moves¶

Bindings for protocols::moves namespace

pyrosetta.rosetta.protocols.moves.AddPyMOLObserver(*args, **kwargs)¶

Overloaded function.

AddPyMOLObserver(p: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool, update_interval: float) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver

Helper function that create PyMOLObserver Object and add it to the give Pose.: This is the most likely the only function that you need to call…

C++: protocols::moves::AddPyMOLObserver(class core::pose::Pose &, bool, double) –> class std::shared_ptr<class protocols::moves::PyMOLObserver>

pyrosetta.rosetta.protocols.moves.AddPyMOLObserver_to_conformation(*args, **kwargs)¶

Overloaded function.

AddPyMOLObserver_to_conformation(p: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_conformation(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_conformation(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool, update_interval: float) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver

Helper function that create PyMOLObserver Object and add it to the give Pose conformation object so pymol only updates on conformation changes.

C++: protocols::moves::AddPyMOLObserver_to_conformation(class core::pose::Pose &, bool, double) –> class std::shared_ptr<class protocols::moves::PyMOLObserver>

pyrosetta.rosetta.protocols.moves.AddPyMOLObserver_to_energies(*args, **kwargs)¶

Overloaded function.

AddPyMOLObserver_to_energies(p: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_energies(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver
AddPyMOLObserver_to_energies(p: pyrosetta.rosetta.core.pose.Pose, keep_history: bool, update_interval: float) -> pyrosetta.rosetta.protocols.moves.PyMOLObserver

Helper function that create PyMOLObserver Object and add it to the give Pose energies object so pymol only updates on energy changes.

C++: protocols::moves::AddPyMOLObserver_to_energies(class core::pose::Pose &, bool, double) –> class std::shared_ptr<class protocols::moves::PyMOLObserver>

class pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover¶

Bases: Mover

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

Apply the stored fold tree to the pose

C++: protocols::moves::ChangeFoldTreeMover::apply(class core::pose::Pose &) –> void

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

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.moves.ChangeFoldTreeMover) → str¶: C++: protocols::moves::ChangeFoldTreeMover::get_name() const –> std::string

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

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

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

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

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

non-const accessor

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

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

static 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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

set_foldtree(self: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: protocols::moves::ChangeFoldTreeMover::set_foldtree(class core::kinematics::FoldTree) –> void

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.CompositionMover¶

Bases: Mover

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

apply(*args, **kwargs)¶

Overloaded function.

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

C++: protocols::moves::CompositionMover::apply(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.moves.CompositionMover, pose: pyrosetta.rosetta.core.pose.Pose, i: int, j: int) -> None

C++: protocols::moves::CompositionMover::apply(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

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

clear(self: pyrosetta.rosetta.protocols.moves.CompositionMover) → None¶: C++: protocols::moves::CompositionMover::clear() –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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_movers(self: pyrosetta.rosetta.protocols.moves.CompositionMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::CompositionMover::get_movers() –> class utility::vector1<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > >

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

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

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

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

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

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

non-const accessor

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

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

static 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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.CycleMover¶

Bases: MoverContainer

CycleMover iterates through its vector of Movers one at a time over many calls to apply().

Each time CycleMover.apply() is called, it calls apply() on the next Mover in its sequence,: until reaching the end of the list and starting over. Useful for things like doing a full repack one out of every eight cycles, and a rotamer trials on the other seven.

add_mover(*args, **kwargs)¶

Overloaded function.

add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover) -> None
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover, weight_in: float) -> None

Adds a mover to the end of this container

C++: protocols::moves::MoverContainer::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void

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

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

clear(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → None¶: C++: protocols::moves::MoverContainer::clear() –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

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

Clone returns a new instance of CycleMover representing a deep copy of this mover.

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

front(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::MoverContainer::front() –> 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_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, index: int) → str¶: C++: protocols::moves::MoverContainer::get_mover(unsigned long) const –> std::string

get_name(self: pyrosetta.rosetta.protocols.moves.CycleMover) → str¶: C++: protocols::moves::CycleMover::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

movers(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::MoverContainer::movers() const –> const class utility::vector0<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &

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

nr_moves(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::nr_moves() –> 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

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

Provide the citation.

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

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

Sets the input Pose for both the container: and the contained movers, for rmsd

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

set_native_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoverContainer::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

weights(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_double¶: C++: protocols::moves::MoverContainer::weights() const –> const class utility::vector0<double, class std::allocator<double> > &

class pyrosetta.rosetta.protocols.moves.CyclicMover¶

Bases: Mover

A simple class for cycling between movers in consecutive calls to apply()

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

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

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

enqueue(self: pyrosetta.rosetta.protocols.moves.CyclicMover, mover: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Enqueue the specified mover for execution

C++: protocols::moves::CyclicMover::enqueue(class std::shared_ptr<class protocols::moves::Mover>) –> void

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

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

fpd

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

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

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

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

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

static 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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.DsspMover¶

Bases: Mover

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

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

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.DsspMover) → pyrosetta.rosetta.protocols.moves.Mover¶

clone this object

C++: protocols::moves::DsspMover::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.DsspMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of object

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

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

fpd

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

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

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

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

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

static mover_name() → str¶: C++: protocols::moves::DsspMover::mover_name() –> std::string

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

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

set_asu_only(self: pyrosetta.rosetta.protocols.moves.DsspMover, asu_only: bool) → None¶

Select only the asymmetric unit residues or not.

C++: protocols::moves::DsspMover::set_asu_only(const bool) –> void

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.DsspMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.moves.DualMonteCarlo¶

Bases: pybind11_object

DualMonteCarlo is a wrapper class around MonteCarlo. Its original purpose is to allow for Boltzmann scoring a pose in centroid mode while simultaneously tracking a fullatom equivalent. It should work for any paired poses. Generally, “DMC_pose” refers to the pose this class tracks, whereas “MC_pose” refers to the one used by the underlying MC object. While this class contains a MonteCarlo object (by composition, not inheritance); you cannot pass in a MC object to it, nor can you get an OP to that object. const access to the underlying MC is provided at this time; if you want nonconst access you can write it in but beware that the user can then ruin the bookkeeping! Also note that I (SML) left the framework in place in comments for a lot of MC’s functions within DMC like checkpointing and counters. Flesh these out if you want them…

MC(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶

const access to MC object

C++: protocols::moves::DualMonteCarlo::MC() const –> const class protocols::moves::MonteCarlo &

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool

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

last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶

this gets you only the DMC’s pose; call MC directly for its. Note that this pose is accepted based on the partner pose in the underlying MC.

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

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

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

lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::DualMonteCarlo::lowest_score_pose() const –> const class core::pose::Pose &

recover_low(*args, **kwargs)¶

Overloaded function.

recover_low(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose) -> None

Copies the lowest_score_ pose into the input pose, as well as into: last_accepted_pose_. Copies action for underlying MC but does not return that pose.

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

recover_low(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose) -> None

Copies the lowest_score_ pose into the input pose, as well as into: last_accepted_pose_. Always copies action for underlying MC. This version returns the MC’s pose.

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

reset(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo, DMC_pose: pyrosetta.rosetta.core.pose.Pose, MC_pose: pyrosetta.rosetta.core.pose.Pose) → None¶

sets lowest and last_accepted poses to pose; calls MC’s reset too

C++: protocols::moves::DualMonteCarlo::reset(const class core::pose::Pose &, const class core::pose::Pose &) –> void

score_function(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::moves::DualMonteCarlo::score_function() const –> const class core::scoring::ScoreFunction &

show_scores(self: pyrosetta.rosetta.protocols.moves.DualMonteCarlo) → None¶: C++: protocols::moves::DualMonteCarlo::show_scores() const –> void

class pyrosetta.rosetta.protocols.moves.EXCN_Converged¶

Bases: Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::add_msg(const std::string &) –> void

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Invoke a crash log for throwing this exception.: If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None¶

Present this exception to the user.: Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int¶: C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)¶

Overloaded function.

msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None¶: C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str¶

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str¶: C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.moves.FastLinearFunc¶

Bases: RampingFunc

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

func(self: pyrosetta.rosetta.protocols.moves.FastLinearFunc, x: float) → float¶: C++: protocols::moves::FastLinearFunc::func(double) const –> double

class pyrosetta.rosetta.protocols.moves.FilterMover¶

Bases: Mover

add_filter(self: pyrosetta.rosetta.protocols.moves.FilterMover, my_filter: pyrosetta.rosetta.protocols.filters.Filter) → None¶: C++: protocols::moves::FilterMover::add_filter(const class std::shared_ptr<class protocols::filters::Filter> &) –> void

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

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

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.moves.FilterMover) → str¶: C++: protocols::moves::FilterMover::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

max_tries(self: pyrosetta.rosetta.protocols.moves.FilterMover, mt: int) → None¶

set maximum tries of making a move with my_mover

C++: protocols::moves::FilterMover::max_tries(const unsigned long) –> void

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

set_mover(self: pyrosetta.rosetta.protocols.moves.FilterMover, my_mover: pyrosetta.rosetta.protocols.moves.Mover) → None¶

set mover

C++: protocols::moves::FilterMover::set_mover(const 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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover¶

Bases: Mover

This Mover runs a Filter and dumps the report_sm value to Pose’s extra scores (for later JD reporting) To do the same for all filters, use WriteFiltersToPose.

