monte_carlo¶

Bindings for protocols::monte_carlo namespace

class pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores¶

Bases: vector1_double

Represents a set of filter scores that have been accepted

append(self: pyrosetta.rosetta.utility.vector1_double, arg0: float) → None¶: adds an element to the end

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

back(self: pyrosetta.rosetta.utility.vector1_double) → float¶: access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_double) → int¶: returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_double) → None¶: clears the contents

count(self: pyrosetta.rosetta.utility.vector1_double, arg0: float) → int¶: counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) → None¶: erases element at index

extend(othervec)¶

front(self: pyrosetta.rosetta.utility.vector1_double) → float¶: access the first element

iteration(self: pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores) → int¶: C++: protocols::monte_carlo::AcceptedScores::iteration() const –> unsigned long

l(self: pyrosetta.rosetta.utility.vector1_double) → int¶: lower index

max_size(self: pyrosetta.rosetta.utility.vector1_double) → int¶: returns the maximum possible number of elements

pop(*args, **kwargs)¶

Overloaded function.

pop(self: pyrosetta.rosetta.utility.vector1_double) -> float

remove and return last item

pop(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) -> float

remove and return item at index

rank_score(self: pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores) → float¶: C++: protocols::monte_carlo::AcceptedScores::rank_score() const –> double

remove(self: pyrosetta.rosetta.utility.vector1_double, arg0: float) → None¶: Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) → None¶: reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) → None¶: changes the number of elements stored

set_rank_score(self: pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores, rank_score: float) → None¶: C++: protocols::monte_carlo::AcceptedScores::set_rank_score(const double) –> void

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_double) → None¶: reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_double) → int¶: upper index

class pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover¶

Bases: MoverApplyingMover

accept(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, provisional_scores: pyrosetta.rosetta.utility.vector1_double, mca_status: pyrosetta.rosetta.protocols.moves.MCA) → None¶

Does what the mover needs to do when a pose is accepted, given a pose and scores

C++: protocols::monte_carlo::GenericMonteCarloMover::accept(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &, const enum protocols::moves::MCA) –> void

accept_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::accept_counter() const –> unsigned long

adaptation_period(*args, **kwargs)¶

Overloaded function.

adaptation_period(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, a: int) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptation_period(const unsigned long) –> void

adaptation_period(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> int

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptation_period() const –> unsigned long

adaptive(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive() const –> const class utility::vector1<bool, class std::allocator<bool> > &

adaptive_movers(*args, **kwargs)¶

Overloaded function.

adaptive_movers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, a: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers(const bool) –> void

adaptive_movers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers() const –> bool

add_filter(*args, **kwargs)¶

Overloaded function.

add_filter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str) -> None
add_filter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str, rank_by: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::add_filter(class std::shared_ptr<class protocols::filters::Filter>, const bool, const double, const std::string &, bool) –> void

add_trigger(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, trigger: std::function<bool (unsigned long, unsigned long, core::pose::Pose const&, std::shared_ptr<core::scoring::ScoreFunction>)>) → int¶

Adds a new trigger, returning its id.

Example: #include <functional>

bool no_op(core::Size stage,
core::Size num_stages, core::Size cycle, core::Size num_cycles, const core::pose::Pose&, core::scoring::ScoreFunctionOP) {}

Trigger callback = std::bind(&no_op, STAGE, NUM_STAGES, _1, _2, _3, _4); core::Size trigger_id = add_trigger(callback);

The current stage and number of stages must be bound at creation time. This information provides the triggers with context about the current progress of the simulation as a whole.

If the trigger returns true, rescoring occurs.

C++: protocols::monte_carlo::GenericMonteCarloMover::add_trigger(const class std::function<bool (unsigned long, unsigned long, const class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>)> &) –> unsigned long

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

apply GenericMonteCarloMover (Mover)

C++: protocols::monte_carlo::GenericMonteCarloMover::apply(class core::pose::Pose &) –> void

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

boltz_rank(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::boltz_rank() const –> bool

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

core of MC

C++: protocols::monte_carlo::GenericMonteCarloMover::boltzmann(class core::pose::Pose &) –> bool

boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, random_nums: pyrosetta.rosetta.utility.vector1_double) -> bool

core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria

C++: protocols::monte_carlo::GenericMonteCarloMover::boltzmann(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) –> bool

