sampler¶

rna

Bindings for protocols::recces::sampler namespace

class pyrosetta.rosetta.protocols.recces.sampler.MC_Any¶

Bases: MC_Comb

add_rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, rotamer: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → None¶

Add one more rotamer sampler to this sampler

C++: protocols::recces::sampler::MC_Comb::add_rotamer(const class std::shared_ptr<class protocols::recces::sampler::MC_Sampler> &) –> void

apply(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the current rotamer to pose

C++: protocols::recces::sampler::MC_Any::apply(class core::pose::Pose &) –> void

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

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

clear_rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Clear all rotamer samplers stored in this sampler

C++: protocols::recces::sampler::MC_Comb::clear_rotamer() –> 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>

curr_id(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → int¶: C++: protocols::recces::sampler::MC_Any::curr_id() const –> unsigned long

find(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶

return OP to the subsampler that controls exactly this torsion_id (assume only one).

C++: protocols::recces::sampler::MC_Comb::find(const class core::id::TorsionID &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Sampler>

found_move(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

check if ++ did anything to pose.

C++: protocols::recces::sampler::MC_Sampler::found_move() const –> bool

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

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

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

get_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.recces.sampler.MC_Sampler) → str¶

Name of the class

C++: protocols::recces::sampler::MC_Sampler::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 > > &

init(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → None¶

Initialization

C++: protocols::recces::sampler::MC_Any::init() –> void

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

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

num_rotamers(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → int¶: C++: protocols::recces::sampler::MC_Comb::num_rotamers() const –> unsigned long

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

pre_increment(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → None¶

Move to next rotamer

C++: protocols::recces::sampler::MC_Any::operator++() –> void

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

reset(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Reset to the first (or random if random()) rotamer

C++: protocols::recces::sampler::MC_Comb::reset() –> 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

restore(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, : pyrosetta.rosetta.core.pose.Pose) → None¶

restore pose to state prior to this sampler’s apply(). Would enable big speedup in monte carlo by obviating pose copies.

C++: protocols::recces::sampler::MC_Sampler::restore(class core::pose::Pose &) –> void

rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶: C++: protocols::recces::sampler::MC_Any::rotamer() const –> class std::shared_ptr<const class protocols::recces::sampler::MC_Sampler>

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_name(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: str) → None¶

Set name of the class

C++: protocols::recces::sampler::MC_Sampler::set_name(const std::string &) –> 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

set_uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, setting: bool) → None¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Comb::set_uniform_modeler(const bool) –> void

set_update_pose(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, setting: pyrosetta.rosetta.core.pose.Pose) → None¶

set (optional) update_pose

C++: protocols::recces::sampler::MC_Comb::set_update_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any, out: pyrosetta.rosetta.std.ostream, indent: int) -> None

output summary of class

C++: protocols::recces::sampler::MC_Any::show(std::ostream &, const unsigned long) 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(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType¶

Type of class (see enum in SamplerPlusPlusTypes.hh)

C++: protocols::recces::sampler::MC_Any::type() const –> enum protocols::toolbox::SamplerPlusPlusType

uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Sampler::uniform_modeler() const –> bool

update(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Update the DOFs

C++: protocols::recces::sampler::MC_Comb::update() –> void

class pyrosetta.rosetta.protocols.recces.sampler.MC_Comb¶

Bases: MC_Sampler

add_rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, rotamer: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → None¶

Add one more rotamer sampler to this sampler

C++: protocols::recces::sampler::MC_Comb::add_rotamer(const class std::shared_ptr<class protocols::recces::sampler::MC_Sampler> &) –> void

apply(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the current rotamer to pose

C++: protocols::recces::sampler::MC_Comb::apply(class core::pose::Pose &) –> void

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

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

clear_rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Clear all rotamer samplers stored in this sampler

C++: protocols::recces::sampler::MC_Comb::clear_rotamer() –> 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>

find(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶

return OP to the subsampler that controls exactly this torsion_id (assume only one).

C++: protocols::recces::sampler::MC_Comb::find(const class core::id::TorsionID &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Sampler>

found_move(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

check if ++ did anything to pose.

