provide a TemperatureController to use for this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::set_tempering(class std::shared_ptr<class protocols::canonical_sampling::TemperatureController>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

tempering(self: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController¶

Return the TemperatureController being used by this simulation.

C++: protocols::canonical_sampling::MetropolisHastingsMover::tempering() const –> class std::shared_ptr<const class protocols::canonical_sampling::TemperatureController>

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator¶

Bases: MoverCreator

RosettaScripts factory for SidechainMetropolisHastingsMover.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator, : pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator) → pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator::operator=(const class protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator &) –> class protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator) → str¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder¶

Bases: TrajectoryRecorder

Record a trajectory to the rosetta-specific silent file format.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver¶: C++: protocols::canonical_sampling::ThermodynamicObserver::operator=(const class protocols::canonical_sampling::ThermodynamicObserver &) –> class protocols::canonical_sampling::ThermodynamicObserver &

static attributes_for_trajectory_recorder(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::canonical_sampling::TrajectoryRecorder::attributes_for_trajectory_recorder(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

cache_limit(*args, **kwargs)¶

Overloaded function.

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return the number of poses that can be cached.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit() –> unsigned long

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit(unsigned long) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cumulate_jobs(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs() const –> bool

cumulate_replicas(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas() const –> bool

file_name(*args, **kwargs)¶

Overloaded function.

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str

Return the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name() const –> const std::string &

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name: str) -> None

Set the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name(const std::string &) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder) → str¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle: int) → None¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

model_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of models that have been saved so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::model_count() const –> unsigned long

static mover_name() → str¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Associates relevant options with the TemperedDocking class.

C++: protocols::canonical_sampling::SilentTrajectoryRecorder::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None
reset(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

Callback executed whenever the simulation is initialized or reset.

C++: protocols::canonical_sampling::TrajectoryRecorder::reset(const class protocols::moves::MonteCarlo &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle: int, temp_level: int, temperature: float) → bool¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

step_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of iterations that have occurred so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::step_count() const –> unsigned long

stride(*args, **kwargs)¶

Overloaded function.

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return how often models should be written to the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride() const –> unsigned long

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride(unsigned long) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_after_boltzmann(*args, **kwargs)¶

Overloaded function.

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) -> None
update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class protocols::moves::MonteCarlo &) –> void

class pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator¶

Bases: MoverCreator

RosettaScripts factory for SilentTrajectoryRecorder.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator, : pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator) → pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorderCreator::operator=(const class protocols::canonical_sampling::SilentTrajectoryRecorderCreator &) –> class protocols::canonical_sampling::SilentTrajectoryRecorderCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorderCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator) → str¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::SilentTrajectoryRecorderCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering¶

Bases: TemperingBase

The only way to set the temperature range used for simulated annealing is to use the command line. The relevant options are:

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::SimulatedTempering::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering, : pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering) → pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering¶: C++: protocols::canonical_sampling::SimulatedTempering::operator=(const class protocols::canonical_sampling::SimulatedTempering &) –> class protocols::canonical_sampling::SimulatedTempering &

static attributes_for_tempering_base(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, : utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::TemperingBase::attributes_for_tempering_base(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, class utility::tag::XMLSchemaDefinition &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SimulatedTempering::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

exchange_grid_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶: C++: protocols::canonical_sampling::TemperatureController::exchange_grid_dim() const –> unsigned long

finalize_simulation(*args, **kwargs)¶

Overloaded function.

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) -> None

callback executed after all Monte Carlo trials

C++: protocols::canonical_sampling::SimulatedTempering::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering, output_name: str) -> None

C++: protocols::canonical_sampling::SimulatedTempering::finalize_simulation(const std::string &) –> void

finished_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, trials: int, ntrials: int) → bool¶

Return true if the simulation has been completed.

C++: protocols::canonical_sampling::TemperatureController::finished_simulation(unsigned long, unsigned long) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SimulatedTempering::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering) → str¶: C++: protocols::canonical_sampling::SimulatedTempering::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle: int) → None¶

callback executed before any Monte Carlo trials

C++: protocols::canonical_sampling::SimulatedTempering::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

level_2_grid_coord(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, level: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::canonical_sampling::TemperatureController::level_2_grid_coord(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → protocols::moves::MonteCarlo¶

Return const access to the MonteCarlo object being controlled.