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.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::monte_carlo::GenericMonteCarloMover::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_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → float¶

return the lowest score

C++: protocols::monte_carlo::GenericMonteCarloMover::current_score() const –> double

static define_composition_schema(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

drift(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::drift() const –> bool

filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t¶: C++: protocols::monte_carlo::GenericMonteCarloMover::filters() const –> const class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > > &

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

create this type of objectt

C++: protocols::monte_carlo::GenericMonteCarloMover::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.monte_carlo.GenericMonteCarloMover) → str¶: C++: protocols::monte_carlo::GenericMonteCarloMover::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(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → None¶

initialize object used in constructor

C++: protocols::monte_carlo::GenericMonteCarloMover::initialize() –> void

keep_filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::keep_filters() const –> bool

last_accepted_pose(*args, **kwargs)¶

Overloaded function.

last_accepted_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the last accepted pose

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose() const –> class std::shared_ptr<class core::pose::Pose>

last_accepted_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose(class std::shared_ptr<class core::pose::Pose>) –> void

last_accepted_score(*args, **kwargs)¶

Overloaded function.

last_accepted_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> float

return the last accepted score

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score() const –> double

last_accepted_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, score: float) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score(const double) –> void

last_accepted_scores(*args, **kwargs)¶

Overloaded function.

last_accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

last_accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

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

last_tested_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::monte_carlo::GenericMonteCarloMover::last_tested_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

load_trial_number_from_checkpoint(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::load_trial_number_from_checkpoint(class core::pose::Pose &) –> unsigned long

lowest_score(*args, **kwargs)¶

Overloaded function.

lowest_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> float

return the lowest score

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score() const –> double

lowest_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, score: float) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score(const double) –> void

lowest_score_pose(*args, **kwargs)¶

Overloaded function.

lowest_score_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the lowest score pose

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose() const –> class std::shared_ptr<class core::pose::Pose>

lowest_score_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose(class std::shared_ptr<class core::pose::Pose>) –> void

lowest_scores(*args, **kwargs)¶

Overloaded function.

lowest_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

lowest_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

max_accepted_trials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns maximum number of accepted trials

C++: protocols::monte_carlo::GenericMonteCarloMover::max_accepted_trials() const –> unsigned long

maxtrials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns maximum number of trials

C++: protocols::monte_carlo::GenericMonteCarloMover::maxtrials() const –> unsigned long

mc_accpeted(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.protocols.moves.MCA¶

return mc_accepted

C++: protocols::monte_carlo::GenericMonteCarloMover::mc_accpeted() const –> enum protocols::moves::MCA

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

static mover_name() → str¶: C++: protocols::monte_carlo::GenericMonteCarloMover::mover_name() –> std::string

mover_stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → basic::datacache::DataMapObj<bool>¶: C++: protocols::monte_carlo::GenericMonteCarloMover::mover_stopping_condition() const –> class std::shared_ptr<class basic::datacache::DataMapObj<bool> >

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

num_designable(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::num_designable(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask> &) –> unsigned long

num_rejections(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::monte_carlo::GenericMonteCarloMover::num_rejections() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

num_triggers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns the number of triggers

C++: protocols::monte_carlo::GenericMonteCarloMover::num_triggers() const –> unsigned long

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

parse_task_operations(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::monte_carlo::GenericMonteCarloMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void

preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::preapply() const –> bool

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

Provide the citation.

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

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

recover_low(*args, **kwargs)¶

Overloaded function.

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

return the simulation state to the lowest energy structure we’ve seen

C++: protocols::monte_carlo::GenericMonteCarloMover::recover_low(class core::pose::Pose &) –> void

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::recover_low() const –> bool

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

remove_trigger(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, trigger_id: int) → None¶

Removes the trigger with the specified id

C++: protocols::monte_carlo::GenericMonteCarloMover::remove_trigger(unsigned long) –> void

reset(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

reset MC iterations, with pose used for the last & best structures

C++: protocols::monte_carlo::GenericMonteCarloMover::reset(class core::pose::Pose &) –> void

reset_baselines(*args, **kwargs)¶

Overloaded function.

reset_baselines(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, r: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::reset_baselines(const bool) –> void

reset_baselines(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::reset_baselines() 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

sample_types(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::monte_carlo::GenericMonteCarloMover::sample_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

save_trial_number_to_checkpoint(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, i: int) → None¶: C++: protocols::monte_carlo::GenericMonteCarloMover::save_trial_number_to_checkpoint(const unsigned long) const –> void

saved_accept_file_name(*args, **kwargs)¶

Overloaded function.