C++: protocols::recces::sampler::MC_Sampler::found_move() const –> bool

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

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

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

get_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.recces.sampler.MC_Sampler) → str¶

Name of the class

C++: protocols::recces::sampler::MC_Sampler::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 > > &

init(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Initialization

C++: protocols::recces::sampler::MC_Comb::init() –> void

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

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

num_rotamers(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → int¶: C++: protocols::recces::sampler::MC_Comb::num_rotamers() const –> unsigned long

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

pre_increment(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Move to next rotamer

C++: protocols::recces::sampler::MC_Comb::operator++() –> void

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

reset(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Reset to the first (or random if random()) rotamer

C++: protocols::recces::sampler::MC_Comb::reset() –> 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

restore(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, : pyrosetta.rosetta.core.pose.Pose) → None¶

restore pose to state prior to this sampler’s apply(). Would enable big speedup in monte carlo by obviating pose copies.

C++: protocols::recces::sampler::MC_Sampler::restore(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_name(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: str) → None¶

Set name of the class

C++: protocols::recces::sampler::MC_Sampler::set_name(const std::string &) –> 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

set_uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, setting: bool) → None¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Comb::set_uniform_modeler(const bool) –> void

set_update_pose(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, setting: pyrosetta.rosetta.core.pose.Pose) → None¶

set (optional) update_pose

C++: protocols::recces::sampler::MC_Comb::set_update_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, out: pyrosetta.rosetta.std.ostream, indent: int) -> None

output summary of class

C++: protocols::recces::sampler::MC_Comb::show(std::ostream &, const unsigned long) 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(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType¶

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

C++: protocols::recces::sampler::MC_Comb::type() const –> enum protocols::toolbox::SamplerPlusPlusType

uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Sampler::uniform_modeler() const –> bool

update(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Update the DOFs

C++: protocols::recces::sampler::MC_Comb::update() –> void

class pyrosetta.rosetta.protocols.recces.sampler.MC_Loop¶

Bases: MC_Any

add_rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, rotamer: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → None¶

Add one more rotamer sampler to this sampler

C++: protocols::recces::sampler::MC_Comb::add_rotamer(const class std::shared_ptr<class protocols::recces::sampler::MC_Sampler> &) –> void

apply(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the current rotamer to pose

C++: protocols::recces::sampler::MC_Any::apply(class core::pose::Pose &) –> void

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

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

clear_rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Clear all rotamer samplers stored in this sampler

C++: protocols::recces::sampler::MC_Comb::clear_rotamer() –> 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>

curr_id(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → int¶: C++: protocols::recces::sampler::MC_Any::curr_id() const –> unsigned long

find(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶

return OP to the subsampler that controls exactly this torsion_id (assume only one).

C++: protocols::recces::sampler::MC_Comb::find(const class core::id::TorsionID &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Sampler>

found_move(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

check if ++ did anything to pose.

C++: protocols::recces::sampler::MC_Sampler::found_move() const –> bool

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

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

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

get_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.recces.sampler.MC_Sampler) → str¶

Name of the class

C++: protocols::recces::sampler::MC_Sampler::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 > > &

init(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → None¶

Initialization

C++: protocols::recces::sampler::MC_Any::init() –> void

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

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

num_rotamers(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → int¶: C++: protocols::recces::sampler::MC_Comb::num_rotamers() const –> unsigned long

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

pre_increment(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Loop) → None¶

Move to next rotamer

C++: protocols::recces::sampler::MC_Loop::operator++() –> void

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

reset(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Reset to the first (or random if random()) rotamer

C++: protocols::recces::sampler::MC_Comb::reset() –> 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

restore(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, : pyrosetta.rosetta.core.pose.Pose) → None¶

restore pose to state prior to this sampler’s apply(). Would enable big speedup in monte carlo by obviating pose copies.

C++: protocols::recces::sampler::MC_Sampler::restore(class core::pose::Pose &) –> void

rotamer(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Any) → pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶: C++: protocols::recces::sampler::MC_Any::rotamer() const –> class std::shared_ptr<const class protocols::recces::sampler::MC_Sampler>

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_name(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: str) → None¶

Set name of the class

C++: protocols::recces::sampler::MC_Sampler::set_name(const std::string &) –> 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

set_uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, setting: bool) → None¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Comb::set_uniform_modeler(const bool) –> void

set_update_pose(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb, setting: pyrosetta.rosetta.core.pose.Pose) → None¶

set (optional) update_pose

C++: protocols::recces::sampler::MC_Comb::set_update_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Loop, out: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Loop, out: pyrosetta.rosetta.std.ostream, indent: int) -> None

output summary of class

C++: protocols::recces::sampler::MC_Loop::show(std::ostream &, const unsigned long) 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(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Loop) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType¶