C++: protocols::canonical_sampling::TemperatureController::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

static mover_name() → str¶: C++: protocols::canonical_sampling::SimulatedTempering::mover_name() –> std::string

n_temp_levels(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::n_temp_levels() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nlevels_per_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : int) → int¶: C++: protocols::canonical_sampling::TemperatureController::nlevels_per_dim(unsigned long) const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperingBase::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::SimulatedTempering::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::SimulatedTempering::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶: C++: protocols::canonical_sampling::SimulatedTempering::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo: protocols::moves::MonteCarlo) → None¶

Set the MonteCarlo object to be controlled.

C++: protocols::canonical_sampling::TemperatureController::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) -> float

Return the temperature of the underlying MonteCarlo object.

C++: protocols::canonical_sampling::TemperingBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, level: int) -> float

Return the temperature of the given level.

C++: protocols::canonical_sampling::TemperingBase::temperature(unsigned long) const –> double

temperature_level(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::temperature_level() const –> unsigned long

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering, score: float) → float¶

execute the temperatur move ( called by observer_after_metropolis ): returns the current temperatur in kT.

C++: protocols::canonical_sampling::SimulatedTempering::temperature_move(double) –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator¶

Bases: MoverCreator

RosettaScripts factory for SimulatedTempering.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator, : pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator) → pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator¶: C++: protocols::canonical_sampling::SimulatedTemperingCreator::operator=(const class protocols::canonical_sampling::SimulatedTemperingCreator &) –> class protocols::canonical_sampling::SimulatedTemperingCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::SimulatedTemperingCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator) → str¶: C++: protocols::canonical_sampling::SimulatedTemperingCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::SimulatedTemperingCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController¶

Bases: 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.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : pyrosetta.rosetta.core.pose.Pose) → None¶

No-op implemented only to satisfy the Mover interface.

C++: protocols::canonical_sampling::TemperatureController::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController¶

This has substantially different behavior than the copy constructor.

C++: protocols::canonical_sampling::TemperatureController::operator=(const class protocols::canonical_sampling::TemperatureController &) –> class protocols::canonical_sampling::TemperatureController &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

exchange_grid_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶: C++: protocols::canonical_sampling::TemperatureController::exchange_grid_dim() const –> unsigned long

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

finished_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, trials: int, ntrials: int) → bool¶

Return true if the simulation has been completed.

C++: protocols::canonical_sampling::TemperatureController::finished_simulation(unsigned long, unsigned long) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → str¶

Return the name of this class.

C++: protocols::canonical_sampling::TemperatureController::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(*args, **kwargs)¶

Overloaded function.

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, level: int, temperature: float, cycle: int) -> None

C++: protocols::canonical_sampling::TemperatureController::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long, double, unsigned long) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) -> None

C++: protocols::canonical_sampling::TemperatureController::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

level_2_grid_coord(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, level: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::canonical_sampling::TemperatureController::level_2_grid_coord(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → protocols::moves::MonteCarlo¶

Return const access to the MonteCarlo object being controlled.

C++: protocols::canonical_sampling::TemperatureController::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

n_temp_levels(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶

Return the number of temperature levels used by this controller.

temperature_level()

C++: protocols::canonical_sampling::TemperatureController::n_temp_levels() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nlevels_per_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : int) → int¶: C++: protocols::canonical_sampling::TemperatureController::nlevels_per_dim(unsigned long) const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperatureController::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo: protocols::moves::MonteCarlo) → None¶

Set the MonteCarlo object to be controlled.

C++: protocols::canonical_sampling::TemperatureController::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) -> float

Return the current temperature.

C++: protocols::canonical_sampling::TemperatureController::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, level: int) -> float

Set the current temperature to match given level.