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

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

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.FilterReportAsPoseExtraScoresMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::moves::FilterReportAsPoseExtraScoresMover::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.FilterReportAsPoseExtraScoresMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::moves::FilterReportAsPoseExtraScoresMover::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_filter(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::moves::FilterReportAsPoseExtraScoresMover::get_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover) → str¶: C++: protocols::moves::FilterReportAsPoseExtraScoresMover::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_report_as(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover) → str¶: C++: protocols::moves::FilterReportAsPoseExtraScoresMover::get_report_as() const –> const std::string &

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

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

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

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

non-const accessor

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

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

static mover_name() → str¶: C++: protocols::moves::FilterReportAsPoseExtraScoresMover::mover_name() –> std::string

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

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

parse XML tag (to use this Mover in Rosetta Scripts)

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

set_filter(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, filter: pyrosetta.rosetta.protocols.filters.Filter) → None¶

set filter we report from

C++: protocols::moves::FilterReportAsPoseExtraScoresMover::set_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

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

setter for poses contained for rms

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

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

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

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

set_report_as(self: pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover, report_as: str) → None¶: C++: protocols::moves::FilterReportAsPoseExtraScoresMover::set_report_as(const std::string &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.moves.FilterReporterMover¶

Bases: Mover

A FilterMover that also calls report() on apply()

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

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

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.FilterReporterMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::FilterReporterMover::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.FilterReporterMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::FilterReporterMover::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_filter(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::moves::FilterReporterMover::get_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

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

get_name(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover) → str¶: C++: protocols::moves::FilterReporterMover::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_out(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover) → pyrosetta.rosetta.std.ostream¶: C++: protocols::moves::FilterReporterMover::get_out() –> std::ostream &

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

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

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

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

non-const accessor

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

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

static 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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

set_filter(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, filter: pyrosetta.rosetta.protocols.filters.Filter) → None¶: C++: protocols::moves::FilterReporterMover::set_filter(const class std::shared_ptr<class protocols::filters::Filter> &) –> 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_mover(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, mover: pyrosetta.rosetta.protocols.moves.Mover) → None¶: C++: protocols::moves::FilterReporterMover::set_mover(const 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_out(self: pyrosetta.rosetta.protocols.moves.FilterReporterMover, out: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::moves::FilterReporterMover::set_out(const std::ostream &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.GeometricFunc¶

Bases: RampingFunc

Ramps rapidly from the starting value to the final value. Not 1 at x=1. Doesn’t really finish at (1,1). func(x) = 1 - exp( -1 * x * inv_xval_at_0p5 * 0.6931 );

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

func(self: pyrosetta.rosetta.protocols.moves.GeometricFunc, x: float) → float¶: C++: protocols::moves::GeometricFunc::func(double) const –> double

class pyrosetta.rosetta.protocols.moves.IfMover¶

Bases: Mover

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

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

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

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

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

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

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

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

static mover_name() → str¶: C++: protocols::moves::IfMover::mover_name() –> std::string

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

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.IfMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.moves.InvGeometricFunc¶

Bases: RampingFunc

Ramps slowly from the starting value to the final value Non-zero for x = 0. Doesn’t really start at (0,0). func(x) = exp( -1 * ( 1 - x ) / ( 1 - xval_at_0p5 ) * 0.6931 );

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

func(self: pyrosetta.rosetta.protocols.moves.InvGeometricFunc, x: float) → float¶: C++: protocols::moves::InvGeometricFunc::func(double) const –> double

class pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover¶

Bases: Mover

A mover that repeatedly applies a sub-mover (up to a given maximum) until the given filter returns values within a certain delta for a given number of cycles.

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

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

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.IteratedConvergenceMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::moves::IteratedConvergenceMover::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>

cycles(*args, **kwargs)¶

Overloaded function.

cycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, cycles: int) -> None

C++: protocols::moves::IteratedConvergenceMover::cycles(unsigned long) –> void

cycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> int

C++: protocols::moves::IteratedConvergenceMover::cycles() const –> unsigned long

delta(*args, **kwargs)¶

Overloaded function.

delta(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, delta: float) -> None

C++: protocols::moves::IteratedConvergenceMover::delta(double) –> void

delta(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> float

C++: protocols::moves::IteratedConvergenceMover::delta() const –> double

filter(*args, **kwargs)¶

Overloaded function.

filter(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, filter: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::moves::IteratedConvergenceMover::filter(class std::shared_ptr<const class protocols::filters::Filter>) –> void

filter(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> pyrosetta.rosetta.protocols.filters.Filter

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

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

required in the context of the parser/scripting scheme

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

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

fpd

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

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

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

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

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) → str¶: C++: protocols::moves::IteratedConvergenceMover::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

maxcycles(*args, **kwargs)¶

Overloaded function.

maxcycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, maxcycles: int) -> None

C++: protocols::moves::IteratedConvergenceMover::maxcycles(unsigned long) –> void

maxcycles(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> int

C++: protocols::moves::IteratedConvergenceMover::maxcycles() const –> unsigned long

static mover_name() → str¶: C++: protocols::moves::IteratedConvergenceMover::mover_name() –> std::string

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

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

parse XML (specifically in the context of the parser/scripting scheme)

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

submover(*args, **kwargs)¶

Overloaded function.

submover(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover, mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::moves::IteratedConvergenceMover::submover(class std::shared_ptr<class protocols::moves::Mover>) –> void

submover(self: pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover) -> pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.moves.JumpOutMover¶

Bases: Mover

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

Applies a move, and conditionally applies a second move.

This mover applies the first move, and checks if the score difference between the initial score and the score after the first move is within a tolerance. If the score after the first move is within the tolerance, the second move is applied.

C++: protocols::moves::JumpOutMover::apply(class core::pose::Pose &) –> void

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

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.moves.JumpOutMover) → str¶: C++: protocols::moves::JumpOutMover::get_name() const –> std::string

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

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

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

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

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

non-const accessor

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

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

static 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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.LinearFunc¶

Bases: RampingFunc

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

func(self: pyrosetta.rosetta.protocols.moves.LinearFunc, x: float) → float¶: C++: protocols::moves::LinearFunc::func(double) const –> double

class pyrosetta.rosetta.protocols.moves.MCA¶

Bases: pybind11_object

Members:

MCA_accepted_score_beat_low

MCA_accepted_score_beat_last

MCA_accepted_thermally

MCA_rejected

MCA_accepted_score_beat_last = <MCA.MCA_accepted_score_beat_last: 2>¶

MCA_accepted_score_beat_low = <MCA.MCA_accepted_score_beat_low: 3>¶

MCA_accepted_thermally = <MCA.MCA_accepted_thermally: 1>¶

MCA_rejected = <MCA.MCA_rejected: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.moves.MCShowMover¶

Bases: Mover

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

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

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.moves.MCShowMover) → str¶: C++: protocols::moves::MCShowMover::get_name() const –> std::string

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

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

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

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

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

non-const accessor

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

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

static 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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.MixedMonteCarlo¶

Bases: pybind11_object

A wrapper class around MonteCarlo that uses both centroid and FA scorefxns.

A Hybrid Monte Carlo mover that employs both centroid and ful-atom score functions. The purpose of this object is to use a combination of centroid and full-atom scorefxn for Boltzmann scoring but only use only the full-atom pose for bookkeeping. This object is particularly important for Resolution Exchange MC based docking.

AmeyaHarmalkar (harmalkar.ameya24.com)

MC(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶

Const access to the MC object

C++: protocols::moves::MixedMonteCarlo::MC() const –> const class protocols::moves::MonteCarlo &

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool

This method should evaluate net score from CG and AA modes

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

highres_score_function(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Returns the highres scorefxn

C++: protocols::moves::MixedMonteCarlo::highres_score_function() const –> const class core::scoring::ScoreFunction &

last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶

this gets you only the low-res pose

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

last_accepted_score(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) → float¶

Returns the score value of the last accepted pose

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

lowest_score(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) → float¶

Returns the score value of the lowest score pose encountered

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

lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶

this gets you only the low-res pose

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

lowres_score_function(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Returns the lowres scorefxn

C++: protocols::moves::MixedMonteCarlo::lowres_score_function() const –> const class core::scoring::ScoreFunction &

recover_low(*args, **kwargs)¶

Overloaded function.

recover_low(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, high_pose: pyrosetta.rosetta.core.pose.Pose) -> None

Copies the lowest_score_ pose into the input pose as well as in the: last_accepted_ pose

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

recover_low(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose) -> None

Copies the lowest_score_ pose into the input pose as well as in the: last_accepted_ pose. Returns the highres pose

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

reset(self: pyrosetta.rosetta.protocols.moves.MixedMonteCarlo, low_pose: pyrosetta.rosetta.core.pose.Pose, high_pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sets the lowest and last accepted poses to pose and calls MC reset

C++: protocols::moves::MixedMonteCarlo::reset(const class core::pose::Pose &, const class core::pose::Pose &) –> void

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

Displays the last accepted and lowest scores

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

class pyrosetta.rosetta.protocols.moves.MonteCarlo¶

Bases: pybind11_object

This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics.

Output Methods:: MonteCarlo.show_counters() MonteCarlo.show_scores() MonteCarlo.show_state()
Common Methods:: MonteCarlo.last_accepted_score MonteCarlo.last_accepted_pose MonteCarlo.lowest_score MonteCarlo.lowest_score_pose MonteCarlo.score_function MonteCarlo.set_temperature MonteCarlo.temperature

boltzmann(*args, **kwargs)¶

Overloaded function.