saved_accept_file_name(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> str

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name() const –> std::string

saved_accept_file_name(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : str) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name(const std::string) –> void

saved_trial_number_file(*args, **kwargs)¶

Overloaded function.

saved_trial_number_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> str

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file() const –> std::string

saved_trial_number_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : str) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file(const std::string) –> void

score_function(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Return the score function in use

C++: protocols::monte_carlo::GenericMonteCarloMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::monte_carlo::GenericMonteCarloMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_boltz_rank(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, boltz_rank: bool) → None¶

if boltz_rank=true, rank structures by the temperature-weighted

sum of scores, rather than a single filter

The score used here is the effective combined energy function that the Monte Carlo sampler is sampling over.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_boltz_rank(const bool) –> 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_drift(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, drift: bool) → None¶

if drift=false, the pose is set back to the initial pose at each MC trial: Of course, this is not MC sampling.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_drift(const bool) –> 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_keep_filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, k: bool) → None¶: C++: protocols::monte_carlo::GenericMonteCarloMover::set_keep_filters(const bool) –> void

set_max_accepted_trials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, n_max_accepted_trial: int) → None¶

set max accepted trials of MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_max_accepted_trials(const unsigned long) –> void

set_maxtrials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, ntrial: int) → None¶

set max trials of MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_maxtrials(const unsigned long) –> void

set_mover(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, mover: pyrosetta.rosetta.protocols.moves.Mover) → None¶

set mover

C++: protocols::monte_carlo::GenericMonteCarloMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> 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_preapply(*args, **kwargs)¶

Overloaded function.

set_preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> None
set_preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, preapply: bool) -> None

if preapply=true, auto-accept the first application of the submover,: ignoring boltzman criteria.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_preapply(const bool) –> void

set_recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, recover_low: bool) → None¶

if recover_low=true, after apply() the structure: is the lowest energy structure, rather than the last accepted structure.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_recover_low(const bool) –> void

set_sampletype(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, type: str) → None¶

set sample type, max or min: when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score

C++: protocols::monte_carlo::GenericMonteCarloMover::set_sampletype(const std::string &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Pose is evaluated by ScoreFunctionOP during MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_stop_sampling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, stop_sampling: bool) → None¶

if set to true, the MC mover will stop sampling

C++: protocols::monte_carlo::GenericMonteCarloMover::set_stop_sampling(const bool) –> void

set_task_scaling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scaling: int) → None¶

set task multiplier to calculate trials from task

C++: protocols::monte_carlo::GenericMonteCarloMover::set_task_scaling(const unsigned long) –> void

set_temperature(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, temp: float) → None¶

set temperature

C++: protocols::monte_carlo::GenericMonteCarloMover::set_temperature(const 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

show_counters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None¶

show counters of ntrial and acceptance ratio

C++: protocols::monte_carlo::GenericMonteCarloMover::show_counters(std::ostream &) const –> void

show_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None¶

show scores of last_accepted_score and “best_score” ( = flip_sign_ * lowest_score )

C++: protocols::monte_carlo::GenericMonteCarloMover::show_scores(std::ostream &) const –> void

stop_sampling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::stop_sampling() const –> bool

stopping_condition(*args, **kwargs)¶

Overloaded function.

stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::stopping_condition(class std::shared_ptr<class protocols::filters::Filter>) –> void

stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::monte_carlo::GenericMonteCarloMover::stopping_condition() const –> class std::shared_ptr<class protocols::filters::Filter>

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

task_factory(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::monte_carlo::GenericMonteCarloMover::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

task_scaling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns the task scaling value

C++: protocols::monte_carlo::GenericMonteCarloMover::task_scaling() const –> unsigned long

temperatures(*args, **kwargs)¶

Overloaded function.

temperatures(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::temperatures() const –> class utility::vector1<double, class std::allocator<double> >

temperatures(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, temps: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::temperatures(const class utility::vector1<double, class std::allocator<double> > &) –> 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

trial_counter(*args, **kwargs)¶

Overloaded function.

trial_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> int

C++: protocols::monte_carlo::GenericMonteCarloMover::trial_counter() const –> unsigned long

trial_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, i: int) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::trial_counter(const unsigned long) –> 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.monte_carlo.GenericMonteCarloMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer¶