C++: protocols::canonical_sampling::TemperatureController::temperature(unsigned long) const –> double

temperature_level(self: pyrosetta.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()

C++: protocols::canonical_sampling::TemperatureController::temperature_level() const –> unsigned long

temperature_move(*args, **kwargs)¶

Overloaded function.

temperature_move(self: pyrosetta.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).

C++: protocols::canonical_sampling::TemperatureController::temperature_move(double) –> double

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, pose: pyrosetta.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.

C++: protocols::canonical_sampling::TemperatureController::temperature_move(class core::pose::Pose &) –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase¶

Bases: 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.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, : pyrosetta.rosetta.core.pose.Pose) → None¶

No-op implemented only to satisfy the Mover interface.

C++: protocols::canonical_sampling::TemperingBase::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, : pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase¶: C++: protocols::canonical_sampling::TemperingBase::operator=(const class protocols::canonical_sampling::TemperingBase &) –> class protocols::canonical_sampling::TemperingBase &

static attributes_for_tempering_base(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, : utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::TemperingBase::attributes_for_tempering_base(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, class utility::tag::XMLSchemaDefinition &) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

exchange_grid_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → int¶: C++: protocols::canonical_sampling::TemperatureController::exchange_grid_dim() const –> unsigned long

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperingBase::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

finished_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, trials: int, ntrials: int) → bool¶

Return true if the simulation has been completed.

C++: protocols::canonical_sampling::TemperatureController::finished_simulation(unsigned long, unsigned long) –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → str¶: C++: protocols::canonical_sampling::TemperingBase::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(*args, **kwargs)¶

Overloaded function.

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) -> None

C++: protocols::canonical_sampling::TemperingBase::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, level: int, temperature: float, cycle: int) -> None

C++: protocols::canonical_sampling::TemperingBase::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long, double, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

level_2_grid_coord(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, level: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::canonical_sampling::TemperatureController::level_2_grid_coord(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → protocols::moves::MonteCarlo¶

Return const access to the MonteCarlo object being controlled.

C++: protocols::canonical_sampling::TemperatureController::monte_carlo() const –> class std::shared_ptr<const class protocols::moves::MonteCarlo>

n_temp_levels(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::n_temp_levels() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nlevels_per_dim(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, : int) → int¶: C++: protocols::canonical_sampling::TemperatureController::nlevels_per_dim(unsigned long) const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TemperingBase::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::TemperingBase::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Register the options used by this mover with the global options: system.

C++: protocols::canonical_sampling::TemperingBase::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: each job.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController) → bool¶

Return false. This class does not need to be reinitialized for: new input.

C++: protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_monte_carlo(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, monte_carlo: protocols::moves::MonteCarlo) → None¶

Set the MonteCarlo object to be controlled.

C++: protocols::canonical_sampling::TemperatureController::set_monte_carlo(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) -> float

Return the temperature of the underlying MonteCarlo object.

C++: protocols::canonical_sampling::TemperingBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase, level: int) -> float

Return the temperature of the given level.

C++: protocols::canonical_sampling::TemperingBase::temperature(unsigned long) const –> double

temperature_level(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase) → int¶: C++: protocols::canonical_sampling::TemperingBase::temperature_level() const –> unsigned long

temperature_move(*args, **kwargs)¶

Overloaded function.

temperature_move(self: pyrosetta.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).

C++: protocols::canonical_sampling::TemperatureController::temperature_move(double) –> double

temperature_move(self: pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController, pose: pyrosetta.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.

C++: protocols::canonical_sampling::TemperatureController::temperature_move(class core::pose::Pose &) –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover¶

Bases: 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.

apply(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.core.pose.Pose) → None¶

Main Method

C++: protocols::moves::Mover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover¶: C++: protocols::canonical_sampling::ThermodynamicMover::operator=(const class protocols::canonical_sampling::ThermodynamicMover &) –> class protocols::canonical_sampling::ThermodynamicMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

Each derived class must specify its name. The class name.

C++: protocols::moves::Mover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.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()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.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()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.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()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if detailed balance is being preserved (i.e. no branch: angle optimization).

C++: protocols::canonical_sampling::ThermodynamicMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, preserve_detailed_balance: bool) → None¶

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.