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

Applies the Metropolis Criterion on pose based on

the ScoreFunction, temperature, and the last accepted pose. This method evaluates the change in score, compares the trial pose to the last accepted pose, and updates the pose structure and simulation statistics appropriately

example(s):: mc.boltzmann( pose )
See also:: MonteCarlo MonteCarlo.last_accepted_score MonteCarlo.lowest_score

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

boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str, proposal_density_ratio: float, inner_score_temperature_delta: float) -> bool

Applies the Metropolis Criterion on pose based on

the externally computes score, temperature, and the last accepted pose. This method evaluates the change in score, compares the trial pose to the last accepted pose, and updates the pose structure and simulation statistics appropriately

example(s):: mc.boltzmann( pose, score )
See also:: MonteCarlo MonteCarlo.last_accepted_score MonteCarlo.lowest_score

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

boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float, check_lowest_score: bool) -> bool

Applies the Metropolis Criterion on the inputted

pose based on the supplied score delta

example(s):

See also:: MonteCarlo

C++: protocols::moves::MonteCarlo::boltzmann(double, const std::string &, const double, const double, bool) –> bool

boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float, check_lowest_score: bool) -> bool

Applies the Metropolis Criterion on the inputted

pose based on the supplied score delta. Updates the Pose Structure accordingly.

example(s):

See also:: MonteCarlo

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

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

Change the weight on a score term in the object’s scorefunction. Useful when we don’t want to reset the whole scorefunction during an annealing step.

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

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

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

Removes last accepted pose and lowest score pose

example(s):
mc.clear_poses()

See also:
MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.lowest_score_pose MonteCarlo.recover_low MonteCarlo.reset MonteCarlo.set_last_accepted_pose MonteCarlo.set_lowest_score_pose

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

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

eval_lowest_score_pose(*args, **kwargs)¶

Overloaded function.

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

Compares score of <pose> to the lowest score found.

If lower, sets the current lowest score pose and lowest score. Use internal pose energies if score_pose is false. Used to evaluate lowest score without boltzmann. Does not change pose structure.

Does not update simulation statistics or last accepts by default.

example(s):: mc.eval_lowest_score_pose( pose )
See also:: MonteCarlo MonteCarlo.lowest_score MonteCarlo.lowest_score_pose MonteCarlo.recover_low

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

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

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

no brief for now

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

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

Returns the number of trials since last acceptance

example(s):
mc.last_accept()

See also:
MonteCarlo MonteCarlo.show_counters MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score

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

last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶

Returns the last accepted pose

example(s):
mc.last_accepted_pose()

See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_score

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

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

Returns the score value of the last accepted pose

example(s):
mc.last_accepted_score()

See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state

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

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

Returns the score value of the last score

example(s):
mc.last_accepted_score()

See also:
MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state

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

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

Returns the score value of the lowest score pose encountered

example(s):
mc.lowest_score()

See also:
MonteCarlo MonteCarlo.lowest_score_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state

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

lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → pyrosetta.rosetta.core.pose.Pose¶

Returns the lowest score pose encountered

example(s):
mc.lowest_score_pose()

See also:
MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.lowest_score

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

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

Returns mc_accepted, informative of the last move applied

Note: Returns true for an accept, false otherwise
3 = accepted:score beat low score and last_accepted score 2 = accepted:score beat last_accepted score 1 = thermally accepted: score worse than last_accepted score 0 = not accepted

example(s):
mc.mc_accepted()

See also:
MonteCarlo MonteCarlo.show_state

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

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

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

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

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

no brief for now

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

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

Sets the input <pose> and last accepted pose to

the lowest score pose

example(s):: mc.recover_low( pose )
See also:: MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_score_pose

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

reset(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, 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::moves::MonteCarlo::reset(const class core::pose::Pose &) –> void

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

Sets lowest score pose and last accepted pose to

the score of <pose>

(does not reset counters)

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

C++: protocols::moves::MonteCarlo::reset(const class core::pose::Pose &, const double) –> 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(*args, **kwargs)¶

Overloaded function.

score_function(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <scorefxn> , re-scores

last accepted pose and lowest score pose

example(s):: mc.score_function( scorefxn )
See also:: MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function

C++: protocols::moves::MonteCarlo::score_function(const class core::scoring::ScoreFunction &) –> void

score_function(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the MonteCarlo ScoreFunction

example(s):
mc.score_function() mc.score_function()( pose )

See also:
MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function

C++: protocols::moves::MonteCarlo::score_function() const –> const class core::scoring::ScoreFunction &

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

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

MonteCarlo MonteCarlo.autotemp MonteCarlo.show_state

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

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

no brief for now

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

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

set_last_accepted_pose(*args, **kwargs)¶

Overloaded function.

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

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

(does not reset counters)

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

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

Sets the last accepted pose and last accepted score

(does not reset counters)

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

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

Set the last score.

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

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

set_lowest_score_pose(*args, **kwargs)¶

Overloaded function.

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

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

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

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

set_temperature(self: pyrosetta.rosetta.protocols.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_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.moves.MonteCarloExceptionConverge¶

Bases: pybind11_object

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

class pyrosetta.rosetta.protocols.moves.MonteCarloUtil¶

Bases: Mover

the MCResetMover applies a monte carlo reset

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

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

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

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

fpd

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

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

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

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

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.MoveMapMover¶

Bases: Mover

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

Main Method

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

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

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.moves.Mover) → str¶

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

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

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

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

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

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

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

non-const accessor

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

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

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

movemap(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.MoveMap¶

Get a movemap for the given pose: (As the movemap may vary based on the Pose (e.g. MoveMapFactory), we need the Pose information)

C++: protocols::moves::MoveMapMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

set_movemap(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.kinematics.MoveMap) → None¶: C++: protocols::moves::MoveMapMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.Mover¶

Bases: pybind11_object

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

Main Method

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

assign(self: pyrosetta.rosetta.protocols.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 &

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.moves.Mover) → str¶

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

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

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

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

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

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

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

non-const accessor

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

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.moves.MoverApplyingMover¶

Bases: Mover

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

Main Method

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

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

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.moves.Mover) → str¶

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

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

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

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

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

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

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

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover(self: pyrosetta.rosetta.protocols.moves.MoverApplyingMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::MoverApplyingMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_mover(self: pyrosetta.rosetta.protocols.moves.MoverApplyingMover, : pyrosetta.rosetta.protocols.moves.Mover) → None¶: C++: protocols::moves::MoverApplyingMover::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.MoverContainer¶

Bases: Mover

add_mover(*args, **kwargs)¶

Overloaded function.

add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover) -> None
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover, weight_in: float) -> None

Adds a mover to the end of this container

C++: protocols::moves::MoverContainer::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void

apply(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoverContainer::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.MoverContainer, : pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.protocols.moves.MoverContainer¶: C++: protocols::moves::MoverContainer::operator=(const class protocols::moves::MoverContainer &) –> class protocols::moves::MoverContainer &

clear(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → None¶: C++: protocols::moves::MoverContainer::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

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>

front(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::MoverContainer::front() –> 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_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, index: int) → str¶: C++: protocols::moves::MoverContainer::get_mover(unsigned long) const –> std::string

get_name(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

Each derived class must specify its name. The class name.

C++: protocols::moves::Mover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movers(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::MoverContainer::movers() const –> const class utility::vector0<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nr_moves(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::nr_moves() –> 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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.MoverContainer, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::moves::MoverContainer::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.MoverContainer, new_tag: str) → None¶: C++: protocols::moves::MoverContainer::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sets the input Pose for both the container: and the contained movers, for rmsd

C++: protocols::moves::MoverContainer::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoverContainer::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

size(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::size() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

weights(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_double¶: C++: protocols::moves::MoverContainer::weights() const –> const class utility::vector0<double, class std::allocator<double> > &

class pyrosetta.rosetta.protocols.moves.MoverCreator¶

Bases: pybind11_object

Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class.

assign(self: pyrosetta.rosetta.protocols.moves.MoverCreator, : pyrosetta.rosetta.protocols.moves.MoverCreator) → pyrosetta.rosetta.protocols.moves.MoverCreator¶: C++: protocols::moves::MoverCreator::operator=(const class protocols::moves::MoverCreator &) –> class protocols::moves::MoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.moves.MoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a new mover.

C++: protocols::moves::MoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.moves.MoverCreator) → str¶

Return the tag name associated with this factory.

C++: protocols::moves::MoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.moves.MoverFactory¶

Bases: SingletonBase_protocols_moves_MoverFactory_t

define_mover_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverFactory, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::MoverFactory::define_mover_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.protocols.moves.MoverFactory, creator: pyrosetta.rosetta.protocols.moves.MoverCreator) → None¶: C++: protocols::moves::MoverFactory::factory_register(class std::shared_ptr<class protocols::moves::MoverCreator>) –> void

get_citation_humanreadable(self: pyrosetta.rosetta.protocols.moves.MoverFactory, mover_name: str) → str¶

Get a human-readable listing of the citations for a given mover, by mover name.

Returns an empty string if there are no citations.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::moves::MoverFactory::get_citation_humanreadable(const std::string &) const –> std::string

static get_instance() → protocols::moves::MoverFactory¶: C++: utility::SingletonBase<protocols::moves::MoverFactory>::get_instance() –> class protocols::moves::MoverFactory *

mover_creator_map(self: pyrosetta.rosetta.protocols.moves.MoverFactory) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_moves_MoverCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_moves_MoverCreator_t¶

Read access to the set of all MoverCreators; for unit testing purposes

C++: protocols::moves::MoverFactory::mover_creator_map() const –> const class std::map<std::string, class std::shared_ptr<class protocols::moves::MoverCreator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class protocols::moves::MoverCreator> > > > &

mover_exists(self: pyrosetta.rosetta.protocols.moves.MoverFactory, mover_name: str) → bool¶

Is there a mover with the given name that’s known to Rosetta?