Bases: GenericMonteCarloMover

GenericSimulatedAnnealer mover for performing simulated annealing trajectories

This class extends GenericMonteCarloMover to provide temperature scaling

accept(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, provisional_scores: pyrosetta.rosetta.utility.vector1_double, mca_status: pyrosetta.rosetta.protocols.moves.MCA) → None¶

Does what the mover needs to do when a pose is accepted, given a pose and scores

C++: protocols::monte_carlo::GenericMonteCarloMover::accept(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &, const enum protocols::moves::MCA) –> void

accept_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::accept_counter() const –> unsigned long

accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, i: int) → pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores¶

gets a list of scores for acceptance number i

C++: protocols::monte_carlo::GenericSimulatedAnnealer::accepted_scores(const unsigned long) const –> const class protocols::monte_carlo::AcceptedScores &

adaptation_period(*args, **kwargs)¶

Overloaded function.

adaptation_period(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, a: int) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptation_period(const unsigned long) –> void

adaptation_period(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> int

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptation_period() const –> unsigned long

adaptive(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive() const –> const class utility::vector1<bool, class std::allocator<bool> > &

adaptive_movers(*args, **kwargs)¶

Overloaded function.

adaptive_movers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, a: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers(const bool) –> void

adaptive_movers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers() const –> bool

add_filter(*args, **kwargs)¶

Overloaded function.

add_filter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str) -> None
add_filter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str, rank_by: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::add_filter(class std::shared_ptr<class protocols::filters::Filter>, const bool, const double, const std::string &, bool) –> void

add_trigger(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, trigger: std::function<bool (unsigned long, unsigned long, core::pose::Pose const&, std::shared_ptr<core::scoring::ScoreFunction>)>) → int¶

Adds a new trigger, returning its id.

Example: #include <functional>

bool no_op(core::Size stage,
core::Size num_stages, core::Size cycle, core::Size num_cycles, const core::pose::Pose&, core::scoring::ScoreFunctionOP) {}

Trigger callback = std::bind(&no_op, STAGE, NUM_STAGES, _1, _2, _3, _4); core::Size trigger_id = add_trigger(callback);

The current stage and number of stages must be bound at creation time. This information provides the triggers with context about the current progress of the simulation as a whole.

If the trigger returns true, rescoring occurs.

C++: protocols::monte_carlo::GenericMonteCarloMover::add_trigger(const class std::function<bool (unsigned long, unsigned long, const class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>)> &) –> unsigned long

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

apply GenericSimulatedAnnealer (Mover)

C++: protocols::monte_carlo::GenericSimulatedAnnealer::apply(class core::pose::Pose &) –> void

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

boltz_rank(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::boltz_rank() const –> bool

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

core of MC

C++: protocols::monte_carlo::GenericMonteCarloMover::boltzmann(class core::pose::Pose &) –> bool

boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, random_nums: pyrosetta.rosetta.utility.vector1_double) -> bool

core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria

C++: protocols::monte_carlo::GenericMonteCarloMover::boltzmann(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) –> bool

boltzmann_result(*args, **kwargs)¶

Overloaded function.

boltzmann_result(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.monte_carlo.TrialResult

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly: uses randomly generated numbers to assess acceptance of scores with temperatures

C++: protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result(class core::pose::Pose &) –> enum protocols::monte_carlo::TrialResult

boltzmann_result(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose, random_nums: pyrosetta.rosetta.utility.vector1_double) -> pyrosetta.rosetta.protocols.monte_carlo.TrialResult

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly

C++: protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) –> enum protocols::monte_carlo::TrialResult

calc_boltz_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, scores: pyrosetta.rosetta.utility.vector1_double) → float¶

if boltz_rank is used, this will calculate the ranking score from a list of filter scores

C++: protocols::monte_carlo::GenericSimulatedAnnealer::calc_boltz_score(const class utility::vector1<double, class std::allocator<double> > &) const –> double

checkpoint_exists(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer) → bool¶

tests to see if the checkpoint files exist and have been generated

C++: protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_exists() const –> bool

checkpoint_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, check_file: str) → None¶

set the checkpoint file name

C++: protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_file(const std::string &) –> 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.monte_carlo.GenericSimulatedAnnealer) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::monte_carlo::GenericSimulatedAnnealer::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>

create_tag(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, suffix: str) → str¶

create a silent struct tag for checkpointing with the given suffix

C++: protocols::monte_carlo::GenericSimulatedAnnealer::create_tag(const std::string &) const –> std::string

current_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → float¶

return the lowest score

C++: protocols::monte_carlo::GenericMonteCarloMover::current_score() const –> double

static define_composition_schema(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

drift(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::drift() const –> bool

filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t¶: C++: protocols::monte_carlo::GenericMonteCarloMover::filters() const –> const class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > > &

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

create this type of objectt

C++: protocols::monte_carlo::GenericSimulatedAnnealer::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.monte_carlo.GenericSimulatedAnnealer) → str¶: C++: protocols::monte_carlo::GenericSimulatedAnnealer::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(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → None¶

initialize object used in constructor

C++: protocols::monte_carlo::GenericMonteCarloMover::initialize() –> void

keep_checkpoint_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, keep_checkpoint: bool) → None¶

sets whether or not to delete checkpoint files when done – useful for debugging

C++: protocols::monte_carlo::GenericSimulatedAnnealer::keep_checkpoint_file(const bool) –> void

keep_filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::keep_filters() const –> bool

last_accepted_pose(*args, **kwargs)¶

Overloaded function.

last_accepted_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the last accepted pose

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose() const –> class std::shared_ptr<class core::pose::Pose>

last_accepted_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose(class std::shared_ptr<class core::pose::Pose>) –> void

last_accepted_score(*args, **kwargs)¶

Overloaded function.

last_accepted_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> float

return the last accepted score

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score() const –> double

last_accepted_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, score: float) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score(const double) –> void

last_accepted_scores(*args, **kwargs)¶

Overloaded function.

last_accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

last_accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

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

last_tested_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::monte_carlo::GenericMonteCarloMover::last_tested_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

load_checkpoint_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

loads checkpoint data and attempts to resume a run with pose as the pose

C++: protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(class core::pose::Pose &) –> void

load_trial_number_from_checkpoint(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::load_trial_number_from_checkpoint(class core::pose::Pose &) –> unsigned long

lowest_score(*args, **kwargs)¶

Overloaded function.

lowest_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> float

return the lowest score

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score() const –> double

lowest_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, score: float) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score(const double) –> void

lowest_score_pose(*args, **kwargs)¶

Overloaded function.

lowest_score_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the lowest score pose

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose() const –> class std::shared_ptr<class core::pose::Pose>

lowest_score_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose(class std::shared_ptr<class core::pose::Pose>) –> void

lowest_scores(*args, **kwargs)¶

Overloaded function.

lowest_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

lowest_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

max_accepted_trials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns maximum number of accepted trials

C++: protocols::monte_carlo::GenericMonteCarloMover::max_accepted_trials() const –> unsigned long

maxtrials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns maximum number of trials

C++: protocols::monte_carlo::GenericMonteCarloMover::maxtrials() const –> unsigned long

mc_accpeted(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.protocols.moves.MCA¶

return mc_accepted

C++: protocols::monte_carlo::GenericMonteCarloMover::mc_accpeted() const –> enum protocols::moves::MCA

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

static mover_name() → str¶: C++: protocols::monte_carlo::GenericSimulatedAnnealer::mover_name() –> std::string

mover_stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → basic::datacache::DataMapObj<bool>¶: C++: protocols::monte_carlo::GenericMonteCarloMover::mover_stopping_condition() const –> class std::shared_ptr<class basic::datacache::DataMapObj<bool> >

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

num_accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer) → int¶

number of acceptances

C++: protocols::monte_carlo::GenericSimulatedAnnealer::num_accepted_scores() const –> unsigned long

num_designable(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::num_designable(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask> &) –> unsigned long

num_rejections(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::monte_carlo::GenericMonteCarloMover::num_rejections() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

num_triggers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns the number of triggers

C++: protocols::monte_carlo::GenericMonteCarloMover::num_triggers() const –> unsigned long

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

XML interface to this mover

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

parse_task_operations(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::monte_carlo::GenericMonteCarloMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void

preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::preapply() const –> bool

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

Provide the citation.

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

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

recover_low(*args, **kwargs)¶

Overloaded function.