C++: protocols::canonical_sampling::ThermodynamicMover::set_preserve_detailed_balance(bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver¶

Bases: Mover

Base class for reporting and recording data from a simulation.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose) → None¶

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.

C++: protocols::canonical_sampling::ThermodynamicObserver::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver¶: C++: protocols::canonical_sampling::ThermodynamicObserver::operator=(const class protocols::canonical_sampling::ThermodynamicObserver &) –> class protocols::canonical_sampling::ThermodynamicObserver &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

Each derived class must specify its name. The class name.

C++: protocols::moves::Mover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicObserver::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicObserver::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec¶

Bases: pybind11_object

A simple class to hold info about torsions to use (deferred parsing)

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec, : pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec) → pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec¶: C++: protocols::canonical_sampling::TorsionSpec::operator=(const struct protocols::canonical_sampling::TorsionSpec &) –> struct protocols::canonical_sampling::TorsionSpec &

property name¶

property number¶

property rsd¶

property style¶

property type¶

class pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpecStyle¶

Bases: pybind11_object

Members:

Single

AllChi

AllBB

AllBB = <TorsionSpecStyle.AllBB: 2>¶

AllChi = <TorsionSpecStyle.AllChi: 1>¶

Single = <TorsionSpecStyle.Single: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder¶

Bases: 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.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver¶: C++: protocols::canonical_sampling::ThermodynamicObserver::operator=(const class protocols::canonical_sampling::ThermodynamicObserver &) –> class protocols::canonical_sampling::ThermodynamicObserver &

static attributes_for_trajectory_recorder(: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::canonical_sampling::TrajectoryRecorder::attributes_for_trajectory_recorder(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

cache_limit(*args, **kwargs)¶

Overloaded function.

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return the number of poses that can be cached.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit() –> unsigned long

cache_limit(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, limit: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cache_limit(unsigned long) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cumulate_jobs(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs() const –> bool

cumulate_replicas(self: pyrosetta.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.

C++: protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas() const –> bool

file_name(*args, **kwargs)¶

Overloaded function.

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> str

Return the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name() const –> const std::string &

file_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, file_name: str) -> None

Set the file name for the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::file_name(const std::string &) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → str¶

Return the name of this mover.

C++: protocols::canonical_sampling::TrajectoryRecorder::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

ThermodynamicObserver::initialize_simulation

C++: protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

model_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of models that have been saved so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::model_count() const –> unsigned long

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

ThermodynamicObserver::observe_after_metropolis

C++: protocols::canonical_sampling::TrajectoryRecorder::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Configure this mover from a RosettaScripts tag.

C++: protocols::canonical_sampling::TrajectoryRecorder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Associate relevant options with the TemperedDocking class.

C++: protocols::canonical_sampling::TrajectoryRecorder::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None
reset(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

Callback executed whenever the simulation is initialized or reset.

C++: protocols::canonical_sampling::TrajectoryRecorder::reset(const class protocols::moves::MonteCarlo &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

step_count(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) → int¶

Return the number of iterations that have occurred so far.

C++: protocols::canonical_sampling::TrajectoryRecorder::step_count() const –> unsigned long

stride(*args, **kwargs)¶

Overloaded function.

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder) -> int

Return how often models should be written to the trajectory.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride() const –> unsigned long

stride(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, stride: int) -> None

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.

C++: protocols::canonical_sampling::TrajectoryRecorder::stride(unsigned long) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_after_boltzmann(*args, **kwargs)¶

Overloaded function.

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose) -> None
update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover *) –> void

update_after_boltzmann(self: pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> None

ThermodynamicObserver::apply

C++: protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann(const class protocols::moves::MonteCarlo &) –> void

class pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver¶

Bases: 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.

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose) → None¶

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.