Vikram K. Mulligan (vmullig.edu)

C++: protocols::moves::MoverFactory::mover_exists(const std::string &) const –> bool

static mover_xml_schema_group_name() → str¶: C++: protocols::moves::MoverFactory::mover_xml_schema_group_name() –> std::string

newMover(*args, **kwargs)¶

Overloaded function.

newMover(self: pyrosetta.rosetta.protocols.moves.MoverFactory, : str) -> pyrosetta.rosetta.protocols.moves.Mover

Create a mover given its identifying string

C++: protocols::moves::MoverFactory::newMover(const std::string &) const –> class std::shared_ptr<class protocols::moves::Mover>

newMover(self: pyrosetta.rosetta.protocols.moves.MoverFactory, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.moves.Mover

return new Mover by Tag parsing; the identifying string for the Mover is in the Tag

C++: protocols::moves::MoverFactory::newMover(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> class std::shared_ptr<class protocols::moves::Mover>

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverFactory, mover_name: str, xsd: utility::tag::XMLSchemaDefinition) → None¶

Get the XML schema for a given mover.

Throws an error if the mover is unknown to Rosetta.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::moves::MoverFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.moves.MoverForPoseList¶

Bases: Mover

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::moves::MoverForPoseList::apply(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None

C++: protocols::moves::MoverForPoseList::apply(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

apply(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, viewer_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::moves::MoverForPoseList::apply(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.MoverForPoseList, : pyrosetta.rosetta.protocols.moves.MoverForPoseList) → pyrosetta.rosetta.protocols.moves.MoverForPoseList¶: C++: protocols::moves::MoverForPoseList::operator=(const class protocols::moves::MoverForPoseList &) –> class protocols::moves::MoverForPoseList &

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.moves.Mover) → str¶

Each derived class must specify its name. The class name.

C++: protocols::moves::Mover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.MoverStatistics¶

Bases: pybind11_object

acceptance_rate(self: pyrosetta.rosetta.protocols.moves.MoverStatistics) → float¶: C++: protocols::moves::MoverStatistics::acceptance_rate() const –> double

accepted(self: pyrosetta.rosetta.protocols.moves.MoverStatistics, result: bool) → None¶: C++: protocols::moves::MoverStatistics::accepted(bool) const –> void

add_score(self: pyrosetta.rosetta.protocols.moves.MoverStatistics, score_in: float) → None¶: C++: protocols::moves::MoverStatistics::add_score(double) –> void

assign(self: pyrosetta.rosetta.protocols.moves.MoverStatistics, : pyrosetta.rosetta.protocols.moves.MoverStatistics) → pyrosetta.rosetta.protocols.moves.MoverStatistics¶: C++: protocols::moves::MoverStatistics::operator=(const class protocols::moves::MoverStatistics &) –> class protocols::moves::MoverStatistics &

clear(self: pyrosetta.rosetta.protocols.moves.MoverStatistics) → None¶: C++: protocols::moves::MoverStatistics::clear() –> void

clear_score(self: pyrosetta.rosetta.protocols.moves.MoverStatistics) → None¶: C++: protocols::moves::MoverStatistics::clear_score() –> void

num_accepted(self: pyrosetta.rosetta.protocols.moves.MoverStatistics) → int¶: C++: protocols::moves::MoverStatistics::num_accepted() const –> int

print(self: pyrosetta.rosetta.protocols.moves.MoverStatistics, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, type: str) → None¶: C++: protocols::moves::MoverStatistics::print(class std::shared_ptr<class protocols::moves::MonteCarlo>, const std::string &) –> void

class pyrosetta.rosetta.protocols.moves.MoverStatus¶

Bases: pybind11_object

return status for movers - mover was successful, failed but can be retried, etc; used mostly by job dist.

Documention for individual codes from SML, and reflects the original intent behind them (more than current usage)

Members:

MS_SUCCESS

FAIL_RETRY

FAIL_DO_NOT_RETRY

FAIL_BAD_INPUT

FAIL

MS_FAIL_RETRY

MS_FAIL_DO_NOT_RETRY

MS_FAIL_BAD_INPUT

MS_FAIL

FAIL = <MoverStatus.FAIL: 4>¶

FAIL_BAD_INPUT = <MoverStatus.FAIL_BAD_INPUT: 3>¶

FAIL_DO_NOT_RETRY = <MoverStatus.FAIL_DO_NOT_RETRY: 2>¶

FAIL_RETRY = <MoverStatus.FAIL_RETRY: 1>¶

MS_FAIL = <MoverStatus.FAIL: 4>¶

MS_FAIL_BAD_INPUT = <MoverStatus.FAIL_BAD_INPUT: 3>¶

MS_FAIL_DO_NOT_RETRY = <MoverStatus.FAIL_DO_NOT_RETRY: 2>¶

MS_FAIL_RETRY = <MoverStatus.FAIL_RETRY: 1>¶

MS_SUCCESS = <MoverStatus.MS_SUCCESS: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.moves.NullMover¶

Bases: MoveMapMover

apply(self: pyrosetta.rosetta.protocols.moves.NullMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::NullMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.NullMover, : pyrosetta.rosetta.protocols.moves.NullMover) → pyrosetta.rosetta.protocols.moves.NullMover¶: C++: protocols::moves::NullMover::operator=(const class protocols::moves::NullMover &) –> class protocols::moves::NullMover &

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.NullMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::NullMover::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.NullMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::NullMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.NullMover) → str¶: C++: protocols::moves::NullMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

movemap(self: pyrosetta.rosetta.protocols.moves.NullMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.MoveMap¶: C++: protocols::moves::NullMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_movemap(self: pyrosetta.rosetta.protocols.moves.NullMover, : pyrosetta.rosetta.core.kinematics.MoveMap) → None¶: C++: protocols::moves::NullMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.NullMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::NullMover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.PDBDumpMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.moves.PDBDumpMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::PDBDumpMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.PDBDumpMover, : pyrosetta.rosetta.protocols.moves.PDBDumpMover) → pyrosetta.rosetta.protocols.moves.PDBDumpMover¶: C++: protocols::moves::PDBDumpMover::operator=(const class protocols::moves::PDBDumpMover &) –> class protocols::moves::PDBDumpMover &

clear(self: pyrosetta.rosetta.protocols.moves.PDBDumpMover) → None¶: C++: protocols::moves::PDBDumpMover::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.PDBDumpMover) → str¶: C++: protocols::moves::PDBDumpMover::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

name(self: pyrosetta.rosetta.protocols.moves.PDBDumpMover, name_in: str) → None¶: C++: protocols::moves::PDBDumpMover::name(std::string) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.PoseCondition¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.moves.PoseCondition, : pyrosetta.rosetta.protocols.moves.PoseCondition) → pyrosetta.rosetta.protocols.moves.PoseCondition¶: C++: protocols::moves::PoseCondition::operator=(const class protocols::moves::PoseCondition &) –> class protocols::moves::PoseCondition &

class pyrosetta.rosetta.protocols.moves.ProfilerMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.moves.ProfilerMover, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::ProfilerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.ProfilerMover, : pyrosetta.rosetta.protocols.moves.ProfilerMover) → pyrosetta.rosetta.protocols.moves.ProfilerMover¶: C++: protocols::moves::ProfilerMover::operator=(const class protocols::moves::ProfilerMover &) –> class protocols::moves::ProfilerMover &

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.moves.ProfilerMover) → str¶: C++: protocols::moves::ProfilerMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static 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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.PyMOLMover¶

Bases: Mover

Special Mover designed to send Pose information into PyMOL instance running

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::moves::PyMOLMover::apply(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Actually our mover does not change the Pose object, so we have additional const version…

C++: protocols::moves::PyMOLMover::apply(const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.protocols.moves.PyMOLMover) → pyrosetta.rosetta.protocols.moves.PyMOLMover¶: C++: protocols::moves::PyMOLMover::operator=(const class protocols::moves::PyMOLMover &) –> class protocols::moves::PyMOLMover &

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.PyMOLMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::moves::PyMOLMover::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>

energy_type(*args, **kwargs)¶

Overloaded function.

energy_type(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) -> pyrosetta.rosetta.core.scoring.ScoreType

C++: protocols::moves::PyMOLMover::energy_type() –> enum core::scoring::ScoreType

energy_type(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, t: pyrosetta.rosetta.core.scoring.ScoreType) -> None

C++: protocols::moves::PyMOLMover::energy_type(enum core::scoring::ScoreType) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::moves::PyMOLMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_PyMOL_model_name(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, pose: pyrosetta.rosetta.core.pose.Pose) → str¶: C++: protocols::moves::PyMOLMover::get_PyMOL_model_name(const class core::pose::Pose &) const –> std::string

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_link(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) → pyrosetta.rosetta.protocols.moves.UDPSocketClient¶: C++: protocols::moves::PyMOLMover::get_link() const –> const class protocols::moves::UDPSocketClient &

get_name(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) → str¶: C++: protocols::moves::PyMOLMover::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 > > &

keep_history(*args, **kwargs)¶

Overloaded function.

keep_history(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, kh: bool) -> None

Set the keep history flag. If set to True - PyMOL will keep track of all frames that: was sent.

C++: protocols::moves::PyMOLMover::keep_history(bool) –> void

keep_history(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) -> bool

Return current keep_history flag.