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

return the simulation state to the lowest energy structure we’ve seen

C++: protocols::monte_carlo::GenericMonteCarloMover::recover_low(class core::pose::Pose &) –> void

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::recover_low() const –> bool

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

remove_checkpoint_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer) → None¶

Deletes the checkpoint files

C++: protocols::monte_carlo::GenericSimulatedAnnealer::remove_checkpoint_file() const –> void

remove_trigger(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, trigger_id: int) → None¶

Removes the trigger with the specified id

C++: protocols::monte_carlo::GenericMonteCarloMover::remove_trigger(unsigned long) –> void

reset(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Clears accepted data and initialize with new pose

C++: protocols::monte_carlo::GenericSimulatedAnnealer::reset(class core::pose::Pose &) –> void

reset_baselines(*args, **kwargs)¶

Overloaded function.

reset_baselines(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, r: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::reset_baselines(const bool) –> void

reset_baselines(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::reset_baselines() 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

sample_types(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::monte_carlo::GenericMonteCarloMover::sample_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

save_checkpoint_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer) → None¶

Saves the current state of the mover into checkpoint files

C++: protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file() const –> void

save_trial_number_to_checkpoint(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, i: int) → None¶: C++: protocols::monte_carlo::GenericMonteCarloMover::save_trial_number_to_checkpoint(const unsigned long) const –> void

saved_accept_file_name(*args, **kwargs)¶

Overloaded function.

saved_accept_file_name(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> str

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name() const –> std::string

saved_accept_file_name(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : str) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name(const std::string) –> void

saved_trial_number_file(*args, **kwargs)¶

Overloaded function.

saved_trial_number_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> str

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file() const –> std::string

saved_trial_number_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : str) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file(const std::string) –> void

scale_temperatures(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, temp_factor: float) → None¶

scales temperatures by the factor provided

C++: protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures(const double) –> void

score_function(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Return the score function in use

C++: protocols::monte_carlo::GenericMonteCarloMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

score_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores¶

given a pose, score the result

C++: protocols::monte_carlo::GenericSimulatedAnnealer::score_pose(const class core::pose::Pose &) const –> class protocols::monte_carlo::AcceptedScores

scorefxn(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::monte_carlo::GenericMonteCarloMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_boltz_rank(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, boltz_rank: bool) → None¶

if boltz_rank=true, rank structures by the temperature-weighted

sum of scores, rather than a single filter

The score used here is the effective combined energy function that the Monte Carlo sampler is sampling over.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_boltz_rank(const bool) –> 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_drift(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, drift: bool) → None¶

if drift=false, the pose is set back to the initial pose at each MC trial: Of course, this is not MC sampling.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_drift(const bool) –> 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_keep_filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, k: bool) → None¶: C++: protocols::monte_carlo::GenericMonteCarloMover::set_keep_filters(const bool) –> void

set_max_accepted_trials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, n_max_accepted_trial: int) → None¶

set max accepted trials of MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_max_accepted_trials(const unsigned long) –> void

set_maxtrials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, ntrial: int) → None¶

set max trials of MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_maxtrials(const unsigned long) –> void

set_mover(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, mover: pyrosetta.rosetta.protocols.moves.Mover) → None¶

set mover

C++: protocols::monte_carlo::GenericMonteCarloMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> 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_preapply(*args, **kwargs)¶

Overloaded function.

set_preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> None
set_preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, preapply: bool) -> None

if preapply=true, auto-accept the first application of the submover,: ignoring boltzman criteria.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_preapply(const bool) –> void

set_recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, recover_low: bool) → None¶

if recover_low=true, after apply() the structure: is the lowest energy structure, rather than the last accepted structure.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_recover_low(const bool) –> void

set_sampletype(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, type: str) → None¶

set sample type, max or min: when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score

C++: protocols::monte_carlo::GenericMonteCarloMover::set_sampletype(const std::string &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Pose is evaluated by ScoreFunctionOP during MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_stop_sampling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, stop_sampling: bool) → None¶

if set to true, the MC mover will stop sampling

C++: protocols::monte_carlo::GenericMonteCarloMover::set_stop_sampling(const bool) –> void

set_task_scaling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scaling: int) → None¶

set task multiplier to calculate trials from task

C++: protocols::monte_carlo::GenericMonteCarloMover::set_task_scaling(const unsigned long) –> void

set_temperature(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, temp: float) → None¶

set temperature

C++: protocols::monte_carlo::GenericMonteCarloMover::set_temperature(const 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

show_counters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None¶

show counters of ntrial and acceptance ratio

C++: protocols::monte_carlo::GenericMonteCarloMover::show_counters(std::ostream &) const –> void

show_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None¶

show scores of last_accepted_score and “best_score” ( = flip_sign_ * lowest_score )