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

C++: protocols::recces::sampler::MC_Loop::type() const –> enum protocols::toolbox::SamplerPlusPlusType

uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Sampler::uniform_modeler() const –> bool

update(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Comb) → None¶

Update the DOFs

C++: protocols::recces::sampler::MC_Comb::update() –> void

class pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion¶

Bases: MC_Sampler

active_angle(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → float¶

Get the active angle

C++: protocols::recces::sampler::MC_OneTorsion::active_angle() const –> double

apply(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the active torsion to pose

C++: protocols::recces::sampler::MC_OneTorsion::apply(class core::pose::Pose &) –> void

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

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>

find(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶

return OP to the subsampler that controls exactly this torsion_id (assume only one).

C++: protocols::recces::sampler::MC_OneTorsion::find(const class core::id::TorsionID &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Sampler>

found_move(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

check if ++ did anything to pose.

C++: protocols::recces::sampler::MC_Sampler::found_move() const –> bool

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

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

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

get_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.recces.sampler.MC_OneTorsion) → str¶

Name of the class

C++: protocols::recces::sampler::MC_OneTorsion::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_torsion_id(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → pyrosetta.rosetta.core.id.TorsionID¶

Get the TorsionID of the sampler

C++: protocols::recces::sampler::MC_OneTorsion::get_torsion_id() const –> const class core::id::TorsionID &

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 > > &

init(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → None¶

Initialization

C++: protocols::recces::sampler::MC_OneTorsion::init() –> void

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

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

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

pre_increment(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → None¶

Update the active angle based on stored: (do not update stored_angle_)

C++: protocols::recces::sampler::MC_OneTorsion::operator++() –> void

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

reset(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → None¶

Reset to current angle

C++: protocols::recces::sampler::MC_OneTorsion::reset() –> 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

restore(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, : pyrosetta.rosetta.core.pose.Pose) → None¶

restore pose to state prior to this sampler’s apply(). Would enable big speedup in monte carlo by obviating pose copies.

C++: protocols::recces::sampler::MC_Sampler::restore(class core::pose::Pose &) –> void

set_angle(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, setting: float) → None¶

Set the stored angle

C++: protocols::recces::sampler::MC_OneTorsion::set_angle(const double) –> void

set_angle_range(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, min: float, max: float) → None¶

Set the angle range

C++: protocols::recces::sampler::MC_OneTorsion::set_angle_range(const double, const double) –> 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_gaussian_stdev(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, setting: float) → None¶

Set the standard deviation of Gaussian sampler

C++: protocols::recces::sampler::MC_OneTorsion::set_gaussian_stdev(const double) –> 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_name(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: str) → None¶

Set name of the class

C++: protocols::recces::sampler::MC_Sampler::set_name(const std::string &) –> 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_torsion_id(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, setting: pyrosetta.rosetta.core.id.TorsionID) → None¶

Set the TorsionID of the sampler

C++: protocols::recces::sampler::MC_OneTorsion::set_torsion_id(const class core::id::TorsionID &) –> 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

set_uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: bool) → None¶

Set uniform modeler (instead of Gaussian)

C++: protocols::recces::sampler::MC_Sampler::set_uniform_modeler(const bool) –> void

set_update_pose(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: pyrosetta.rosetta.core.pose.Pose) → None¶

set (optional) update_pose

C++: protocols::recces::sampler::MC_Sampler::set_update_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_update_tolerance(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, setting: float) → None¶: C++: protocols::recces::sampler::MC_OneTorsion::set_update_tolerance(const double &) –> void

shared_from_this(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → pyrosetta.rosetta.protocols.moves.Mover¶

show(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion, out: pyrosetta.rosetta.std.ostream, indent: int) → None¶

output summary of class

C++: protocols::recces::sampler::MC_OneTorsion::show(std::ostream &, const unsigned long) const –> void

stored_angle(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → float¶

Get the stored angle

C++: protocols::recces::sampler::MC_OneTorsion::stored_angle() const –> double

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

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

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

type(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType¶

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

C++: protocols::recces::sampler::MC_OneTorsion::type() const –> enum protocols::toolbox::SamplerPlusPlusType

uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Sampler::uniform_modeler() const –> bool

update(self: pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion) → None¶

Update the stored angle to match active angle

C++: protocols::recces::sampler::MC_OneTorsion::update() –> void

class pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶

Bases: SamplerPlusPlus

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

Apply the current rotamer to pose

C++: protocols::toolbox::SamplerPlusPlus::apply(class core::pose::Pose &) –> void

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

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>

find(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler¶

return OP to the subsampler that controls exactly this torsion_id (assume only one).