C++: protocols::moves::PyMOLMover::keep_history() –> bool

label_energy(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, input_pose: pyrosetta.rosetta.core.pose.Pose, energy_type: str) → None¶

Xiyao’s Code

C++: protocols::moves::PyMOLMover::label_energy(const class core::pose::Pose &, std::string) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::moves::PyMOLMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parses tag for rosetta scripts

C++: protocols::moves::PyMOLMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

print(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, message: str) → None¶

Send message for PyMOL to print

C++: protocols::moves::PyMOLMover::print(const std::string &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::PyMOLMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

pymol_name(*args, **kwargs)¶

Overloaded function.

pymol_name(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) -> str

Specify PyMOL model name

C++: protocols::moves::PyMOLMover::pymol_name() –> std::string

pymol_name(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, new_pymol_name: str) -> None

C++: protocols::moves::PyMOLMover::pymol_name(std::string) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

send_RAW_Energies(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose, energyType: str, energies: pyrosetta.rosetta.utility.vector1_int) → None¶

Send RAW energy array for coloring by PyMOL already implemented

C++: protocols::moves::PyMOLMover::send_RAW_Energies(const class core::pose::Pose &, std::string, const class utility::vector1<int, class std::allocator<int> > &) –> void

send_any(*args, **kwargs)¶

Overloaded function.

send_any(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, ptype: str, pose: pyrosetta.rosetta.core.pose.Pose, data: pyrosetta.rosetta.utility.vector1_std_string) -> None
send_any(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, ptype: str, pose: pyrosetta.rosetta.core.pose.Pose, data: pyrosetta.rosetta.utility.vector1_std_string, size: int) -> None

C++: protocols::moves::PyMOLMover::send_any(std::string, const class core::pose::Pose &, class utility::vector1<std::string, class std::allocator<std::string > >, unsigned long) –> void

send_colors(*args, **kwargs)¶

Overloaded function.

send_colors(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose, colors: pyrosetta.rosetta.std.map_int_int) -> None
send_colors(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose, colors: pyrosetta.rosetta.std.map_int_int, default_color: pyrosetta.rosetta.protocols.moves.X11Colors) -> None

Tell PyMOL to color protein with supplied custom colors

C++: protocols::moves::PyMOLMover::send_colors(const class core::pose::Pose &, const class std::map<int, int, struct std::less<int>, class std::allocator<struct std::pair<const int, int> > > &, enum protocols::moves::X11Colors) –> void

send_energy(*args, **kwargs)¶

Overloaded function.

send_energy(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose) -> None
send_energy(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose, stype: pyrosetta.rosetta.core.scoring.ScoreType) -> None

Send specified energy to PyMOL.

C++: protocols::moves::PyMOLMover::send_energy(const class core::pose::Pose &, enum core::scoring::ScoreType) –> void

send_energy(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose, stype: str) -> None

Send specified energy to PyMOL.

C++: protocols::moves::PyMOLMover::send_energy(const class core::pose::Pose &, const std::string &) –> void

send_foldtree(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, pose: pyrosetta.rosetta.core.pose.Pose, foldtree: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: protocols::moves::PyMOLMover::send_foldtree(const class core::pose::Pose &, const class core::kinematics::FoldTree &) –> void

send_hbonds(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::PyMOLMover::send_hbonds(const class core::pose::Pose &) –> void

send_membrane_planes(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, : pyrosetta.rosetta.core.pose.Pose) → None¶

Send Membrane Planes to PyMOL

If pose is a membrane pose pymol viewer will build CGO planes from points specified

C++: protocols::moves::PyMOLMover::send_membrane_planes(const class core::pose::Pose &) –> void

send_movemap(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, pose: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶: C++: protocols::moves::PyMOLMover::send_movemap(const class core::pose::Pose &, const class core::kinematics::MoveMap &) –> void

send_polars(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::PyMOLMover::send_polars(const class core::pose::Pose &) –> void

send_ss(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, pose: pyrosetta.rosetta.core.pose.Pose, ss: str) → None¶: C++: protocols::moves::PyMOLMover::send_ss(class core::pose::Pose &, std::string) –> void

set_PyMOL_model_name(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, name: str) → None¶

Set the pymol model name

C++: protocols::moves::PyMOLMover::set_PyMOL_model_name(std::string) –> 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_link(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, link: pyrosetta.rosetta.protocols.moves.UDPSocketClient) → None¶: C++: protocols::moves::PyMOLMover::set_link(const class protocols::moves::UDPSocketClient &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) -> None
show(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::moves::PyMOLMover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_energy(*args, **kwargs)¶

Overloaded function.

update_energy(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) -> bool

Flag that specify if PyMOL mover should send current Pose energy on every apply. If name set to empty string (default) then name derived from pdb_info will be used

C++: protocols::moves::PyMOLMover::update_energy() –> bool

update_energy(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, f: bool) -> None

C++: protocols::moves::PyMOLMover::update_energy(bool) –> void

update_interval(*args, **kwargs)¶

Overloaded function.

update_interval(self: pyrosetta.rosetta.protocols.moves.PyMOLMover, t: float) -> None

Set current minimum update interval ‘t’ in seconds. Mover will not send anyinformation to: PyMOL before atleast ‘t’ secons has passes since last packet was sent. default value is 0, - no packets are skipped.

C++: protocols::moves::PyMOLMover::update_interval(double) –> void

update_interval(self: pyrosetta.rosetta.protocols.moves.PyMOLMover) -> float

Return current update interval.

C++: protocols::moves::PyMOLMover::update_interval() –> double

class pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator, : pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator) → pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator¶: C++: protocols::moves::PyMOLMoverCreator::operator=(const class protocols::moves::PyMOLMoverCreator &) –> class protocols::moves::PyMOLMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::PyMOLMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator) → str¶: C++: protocols::moves::PyMOLMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::PyMOLMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.moves.PyMOLObserver¶

Bases: CacheableObserver

Special Observer which apply PyMOLMover if Pose is changed

class ObserverType¶

Bases: pybind11_object

Members:

no_observer

general_observer

energy_observer

conformation_observer

conformation_observer = <ObserverType.conformation_observer: 4>¶

energy_observer = <ObserverType.energy_observer: 2>¶

general_observer = <ObserverType.general_observer: 1>¶

property name¶

no_observer = <ObserverType.no_observer: 0>¶

property value¶

add_type(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, setting: pyrosetta.rosetta.protocols.moves.PyMOLObserver.ObserverType) → None¶: C++: protocols::moves::PyMOLObserver::add_type(enum protocols::moves::PyMOLObserver::ObserverType) –> void

assign(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, rval: pyrosetta.rosetta.protocols.moves.PyMOLObserver) → pyrosetta.rosetta.protocols.moves.PyMOLObserver¶: C++: protocols::moves::PyMOLObserver::operator=(const class protocols::moves::PyMOLObserver &) –> class protocols::moves::PyMOLObserver &

attach(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, p: pyrosetta.rosetta.core.pose.Pose) → None¶

Attach observer to the pose object

C++: protocols::moves::PyMOLObserver::attach(class core::pose::Pose &) –> void

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

attach to Pose/Conformation: Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶: C++: protocols::moves::PyMOLObserver::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

conformationEvent(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, ev: pyrosetta.rosetta.core.pose.signals.ConformationEvent) → None¶: C++: protocols::moves::PyMOLObserver::conformationEvent(const struct core::pose::signals::ConformationEvent &) –> void

conformation_observer = <ObserverType.conformation_observer: 4>¶

create(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶: C++: protocols::moves::PyMOLObserver::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

detach(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, p: pyrosetta.rosetta.core.pose.Pose) → None¶

Detach observer from the pose object

C++: protocols::moves::PyMOLObserver::detach(class core::pose::Pose &) –> void

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → None¶

detach from Pose/Conformation

Derived classes do not overload this method – see
detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

energyEvent(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, ev: pyrosetta.rosetta.core.pose.signals.EnergyEvent) → None¶: C++: protocols::moves::PyMOLObserver::energyEvent(const struct core::pose::signals::EnergyEvent &) –> void

energy_observer = <ObserverType.energy_observer: 2>¶

generalEvent(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, ev: pyrosetta.rosetta.core.pose.signals.GeneralEvent) → None¶: C++: protocols::moves::PyMOLObserver::generalEvent(const struct core::pose::signals::GeneralEvent &) –> void

general_observer = <ObserverType.general_observer: 1>¶

get_type(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver) → pyrosetta.rosetta.protocols.moves.PyMOLObserver.ObserverType¶: C++: protocols::moves::PyMOLObserver::get_type() const –> enum protocols::moves::PyMOLObserver::ObserverType

is_attached(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver) → bool¶: C++: protocols::moves::PyMOLObserver::is_attached() const –> bool

no_observer = <ObserverType.no_observer: 0>¶

pymol(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver) → pyrosetta.rosetta.protocols.moves.PyMOLMover¶: C++: protocols::moves::PyMOLObserver::pymol() –> class protocols::moves::PyMOLMover &

set_type(self: pyrosetta.rosetta.protocols.moves.PyMOLObserver, setting: pyrosetta.rosetta.protocols.moves.PyMOLObserver.ObserverType) → None¶: C++: protocols::moves::PyMOLObserver::set_type(enum protocols::moves::PyMOLObserver::ObserverType) –> void

class pyrosetta.rosetta.protocols.moves.RampingFunc¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.moves.RampingFunc, : pyrosetta.rosetta.protocols.moves.RampingFunc) → pyrosetta.rosetta.protocols.moves.RampingFunc¶: C++: protocols::moves::RampingFunc::operator=(const class protocols::moves::RampingFunc &) –> class protocols::moves::RampingFunc &

func(self: pyrosetta.rosetta.protocols.moves.RampingFunc, : float) → float¶

Func must be defined (and finite) over the range from 0 and 1.