C++: protocols::monte_carlo::GenericMonteCarloMover::show_scores(std::ostream &) const –> void

stop_sampling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::stop_sampling() const –> bool

stopping_condition(*args, **kwargs)¶

Overloaded function.

stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::stopping_condition(class std::shared_ptr<class protocols::filters::Filter>) –> void

stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::monte_carlo::GenericMonteCarloMover::stopping_condition() const –> class std::shared_ptr<class protocols::filters::Filter>

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

task_factory(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::monte_carlo::GenericMonteCarloMover::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

task_scaling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns the task scaling value

C++: protocols::monte_carlo::GenericMonteCarloMover::task_scaling() const –> unsigned long

temperatures(*args, **kwargs)¶

Overloaded function.

temperatures(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::temperatures() const –> class utility::vector1<double, class std::allocator<double> >

temperatures(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, temps: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::temperatures(const class utility::vector1<double, class std::allocator<double> > &) –> 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

trial_counter(*args, **kwargs)¶

Overloaded function.

trial_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> int

C++: protocols::monte_carlo::GenericMonteCarloMover::trial_counter() const –> unsigned long

trial_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, i: int) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::trial_counter(const unsigned long) –> 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.monte_carlo.GenericSimulatedAnnealerCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface¶

Bases: MonteCarlo

A MonteCarlo object for optimizing the interface dG as defined using InterfaceAnalyzer. The dG and Total energy can be weighted. This is so that the interface energy itself can be optimized through a protocol.

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, 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 Interface dG and Total Score according to Set weights.

Interface dG is calculated using the InterfaceAnalyzer Application.

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::monte_carlo::MonteCarloInterface::boltzmann(class core::pose::Pose &, const std::string &, const double, const double) –> bool

calculate_score(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Calculate the score given the pose and the weights.

C++: protocols::monte_carlo::MonteCarloInterface::calculate_score(class core::pose::Pose &) –> double

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.monte_carlo.MonteCarloInterface) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶: C++: protocols::monte_carlo::MonteCarloInterface::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.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sets lowest score pose and last accepted pose to

the score of <pose>

(does not reset counters)

example(s):: mc.reset(pose)
See also:: MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_scored_pose

C++: protocols::monte_carlo::MonteCarloInterface::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.monte_carlo.MonteCarloInterface, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::monte_carlo::MonteCarloInterface::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_dG_weight(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, dG_weight: float) → None¶

Set the weight on the dG component of the energy (Default = 1.0)

C++: protocols::monte_carlo::MonteCarloInterface::set_dG_weight(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_interface(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, interface: str) → None¶

Set the interface that we will be using to calculate interface energy.

C++: protocols::monte_carlo::MonteCarloInterface::set_interface(const std::string &) –> 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_pack_interface_separated(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pack_separated: bool) → None¶

Should we pack the interface while separated? Default TRUE.

C++: protocols::monte_carlo::MonteCarloInterface::set_pack_interface_separated(bool) –> void

set_repack_separated(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, repack_separated: bool) → None¶

Should we repack only the interface residues of a cloned pose on calculating the interface energy?: Default TRUE.

C++: protocols::monte_carlo::MonteCarloInterface::set_repack_separated(bool) –> void

set_temperature(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, temp: float) → None¶

Sets the temperature value used in the Metropolis Criterion to <temp>

example(s):
mc.set_temperature( temp )

See also:
MonteCarlo MonteCarlo.temperature MonteCarlo.show_state

C++: protocols::moves::MonteCarlo::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_total_weight(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, total_weight: float) → None¶

Set the weight on the total component of the enegy (Default = 0.0)

C++: protocols::monte_carlo::MonteCarloInterface::set_total_weight(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.monte_carlo.MonteCarloRecover¶

Bases: Mover

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

apply MonteCarloRecover (Mover)

C++: protocols::monte_carlo::MonteCarloRecover::apply(class core::pose::Pose &) –> void

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

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.monte_carlo.MonteCarloRecover) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::monte_carlo::MonteCarloRecover::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>

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

create this type of objectt

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

get_MC(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover) → pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover¶: C++: protocols::monte_carlo::MonteCarloRecover::get_MC() const –> class std::shared_ptr<class protocols::monte_carlo::GenericMonteCarloMover>

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.monte_carlo.MonteCarloRecover) → str¶: C++: protocols::monte_carlo::MonteCarloRecover::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_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::monte_carlo::MonteCarloRecover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::monte_carlo::MonteCarloRecover::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::monte_carlo::MonteCarloRecover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

recover_low(*args, **kwargs)¶

Overloaded function.