C++: protocols::canonical_sampling::ThermodynamicObserver::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver, : pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver) → pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver¶: C++: protocols::canonical_sampling::TrialCounterObserver::operator=(const class protocols::canonical_sampling::TrialCounterObserver &) –> class protocols::canonical_sampling::TrialCounterObserver &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::TrialCounterObserver::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TrialCounterObserver::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver) → str¶: C++: protocols::canonical_sampling::TrialCounterObserver::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover, cycle: int) → None¶: C++: protocols::canonical_sampling::TrialCounterObserver::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::canonical_sampling::TrialCounterObserver::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver, metropolis_hastings_mover: pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::TrialCounterObserver::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::TrialCounterObserver::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver) → bool¶

Return false, as a valid pose is not required for counting trials.

C++: protocols::canonical_sampling::TrialCounterObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator¶

Bases: MoverCreator

RosettaScripts factory for TrialCounterObserver.

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator, : pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator) → pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator¶: C++: protocols::canonical_sampling::TrialCounterObserverCreator::operator=(const class protocols::canonical_sampling::TrialCounterObserverCreator &) –> class protocols::canonical_sampling::TrialCounterObserverCreator &

create_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::canonical_sampling::TrialCounterObserverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator) → str¶: C++: protocols::canonical_sampling::TrialCounterObserverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::canonical_sampling::TrialCounterObserverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy¶

Bases: BiasEnergy

add_values_to_job(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : protocols::jd2::Job) → None¶: C++: protocols::canonical_sampling::BiasEnergy::add_values_to_job(const class core::pose::Pose &, class protocols::jd2::Job &) const –> void

apply(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver, : pyrosetta.rosetta.core.pose.Pose) → None¶

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.

C++: protocols::canonical_sampling::ThermodynamicObserver::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy, : pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy) → pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy¶: C++: protocols::canonical_sampling::WTEBiasEnergy::operator=(const class protocols::canonical_sampling::WTEBiasEnergy &) –> class protocols::canonical_sampling::WTEBiasEnergy &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

evaluate(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::canonical_sampling::BiasEnergy::evaluate(const class core::pose::Pose &) const –> double

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::BiasEnergy::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.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.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.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.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy) → str¶: C++: protocols::canonical_sampling::WTEBiasEnergy::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, : int) → None¶: C++: protocols::canonical_sampling::BiasEnergy::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : protocols::canonical_sampling::MetropolisHastingsMover) → None¶: C++: protocols::canonical_sampling::BiasEnergy::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::canonical_sampling::BiasEnergy::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

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.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.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).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

requires_pose(self: pyrosetta.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.

C++: protocols::canonical_sampling::ThermodynamicObserver::requires_pose() –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

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.

C++: protocols::moves::Mover::reset_status() –> void

restart_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose, : protocols::canonical_sampling::MetropolisHastingsMover, cycle: int, temp_level: int, temperature: float) → bool¶: C++: protocols::canonical_sampling::BiasEnergy::restart_simulation(class core::pose::Pose &, class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long &, unsigned long &, double &) –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, setting: float) → None¶: C++: protocols::canonical_sampling::BiasEnergy::set_temperature(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

swap_replicas(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy) → None¶: C++: protocols::canonical_sampling::BiasEnergy::swap_replicas() –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::canonical_sampling::BiasEnergy::update(const class core::pose::Pose &) –> void

write_to_string(self: pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy, str: str) → None¶: C++: protocols::canonical_sampling::BiasEnergy::write_to_string(std::string &) const –> void

pyrosetta.rosetta.protocols.canonical_sampling.canonical_sampling_main() → int¶: C++: protocols::canonical_sampling::canonical_sampling_main() –> int

pyrosetta.rosetta.protocols.canonical_sampling.interpolation_type_enum_to_string(interp_enum: pyrosetta.rosetta.protocols.canonical_sampling.InterpolationType) → str¶: C++: protocols::canonical_sampling::interpolation_type_enum_to_string(enum protocols::canonical_sampling::InterpolationType) –> std::string

pyrosetta.rosetta.protocols.canonical_sampling.interpolation_type_string_to_enum(interp_string: str) → pyrosetta.rosetta.protocols.canonical_sampling.InterpolationType¶: C++: protocols::canonical_sampling::interpolation_type_string_to_enum(const std::string &) –> enum protocols::canonical_sampling::InterpolationType