monte_carlo

Bindings for protocols::stepwise::monte_carlo namespace

class pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the loop-rebuild protocol to the input pose

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

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

checkpoint_file_exists(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) bool

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::checkpoint_file_exists() const –> 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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

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

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

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

get_name(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) str

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::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

master_mover(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) protocols::stepwise::monte_carlo::mover::StepWiseMasterMover

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::master_mover() const –> class std::shared_ptr<const class protocols::stepwise::monte_carlo::mover::StepWiseMasterMover>

model_tag(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) str

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::model_tag() const –> std::string

move(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::move() const –> class protocols::stepwise::monte_carlo::mover::StepWiseMove

static name() str

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

options(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::options() const –> class std::shared_ptr<const class protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions>

out_path(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) str

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::out_path() const –> std::string

output_checkpoint_file(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, low: pyrosetta.rosetta.core.pose.Pose, k: int) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::output_checkpoint_file(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long) const –> void

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

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

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

pose_from_checkpoint_file(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) pyrosetta.rosetta.core.pose.Pose

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::pose_from_checkpoint_file() const –> class core::pose::Pose

pose_from_checkpoint_file_low(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) pyrosetta.rosetta.core.pose.Pose

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::pose_from_checkpoint_file_low() const –> class core::pose::Pose

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

remove_checkpoint_file(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo) None

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

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

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

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

set_align_pose(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_align_pose(class std::shared_ptr<const class core::pose::Pose>) –> 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_model_tag(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, setting: str) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_model_tag(const std::string &) –> void

set_move(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, setting: pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_move(const class protocols::stepwise::monte_carlo::mover::StepWiseMove &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, 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::stepwise::monte_carlo::StepWiseMonteCarlo::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_options(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, options: protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_options(class std::shared_ptr<const class protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions>) –> void

set_out_file_prefix(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, setting: str) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_out_file_prefix(const std::string &) –> void

set_out_path(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, setting: str) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_out_path(const std::string &) –> void

set_submotif_library(self: pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo, setting: protocols::stepwise::monte_carlo::submotif::SubMotifLibrary) None

C++: protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_submotif_library(class std::shared_ptr<const class protocols::stepwise::monte_carlo::submotif::SubMotifLibrary>) –> 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.

  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(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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

pyrosetta.rosetta.protocols.stepwise.monte_carlo.build_full_model(*args, **kwargs)

Overloaded function.

  1. build_full_model(start_pose: pyrosetta.rosetta.core.pose.Pose, full_model_pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. build_full_model(start_pose: pyrosetta.rosetta.core.pose.Pose, full_model_pose: pyrosetta.rosetta.core.pose.Pose, enumerate: bool) -> None

  3. build_full_model(start_pose: pyrosetta.rosetta.core.pose.Pose, full_model_pose: pyrosetta.rosetta.core.pose.Pose, enumerate: bool, skip_bulge_freq: float) -> None

C++: protocols::stepwise::monte_carlo::build_full_model(const class core::pose::Pose &, class core::pose::Pose &, const bool &, const double &) –> void

  1. build_full_model(start_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::stepwise::monte_carlo::build_full_model(const class core::pose::Pose &) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.stepwise.monte_carlo.get_all_res_list(pose: pyrosetta.rosetta.core.pose.Pose) str

C++: protocols::stepwise::monte_carlo::get_all_res_list(class core::pose::Pose &) –> std::string

pyrosetta.rosetta.protocols.stepwise.monte_carlo.get_move_type_string(swa_move: pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove) str

C++: protocols::stepwise::monte_carlo::get_move_type_string(const class protocols::stepwise::monte_carlo::mover::StepWiseMove &) –> std::string

pyrosetta.rosetta.protocols.stepwise.monte_carlo.output_to_silent_file(*args, **kwargs)

Overloaded function.

  1. output_to_silent_file(out_tag: str, silent_file: str, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. output_to_silent_file(out_tag: str, silent_file: str, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, superimpose_over_all_instantiated: bool) -> None

  3. output_to_silent_file(out_tag: str, silent_file: str, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, superimpose_over_all_instantiated: bool, do_rms_fill_calculation: bool) -> None

C++: protocols::stepwise::monte_carlo::output_to_silent_file(const std::string &, const std::string &, class core::pose::Pose &, class std::shared_ptr<const class core::pose::Pose>, const bool, const bool) –> void

  1. output_to_silent_file(out_tag: str, silent_file: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::stepwise::monte_carlo::output_to_silent_file(const std::string &, const std::string &, const class core::pose::Pose &) –> void

  1. output_to_silent_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, native_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::stepwise::monte_carlo::output_to_silent_file(const std::string &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class std::shared_ptr<const class core::pose::Pose>) –> void

pyrosetta.rosetta.protocols.stepwise.monte_carlo.prepare_silent_struct(*args, **kwargs)

Overloaded function.

  1. prepare_silent_struct(out_tag: str, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.io.silent.SilentStruct

  2. prepare_silent_struct(out_tag: str, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, superimpose_over_all_instantiated: bool) -> pyrosetta.rosetta.core.io.silent.SilentStruct

  3. prepare_silent_struct(out_tag: str, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, superimpose_over_all_instantiated: bool, do_rms_fill_calculation: bool) -> pyrosetta.rosetta.core.io.silent.SilentStruct

  4. prepare_silent_struct(out_tag: str, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, superimpose_over_all_instantiated: bool, do_rms_fill_calculation: bool, full_model_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.io.silent.SilentStruct

C++: protocols::stepwise::monte_carlo::prepare_silent_struct(const std::string &, class core::pose::Pose &, class std::shared_ptr<const class core::pose::Pose>, const bool, const bool, class std::shared_ptr<class core::pose::Pose>) –> class std::shared_ptr<class core::io::silent::SilentStruct>