C++: protocols::moves::RampingFunc::func(double) const –> double

class pyrosetta.rosetta.protocols.moves.RampingMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.moves.RampingMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::RampingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.RampingMover, : pyrosetta.rosetta.protocols.moves.RampingMover) → pyrosetta.rosetta.protocols.moves.RampingMover¶: C++: protocols::moves::RampingMover::operator=(const class protocols::moves::RampingMover &) –> class protocols::moves::RampingMover &

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.RampingMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::RampingMover::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>

end_weight(self: pyrosetta.rosetta.protocols.moves.RampingMover, end_weight_in: float) → None¶: C++: protocols::moves::RampingMover::end_weight(double) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.RampingMover) → str¶: C++: protocols::moves::RampingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::moves::RampingMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.RampingMover, tags: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::moves::RampingMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::RampingMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_func_for_weight(self: pyrosetta.rosetta.protocols.moves.RampingMover, scoretype: pyrosetta.rosetta.core.scoring.ScoreType, func: pyrosetta.rosetta.protocols.moves.RampingFunc) → None¶: C++: protocols::moves::RampingMover::set_func_for_weight(enum core::scoring::ScoreType, class std::shared_ptr<class protocols::moves::RampingFunc>) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

sfxn(self: pyrosetta.rosetta.protocols.moves.RampingMover, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::moves::RampingMover::sfxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

start_weight(self: pyrosetta.rosetta.protocols.moves.RampingMover, start_weight_in: float) → None¶: C++: protocols::moves::RampingMover::start_weight(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

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.RampingMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.moves.RampingMoverCreator, : pyrosetta.rosetta.protocols.moves.RampingMoverCreator) → pyrosetta.rosetta.protocols.moves.RampingMoverCreator¶: C++: protocols::moves::RampingMoverCreator::operator=(const class protocols::moves::RampingMoverCreator &) –> class protocols::moves::RampingMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.moves.RampingMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::RampingMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.moves.RampingMoverCreator) → str¶: C++: protocols::moves::RampingMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.RampingMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::RampingMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.moves.RandomMover¶

Bases: MoverContainer

RandomMover picks a random move and applies it

If nmoves is greater than 1, it repeats this process nmoves times for each call to apply(). This mover supports weights — the individual moves are sampled with frequency proportional to their weight given with add_mover( mover, weight );

add_mover(*args, **kwargs)¶

Overloaded function.

add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover) -> None
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover, weight_in: float) -> None

Adds a mover to the end of this container

C++: protocols::moves::MoverContainer::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void

apply(self: pyrosetta.rosetta.protocols.moves.RandomMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::RandomMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.RandomMover, : pyrosetta.rosetta.protocols.moves.RandomMover) → pyrosetta.rosetta.protocols.moves.RandomMover¶: C++: protocols::moves::RandomMover::operator=(const class protocols::moves::RandomMover &) –> class protocols::moves::RandomMover &

clear(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → None¶: C++: protocols::moves::MoverContainer::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.RandomMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::RandomMover::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.RandomMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::RandomMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

front(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::MoverContainer::front() –> 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_index_of_last_mover_used(self: pyrosetta.rosetta.protocols.moves.RandomMover) → int¶

Get the index of the last Mover used by the RandomMover (0 means RandomMover has not been applied yet)

C++: protocols::moves::RandomMover::get_index_of_last_mover_used() –> unsigned long

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_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, index: int) → str¶: C++: protocols::moves::MoverContainer::get_mover(unsigned long) const –> std::string

get_name(self: pyrosetta.rosetta.protocols.moves.RandomMover) → str¶: C++: protocols::moves::RandomMover::get_name() const –> std::string

get_name_individual_mover(self: pyrosetta.rosetta.protocols.moves.RandomMover, index: int) → str¶: C++: protocols::moves::RandomMover::get_name_individual_mover(unsigned long) –> 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.RandomMover) → float¶: C++: protocols::moves::RandomMover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::moves::RandomMover::mover_name() –> std::string

movers(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::MoverContainer::movers() const –> const class utility::vector0<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nr_moves(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::nr_moves() –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.RandomMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::moves::RandomMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.MoverContainer, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::moves::MoverContainer::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::RandomMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.MoverContainer, new_tag: str) → None¶: C++: protocols::moves::MoverContainer::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sets the input Pose for both the container: and the contained movers, for rmsd

C++: protocols::moves::MoverContainer::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoverContainer::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_repeats(self: pyrosetta.rosetta.protocols.moves.RandomMover, repeats: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Set the repeats for all the movers. Should be the same order that the movers have been added.: Allows probabilistic repeats

C++: protocols::moves::RandomMover::set_repeats(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

size(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::size() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

weights(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_double¶: C++: protocols::moves::MoverContainer::weights() const –> const class utility::vector0<double, class std::allocator<double> > &

class pyrosetta.rosetta.protocols.moves.RandomMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.moves.RandomMoverCreator, : pyrosetta.rosetta.protocols.moves.RandomMoverCreator) → pyrosetta.rosetta.protocols.moves.RandomMoverCreator¶: C++: protocols::moves::RandomMoverCreator::operator=(const class protocols::moves::RandomMoverCreator &) –> class protocols::moves::RandomMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.moves.RandomMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::RandomMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.moves.RandomMoverCreator) → str¶: C++: protocols::moves::RandomMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.RandomMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::RandomMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.moves.RepeatMover¶

Bases: Mover

A Mover that repeats an input Mover a user-specified number of times

Common Methods:: RepeatMover.apply

apply(self: pyrosetta.rosetta.protocols.moves.RepeatMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Repeats the input Mover a specified number of times

C++: protocols::moves::RepeatMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.RepeatMover, : pyrosetta.rosetta.protocols.moves.RepeatMover) → pyrosetta.rosetta.protocols.moves.RepeatMover¶: C++: protocols::moves::RepeatMover::operator=(const class protocols::moves::RepeatMover &) –> class protocols::moves::RepeatMover &

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.RepeatMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::RepeatMover::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.RepeatMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::RepeatMover::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_mover(self: pyrosetta.rosetta.protocols.moves.RepeatMover) → str¶: C++: protocols::moves::RepeatMover::get_mover() const –> std::string

get_name(self: pyrosetta.rosetta.protocols.moves.RepeatMover) → str¶: C++: protocols::moves::RepeatMover::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_nmoves(self: pyrosetta.rosetta.protocols.moves.RepeatMover) → int¶: C++: protocols::moves::RepeatMover::get_nmoves() const –> unsigned long

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static 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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC¶

Bases: MonteCarlo

boltzmann(*args, **kwargs)¶

Overloaded function.

boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float, check_lowest_score: bool) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, score: float, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float, check_lowest_score: bool) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose, score: float, move_type: str, proposal_density_ratio: float, inner_score_temperature_delta: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float) -> bool
boltzmann(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, pose: pyrosetta.rosetta.core.pose.Pose, move_type: str, proposal_density_ratio: float, inner_score_delta_over_temperature: float) -> bool

C++: protocols::moves::ReplicaExchangeMC::boltzmann(class core::pose::Pose &, const std::string &, const double, const double) –> bool

build_temperature_list(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC, elist: float) → None¶: C++: protocols::moves::ReplicaExchangeMC::build_temperature_list(const double *) –> void

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.moves.MonteCarlo) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶: C++: protocols::moves::MonteCarlo::clone() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

eval_lowest_score_pose(*args, **kwargs)¶

Overloaded function.

eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool, update_stats: bool) -> bool
eval_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score_pose: bool, update_stats: bool, move_type: str) -> bool

Compares score of <pose> to the lowest score found.

If lower, sets the current lowest score pose and lowest score. Use internal pose energies if score_pose is false. Used to evaluate lowest score without boltzmann. Does not change pose structure.

Does not update simulation statistics or last accepts by default.

example(s):: mc.eval_lowest_score_pose( pose )
See also:: MonteCarlo MonteCarlo.lowest_score MonteCarlo.lowest_score_pose MonteCarlo.recover_low

C++: protocols::moves::MonteCarlo::eval_lowest_score_pose(class core::pose::Pose &, bool, bool, const std::string &) –> bool

get_update_boinc(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → bool¶: C++: protocols::moves::MonteCarlo::get_update_boinc() const –> bool

heat_after_cycles(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) → int¶

no brief for now

C++: protocols::moves::MonteCarlo::heat_after_cycles() const –> unsigned long

init(self: pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC) → None¶: C++: protocols::moves::ReplicaExchangeMC::init() –> void

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(*args, **kwargs)¶

Overloaded function.

reset(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, 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::moves::MonteCarlo::reset(const class core::pose::Pose &) –> void

reset(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None

Sets lowest score pose and last accepted pose to

the score of <pose>

(does not reset counters)

example(s):: mc.reset(pose, score)
See also:: MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_scored_pose

C++: protocols::moves::MonteCarlo::reset(const class core::pose::Pose &, const double) –> 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(*args, **kwargs)¶

Overloaded function.

score_function(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <scorefxn> , re-scores

last accepted pose and lowest score pose

example(s):: mc.score_function( scorefxn )
See also:: MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function

C++: protocols::moves::MonteCarlo::score_function(const class core::scoring::ScoreFunction &) –> void

score_function(self: pyrosetta.rosetta.protocols.moves.MonteCarlo) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the MonteCarlo ScoreFunction

example(s):
mc.score_function() mc.score_function()( pose )

See also:
MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function

C++: protocols::moves::MonteCarlo::score_function() const –> const class core::scoring::ScoreFunction &

set_autotemp(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: bool, quench_temp: float) → None¶

Sets autotemp to quench_temp: example(s): See also:

MonteCarlo MonteCarlo.autotemp MonteCarlo.show_state

C++: protocols::moves::MonteCarlo::set_autotemp(const bool, const double) –> void

set_heat_after_cycles(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, setting: int) → None¶

no brief for now

C++: protocols::moves::MonteCarlo::set_heat_after_cycles(unsigned long) –> void

set_last_accepted(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) → None¶: C++: protocols::moves::MonteCarlo::set_last_accepted(double) –> void

set_last_accepted_pose(*args, **kwargs)¶

Overloaded function.

set_last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Sets the last accepted pose to the score of <pose>

(does not reset counters)

C++: protocols::moves::MonteCarlo::set_last_accepted_pose(const class core::pose::Pose &) –> void

set_last_accepted_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None

Sets the last accepted pose and last accepted score

(does not reset counters)

C++: protocols::moves::MonteCarlo::set_last_accepted_pose(const class core::pose::Pose &, double) –> void

set_last_score(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) → None¶

Set the last score.