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover) -> bool

C++: protocols::monte_carlo::MonteCarloRecover::recover_low() const –> bool

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover, recover: bool) -> None

C++: protocols::monte_carlo::MonteCarloRecover::recover_low(const bool) –> 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_MC(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover, mover: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → None¶

set mover

C++: protocols::monte_carlo::MonteCarloRecover::set_MC(class std::shared_ptr<class protocols::monte_carlo::GenericMonteCarloMover>) –> 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_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.monte_carlo.MonteCarloRecoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset¶

Bases: Mover

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

apply MonteCarloReset (Mover)

C++: protocols::monte_carlo::MonteCarloReset::apply(class core::pose::Pose &) –> void

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

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.monte_carlo.MonteCarloReset) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::monte_carlo::MonteCarloReset::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>

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

create this type of objectt

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

get_MC(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset) → pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover¶: C++: protocols::monte_carlo::MonteCarloReset::get_MC() const –> class std::shared_ptr<class protocols::monte_carlo::GenericMonteCarloMover>

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.monte_carlo.MonteCarloReset) → str¶: C++: protocols::monte_carlo::MonteCarloReset::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_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::monte_carlo::MonteCarloReset::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::monte_carlo::MonteCarloReset::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::monte_carlo::MonteCarloReset::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

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_MC(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset, mover: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → None¶

set mover

C++: protocols::monte_carlo::MonteCarloReset::set_MC(class std::shared_ptr<class protocols::monte_carlo::GenericMonteCarloMover>) –> 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_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.monte_carlo.MonteCarloResetCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest¶

Bases: Mover

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

apply MonteCarloTest (Mover)

C++: protocols::monte_carlo::MonteCarloTest::apply(class core::pose::Pose &) –> void

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

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.monte_carlo.MonteCarloTest) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::monte_carlo::MonteCarloTest::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>

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

create this type of objectt

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

get_MC(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest) → pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover¶: C++: protocols::monte_carlo::MonteCarloTest::get_MC() const –> class std::shared_ptr<class protocols::monte_carlo::GenericMonteCarloMover>

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.monte_carlo.MonteCarloTest) → str¶: C++: protocols::monte_carlo::MonteCarloTest::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_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::monte_carlo::MonteCarloTest::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::monte_carlo::MonteCarloTest::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::monte_carlo::MonteCarloTest::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

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_MC(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest, mover: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → None¶

set mover

C++: protocols::monte_carlo::MonteCarloTest::set_MC(class std::shared_ptr<class protocols::monte_carlo::GenericMonteCarloMover>) –> 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_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.monte_carlo.MonteCarloTestCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover¶

Bases: Mover

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

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

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.monte_carlo.ResetBaselineMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::monte_carlo::ResetBaselineMover::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>

filter(*args, **kwargs)¶

Overloaded function.

filter(self: pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::monte_carlo::ResetBaselineMover::filter() const –> class std::shared_ptr<class protocols::filters::Filter>

filter(self: pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::monte_carlo::ResetBaselineMover::filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::monte_carlo::ResetBaselineMover::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.monte_carlo.ResetBaselineMover) → str¶: C++: protocols::monte_carlo::ResetBaselineMover::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_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::monte_carlo::ResetBaselineMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::monte_carlo::ResetBaselineMover::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::monte_carlo::ResetBaselineMover::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

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_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.monte_carlo.ResetBaselineMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.monte_carlo.TrialResult¶

Bases: pybind11_object

Describes result of a trial

REJECTEDMove was rejected
ACCEPTED : Move was accepted FAILED : Some failure occurred during the move FINISHED : The stopping condition was met

Members:

REJECTED

ACCEPTED

FAILED

FINISHED

ACCEPTED = <TrialResult.ACCEPTED: 1>¶

FAILED = <TrialResult.FAILED: 2>¶

FINISHED = <TrialResult.FINISHED: 3>¶

REJECTED = <TrialResult.REJECTED: 0>¶

property name¶

property value¶

pyrosetta.rosetta.protocols.monte_carlo.replace_file(origfile: str, newfile: str) → None¶

helper function that safely replaces a file with another

C++: protocols::monte_carlo::replace_file(const std::string &, const std::string &) –> void