C++: protocols::recces::sampler::MC_Sampler::find(const class core::id::TorsionID &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Sampler>

found_move(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

check if ++ did anything to pose.

C++: protocols::recces::sampler::MC_Sampler::found_move() const –> bool

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

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

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

get_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.recces.sampler.MC_Sampler) → str¶

Name of the class

C++: protocols::recces::sampler::MC_Sampler::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 > > &

init(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → None¶

Initialization

C++: protocols::toolbox::SamplerPlusPlus::init() –> void

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

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

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

pre_increment(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → None¶

Move to next rotamer

C++: protocols::toolbox::SamplerPlusPlus::operator++() –> void

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

reset(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → None¶

Reset to the first (or random if random()) rotamer

C++: protocols::toolbox::SamplerPlusPlus::reset() –> 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

restore(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, : pyrosetta.rosetta.core.pose.Pose) → None¶

restore pose to state prior to this sampler’s apply(). Would enable big speedup in monte carlo by obviating pose copies.

C++: protocols::recces::sampler::MC_Sampler::restore(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_name(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: str) → None¶

Set name of the class

C++: protocols::recces::sampler::MC_Sampler::set_name(const std::string &) –> 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

set_uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: bool) → None¶

Set uniform modeler (instead of Gaussian)

C++: protocols::recces::sampler::MC_Sampler::set_uniform_modeler(const bool) –> void

set_update_pose(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler, setting: pyrosetta.rosetta.core.pose.Pose) → None¶

set (optional) update_pose

C++: protocols::recces::sampler::MC_Sampler::set_update_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) -> None
show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, output: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, out: pyrosetta.rosetta.std.ostream, indent: int) -> None

output summary of class

C++: protocols::toolbox::SamplerPlusPlus::show(std::ostream &, const unsigned long) 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(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType¶

Type of class (see enum in SamplerPlusPlusTypes.hh)

C++: protocols::toolbox::SamplerPlusPlus::type() const –> enum protocols::toolbox::SamplerPlusPlusType

uniform_modeler(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → bool¶

Get uniform modeler state

C++: protocols::recces::sampler::MC_Sampler::uniform_modeler() const –> bool

update(self: pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler) → None¶

Update the DOFs

C++: protocols::recces::sampler::MC_Sampler::update() –> void

pyrosetta.rosetta.protocols.recces.sampler.get_recces_turner_sampler(pose: pyrosetta.rosetta.core.pose.Pose, a_form_range: float, secstruct: pyrosetta.rosetta.core.pose.rna.RNA_SecStruct, params: pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters) → pyrosetta.rosetta.protocols.recces.sampler.MC_Comb¶: C++: protocols::recces::sampler::get_recces_turner_sampler(const class core::pose::Pose &, const double &, const class core::pose::rna::RNA_SecStruct &, const class protocols::recces::params::RECCES_Parameters &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Comb>

pyrosetta.rosetta.protocols.recces.sampler.initialize_jump_sampler(pose: pyrosetta.rosetta.core.pose.Pose, num_jump: int, options: pyrosetta.rosetta.protocols.recces.options.RECCES_Options) → pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump¶: C++: protocols::recces::sampler::initialize_jump_sampler(const class core::pose::Pose &, const unsigned long &, const class protocols::recces::options::RECCES_Options &) –> class std::shared_ptr<class protocols::recces::sampler::rna::MC_RNA_OneJump>

pyrosetta.rosetta.protocols.recces.sampler.initialize_sampler(pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.protocols.recces.options.RECCES_Options, params: pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters) → pyrosetta.rosetta.protocols.recces.sampler.MC_Comb¶: C++: protocols::recces::sampler::initialize_sampler(const class core::pose::Pose &, const class protocols::recces::options::RECCES_Options &, const class protocols::recces::params::RECCES_Parameters &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Comb>

pyrosetta.rosetta.protocols.recces.sampler.initialize_thermal_sampler(pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.protocols.recces.options.RECCES_Options) → pyrosetta.rosetta.protocols.recces.sampler.MC_Comb¶: C++: protocols::recces::sampler::initialize_thermal_sampler(const class core::pose::Pose &, const class protocols::recces::options::RECCES_Options &) –> class std::shared_ptr<class protocols::recces::sampler::MC_Comb>