C++: protocols::moves::MonteCarlo::set_last_score(double) –> void

set_lowest(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, score: float) → None¶: C++: protocols::moves::MonteCarlo::set_lowest(double) –> void

set_lowest_score_pose(*args, **kwargs)¶

Overloaded function.

set_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::moves::MonteCarlo::set_lowest_score_pose(const class core::pose::Pose &) –> void

set_lowest_score_pose(self: pyrosetta.rosetta.protocols.moves.MonteCarlo, pose: pyrosetta.rosetta.core.pose.Pose, score: float) -> None

C++: protocols::moves::MonteCarlo::set_lowest_score_pose(const class core::pose::Pose &, double) –> void

set_temperature(self: pyrosetta.rosetta.protocols.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_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.moves.ResId¶

Bases: pybind11_object

/ Override the get and set methods in containers of ResId objects (see CompoundStatementFilter and DockDesignMover for examples)

assign(self: pyrosetta.rosetta.protocols.moves.ResId, : pyrosetta.rosetta.protocols.moves.ResId) → pyrosetta.rosetta.protocols.moves.ResId¶: C++: protocols::moves::ResId::operator=(const class protocols::moves::ResId &) –> class protocols::moves::ResId &

get_resid(self: pyrosetta.rosetta.protocols.moves.ResId, : pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::moves::ResId::get_resid(const class core::pose::Pose &) const –> unsigned long

modifiable(*args, **kwargs)¶

Overloaded function.

modifiable(self: pyrosetta.rosetta.protocols.moves.ResId) -> bool

should another method be able to modify resid_. This is used by modify_ResId_based_object as a test

C++: protocols::moves::ResId::modifiable() const –> bool

modifiable(self: pyrosetta.rosetta.protocols.moves.ResId, u: bool) -> None

C++: protocols::moves::ResId::modifiable(const bool) –> void

set_resid(*args, **kwargs)¶

Overloaded function.

set_resid(self: pyrosetta.rosetta.protocols.moves.ResId, r: int) -> None

C++: protocols::moves::ResId::set_resid(const unsigned long) –> void

set_resid(self: pyrosetta.rosetta.protocols.moves.ResId, r: pyrosetta.rosetta.core.pose.ResidueIndexDescription) -> None

C++: protocols::moves::ResId::set_resid(class std::shared_ptr<const class core::pose::ResidueIndexDescription>) –> void

class pyrosetta.rosetta.protocols.moves.SequenceMover¶

Bases: MoverContainer

A Mover that iterates through a vector of Movers, applying each one sequentially

Common Methods:: SequenceMover.add_mover SequenceMover.apply

add_mover(*args, **kwargs)¶

Overloaded function.

add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover) -> None
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover, weight_in: float) -> None

Adds a mover to the end of this container

C++: protocols::moves::MoverContainer::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void

apply(self: pyrosetta.rosetta.protocols.moves.SequenceMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Applies a series of movers sequentially on a Pose

example(s):
seqmover.apply(pose)

See also:
MinMover RepeatMover SequenceMover TrialMover

C++: protocols::moves::SequenceMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.SequenceMover, : pyrosetta.rosetta.protocols.moves.SequenceMover) → pyrosetta.rosetta.protocols.moves.SequenceMover¶: C++: protocols::moves::SequenceMover::operator=(const class protocols::moves::SequenceMover &) –> class protocols::moves::SequenceMover &

clear(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → None¶: C++: protocols::moves::MoverContainer::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.SequenceMover) → pyrosetta.rosetta.protocols.moves.Mover¶

deep copy of all contained movers.

C++: protocols::moves::SequenceMover::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.SequenceMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::SequenceMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

front(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::MoverContainer::front() –> 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_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, index: int) → str¶: C++: protocols::moves::MoverContainer::get_mover(unsigned long) const –> std::string

get_name(self: pyrosetta.rosetta.protocols.moves.SequenceMover) → str¶: C++: protocols::moves::SequenceMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::moves::SequenceMover::mover_name() –> std::string

movers(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::MoverContainer::movers() const –> const class utility::vector0<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nr_moves(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::nr_moves() –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.SequenceMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::moves::SequenceMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.MoverContainer, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::moves::MoverContainer::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::SequenceMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.MoverContainer, new_tag: str) → None¶: C++: protocols::moves::MoverContainer::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sets the input Pose for both the container: and the contained movers, for rmsd

C++: protocols::moves::MoverContainer::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoverContainer::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

size(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::size() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

use_mover_status(*args, **kwargs)¶

Overloaded function.

use_mover_status(self: pyrosetta.rosetta.protocols.moves.SequenceMover, flag: bool) -> None

MoverStatus of the mover will be evaluated after each mover

C++: protocols::moves::SequenceMover::use_mover_status(const bool) –> void

use_mover_status(self: pyrosetta.rosetta.protocols.moves.SequenceMover) -> bool

C++: protocols::moves::SequenceMover::use_mover_status() –> bool

weights(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_double¶: C++: protocols::moves::MoverContainer::weights() const –> const class utility::vector0<double, class std::allocator<double> > &

class pyrosetta.rosetta.protocols.moves.SequenceMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.moves.SequenceMoverCreator, : pyrosetta.rosetta.protocols.moves.SequenceMoverCreator) → pyrosetta.rosetta.protocols.moves.SequenceMoverCreator¶: C++: protocols::moves::SequenceMoverCreator::operator=(const class protocols::moves::SequenceMoverCreator &) –> class protocols::moves::SequenceMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.moves.SequenceMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::SequenceMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.moves.SequenceMoverCreator) → str¶: C++: protocols::moves::SequenceMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.SequenceMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::SequenceMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.moves.SimulatedTempering¶

Bases: pybind11_object

check_boltzmann(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

Applies the Metropolis Criterion on pose. But does not roll back pose if reject!

C++: protocols::moves::SimulatedTempering::check_boltzmann(class core::pose::Pose &) –> bool

force_next_move_reject(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering) → None¶

Sets the next boltzmann() call to automatically reject

C++: protocols::moves::SimulatedTempering::force_next_move_reject() –> void

score_function(*args, **kwargs)¶

Overloaded function.

score_function(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <scorefxn>

C++: protocols::moves::SimulatedTempering::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

score_function(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the MonteCarlo ScoreFunction

C++: protocols::moves::SimulatedTempering::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_rep_cutoff(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering, setting: float) → None¶

Sets cutoff of repusion filter, use 0 to turn it off

C++: protocols::moves::SimulatedTempering::set_rep_cutoff(const double) –> void

t_jump(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering) → bool¶

Attempt temperature jumping.

C++: protocols::moves::SimulatedTempering::t_jump() –> bool

temp_id(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering) → int¶

Get the id of current temperature

C++: protocols::moves::SimulatedTempering::temp_id() const –> unsigned long

temperature(self: pyrosetta.rosetta.protocols.moves.SimulatedTempering) → float¶

Get the current temperature

C++: protocols::moves::SimulatedTempering::temperature() const –> double

class pyrosetta.rosetta.protocols.moves.StatsType¶

Bases: pybind11_object

A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object.

:

Each derived class should define its own apply() statement the apply (mc) which requires a monte carlo object and only keeps the move if the monte carlo test allows it

Monica Berrondo

Members:

all_stats

accept_reject

no_stats

accept_reject = <StatsType.accept_reject: 2>¶

all_stats = <StatsType.all_stats: 1>¶

property name¶

no_stats = <StatsType.no_stats: 3>¶

property value¶

class pyrosetta.rosetta.protocols.moves.StructureRestrictor¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.moves.StructureRestrictor, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::StructureRestrictor::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.StructureRestrictor, : pyrosetta.rosetta.protocols.moves.StructureRestrictor) → pyrosetta.rosetta.protocols.moves.StructureRestrictor¶: C++: protocols::moves::StructureRestrictor::operator=(const class protocols::moves::StructureRestrictor &) –> class protocols::moves::StructureRestrictor &

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.StructureRestrictor) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::StructureRestrictor::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.StructureRestrictor) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::StructureRestrictor::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.StructureRestrictor) → str¶: C++: protocols::moves::StructureRestrictor::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.StructureRestrictor, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::moves::StructureRestrictor::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pose_name(self: pyrosetta.rosetta.protocols.moves.StructureRestrictor, pose: pyrosetta.rosetta.core.pose.Pose) → str¶: C++: protocols::moves::StructureRestrictor::pose_name(const class core::pose::Pose &) –> std::string

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_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

setup_relevant_chains(self: pyrosetta.rosetta.protocols.moves.StructureRestrictor, relevant_chains_fname: str, chain_map: pyrosetta.rosetta.std.map_std_string_std_string) → None¶: C++: protocols::moves::StructureRestrictor::setup_relevant_chains(const std::string &, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.SwitchMover¶

Bases: MoverContainer

SwitchMover can hold multiple movers and execute only the requested one

In terms of RosettaScripts, it allows to have a single script with N- different behaviours that can be called through the parser:script_vars (for example). And it will log in the scores which mover was used.

add_mover(*args, **kwargs)¶

Overloaded function.

add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover) -> None
add_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, mover_in: pyrosetta.rosetta.protocols.moves.Mover, weight_in: float) -> None

