monte_carlo

Bindings for protocols::monte_carlo namespace

class pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores

Bases: pyrosetta.rosetta.utility.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

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.

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

remove and return last item

2. 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.GenericSimulatedAnnealer

Bases: pyrosetta.rosetta.protocols.monte_carlo.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.

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

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

2. 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.

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

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

2. 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.

1. add_filter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str) -> None
2. 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 class std::basic_string<char> &, bool) –> void

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.

1. 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

2. 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.

1. 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

2. 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) 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

define_composition_schema(: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.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.

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_std_allocator_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.

1. 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>

2. 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.

1. 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

2. 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.

1. 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> > &

2. 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.

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

return the lowest score

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

2. 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.

1. 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>

2. 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.

1. 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> > &

2. 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>

mover_name() → str

C++: protocols::monte_carlo::GenericSimulatedAnnealer::mover_name() –> std::string

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, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → 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 &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t) → 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 &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &) –> void

preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::monte_carlo::GenericSimulatedAnnealer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

recover_low(*args, **kwargs)

Overloaded function.

1. 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

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

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

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.

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

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

2. 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.

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

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

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

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name(const class std::basic_string<char>) –> void

saved_trial_number_file(*args, **kwargs)

Overloaded function.

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

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

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

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file(const class std::basic_string<char>) –> 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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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.

1. set_preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> None
2. 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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
2. 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) 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.

1. 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

2. 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.

1. 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

2. 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.

1. 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> >

2. 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.

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

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

2. 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.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface

Bases: pyrosetta.rosetta.protocols.moves.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.

1. boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
2. boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
3. boltzmann(self: pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
4. 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 class std::basic_string<char> &, 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.

1. eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
2. eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool) -> bool
3. eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool, update_stats: bool) -> bool
4. 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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.

1. 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

2. 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.

1. 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

2. 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.TrialResult

Bases: pybind11_builtins.pybind11_object

Describes result of a trial

REJECTED : Move was rejected

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

Members:

REJECTED

ACCEPTED

FAILED

FINISHED

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 class std::basic_string<char> &, const class std::basic_string<char> &) –> void