Adds a mover to the end of this container

C++: protocols::moves::MoverContainer::add_mover(class std::shared_ptr<class protocols::moves::Mover>, double) –> void

apply(self: pyrosetta.rosetta.protocols.moves.SwitchMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::SwitchMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.SwitchMover, : pyrosetta.rosetta.protocols.moves.SwitchMover) → pyrosetta.rosetta.protocols.moves.SwitchMover¶: C++: protocols::moves::SwitchMover::operator=(const class protocols::moves::SwitchMover &) –> class protocols::moves::SwitchMover &

clear(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → None¶: C++: protocols::moves::MoverContainer::clear() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.SwitchMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::SwitchMover::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.SwitchMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::SwitchMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

front(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::MoverContainer::front() –> 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_mover(self: pyrosetta.rosetta.protocols.moves.MoverContainer, index: int) → str¶: C++: protocols::moves::MoverContainer::get_mover(unsigned long) const –> std::string

get_name(self: pyrosetta.rosetta.protocols.moves.SwitchMover) → str¶: C++: protocols::moves::SwitchMover::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_selected_mover(self: pyrosetta.rosetta.protocols.moves.SwitchMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::SwitchMover::get_selected_mover() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::moves::SwitchMover::mover_name() –> std::string

movers(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::MoverContainer::movers() const –> const class utility::vector0<class std::shared_ptr<class protocols::moves::Mover>, class std::allocator<class std::shared_ptr<class protocols::moves::Mover> > > &

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nr_moves(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::nr_moves() –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.SwitchMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::moves::SwitchMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.MoverContainer, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: protocols::moves::MoverContainer::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::SwitchMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

selected(*args, **kwargs)¶

Overloaded function.

selected(self: pyrosetta.rosetta.protocols.moves.SwitchMover) -> str

C++: protocols::moves::SwitchMover::selected() const –> std::string

selected(self: pyrosetta.rosetta.protocols.moves.SwitchMover, sele: str) -> None

C++: protocols::moves::SwitchMover::selected(std::string) –> 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.MoverContainer, new_tag: str) → None¶: C++: protocols::moves::MoverContainer::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sets the input Pose for both the container: and the contained movers, for rmsd

C++: protocols::moves::MoverContainer::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.MoverContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::MoverContainer::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

size(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → int¶: C++: protocols::moves::MoverContainer::size() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

weights(self: pyrosetta.rosetta.protocols.moves.MoverContainer) → pyrosetta.rosetta.utility.vector0_double¶: C++: protocols::moves::MoverContainer::weights() const –> const class utility::vector0<double, class std::allocator<double> > &

class pyrosetta.rosetta.protocols.moves.SwitchMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.moves.SwitchMoverCreator, : pyrosetta.rosetta.protocols.moves.SwitchMoverCreator) → pyrosetta.rosetta.protocols.moves.SwitchMoverCreator¶: C++: protocols::moves::SwitchMoverCreator::operator=(const class protocols::moves::SwitchMoverCreator &) –> class protocols::moves::SwitchMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.moves.SwitchMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::SwitchMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.moves.SwitchMoverCreator) → str¶: C++: protocols::moves::SwitchMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.SwitchMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::moves::SwitchMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.moves.TrialCounter¶

Bases: pybind11_object

accepted(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : str) → int¶: C++: protocols::moves::TrialCounter::accepted(const std::string &) const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : pyrosetta.rosetta.protocols.moves.TrialCounter) → pyrosetta.rosetta.protocols.moves.TrialCounter¶: C++: protocols::moves::TrialCounter::operator=(const class protocols::moves::TrialCounter &) –> class protocols::moves::TrialCounter &

count_accepted(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : str) → None¶: C++: protocols::moves::TrialCounter::count_accepted(const std::string &) –> void

count_energy_drop(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : str, : float) → None¶: C++: protocols::moves::TrialCounter::count_energy_drop(const std::string &, double) –> void

count_trial(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : str) → None¶: C++: protocols::moves::TrialCounter::count_trial(const std::string &) –> void

energy_drop(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : str) → float¶: C++: protocols::moves::TrialCounter::energy_drop(const std::string &) const –> double

reset(self: pyrosetta.rosetta.protocols.moves.TrialCounter) → None¶: C++: protocols::moves::TrialCounter::reset() –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.TrialCounter) -> None

C++: protocols::moves::TrialCounter::show() const –> void

show(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : pyrosetta.rosetta.std.ostream, line_header: str) -> None
show(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : pyrosetta.rosetta.std.ostream, line_header: str, with_end_line: bool) -> None

C++: protocols::moves::TrialCounter::show(std::ostream &, std::string, bool) const –> void

tags(self: pyrosetta.rosetta.protocols.moves.TrialCounter) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::moves::TrialCounter::tags() const –> const class utility::vector1<std::string, class std::allocator<std::string > >

total_trials(self: pyrosetta.rosetta.protocols.moves.TrialCounter) → int¶: C++: protocols::moves::TrialCounter::total_trials() const –> unsigned long

trial(self: pyrosetta.rosetta.protocols.moves.TrialCounter, : str) → int¶: C++: protocols::moves::TrialCounter::trial(const std::string &) const –> unsigned long

class pyrosetta.rosetta.protocols.moves.TrialMover¶

Bases: Mover

A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object.

Common Methods:: TrialMover.apply TrialMover.set_mc

acceptance_rate(self: pyrosetta.rosetta.protocols.moves.TrialMover) → float¶: C++: protocols::moves::TrialMover::acceptance_rate() const –> double

apply(self: pyrosetta.rosetta.protocols.moves.TrialMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Performs a single trial, apply the Mover and accept or

reject the move based on the MonteCarlo acceptance criteria

example(s):: trialmover.apply(pose)
See Also:: Pose MonteCarlo MonteCarlo.boltzmann RepeatMover SequenceMover TrialMover

C++: protocols::moves::TrialMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.TrialMover, : pyrosetta.rosetta.protocols.moves.TrialMover) → pyrosetta.rosetta.protocols.moves.TrialMover¶: C++: protocols::moves::TrialMover::operator=(const class protocols::moves::TrialMover &) –> class protocols::moves::TrialMover &

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.TrialMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::TrialMover::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.TrialMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::TrialMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.moves.TrialMover) → str¶: C++: protocols::moves::TrialMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_weights(self: pyrosetta.rosetta.protocols.moves.TrialMover, start_weight: float, end_weight: float, score_type: pyrosetta.rosetta.core.scoring.ScoreType, ramp_cycles: int) → None¶: C++: protocols::moves::TrialMover::initialize_weights(const double, const double, enum core::scoring::ScoreType, const int) –> void

keep_stats_type(*args, **kwargs)¶

Overloaded function.

keep_stats_type(self: pyrosetta.rosetta.protocols.moves.TrialMover) -> pyrosetta.rosetta.protocols.moves.StatsType

C++: protocols::moves::TrialMover::keep_stats_type() const –> enum protocols::moves::StatsType

keep_stats_type(self: pyrosetta.rosetta.protocols.moves.TrialMover, setting: pyrosetta.rosetta.protocols.moves.StatsType) -> None

C++: protocols::moves::TrialMover::keep_stats_type(enum protocols::moves::StatsType) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mc(self: pyrosetta.rosetta.protocols.moves.TrialMover) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶

Returns the underlying MonteCarlo object

C++: protocols::moves::TrialMover::mc() const –> const class protocols::moves::MonteCarlo &

mover(self: pyrosetta.rosetta.protocols.moves.TrialMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Returns the underlying Mover

C++: protocols::moves::TrialMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

num_accepts(self: pyrosetta.rosetta.protocols.moves.TrialMover) → int¶

Returns the number of moves accepted by this TrialMover

C++: protocols::moves::TrialMover::num_accepts() const –> int

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.TrialMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Requires that a MonteCarlo object has already been: loaded into the basic::datacache::DataMap in a prior MONTECARLOS objects section.

C++: protocols::moves::TrialMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.TrialMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::TrialMover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_mc(self: pyrosetta.rosetta.protocols.moves.TrialMover, mc_in: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶

Sets the MonteCarlo object to <mc_in>

example(s):
trialmover.set_mc(mc)

See Also:
MonteCarlo MonteCarlo.boltzmann TrialMover

C++: protocols::moves::TrialMover::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.TrialMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::TrialMover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.UDPSocketClient¶

Bases: pybind11_object

PyMOLMover helper class. Handle low level UDP transactions stuff. This is a port of original Python version of UDP socket client written writen for PyRosetta

assign(self: pyrosetta.rosetta.protocols.moves.UDPSocketClient, : pyrosetta.rosetta.protocols.moves.UDPSocketClient) → pyrosetta.rosetta.protocols.moves.UDPSocketClient¶: C++: protocols::moves::UDPSocketClient::operator=(const class protocols::moves::UDPSocketClient &) –> class protocols::moves::UDPSocketClient &

get_address(self: pyrosetta.rosetta.protocols.moves.UDPSocketClient) → str¶: C++: protocols::moves::UDPSocketClient::get_address() const –> std::string

get_max_packet_size(self: pyrosetta.rosetta.protocols.moves.UDPSocketClient) → int¶: C++: protocols::moves::UDPSocketClient::get_max_packet_size() const –> unsigned int

get_port(self: pyrosetta.rosetta.protocols.moves.UDPSocketClient) → int¶: C++: protocols::moves::UDPSocketClient::get_port() const –> unsigned int

sendMessage(self: pyrosetta.rosetta.protocols.moves.UDPSocketClient, msg: str) → None¶: C++: protocols::moves::UDPSocketClient::sendMessage(std::string) –> void

show(self: pyrosetta.rosetta.protocols.moves.UDPSocketClient, output: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::moves::UDPSocketClient::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.moves.VectorPoseMover¶

Bases: Mover

Designates a mover that can be passed multiple poses by the VectorPoseJobDistributor Any movers deriving from this subclass can then act on all of the input poses simultaneously Only accessible through recon application.

apply(self: pyrosetta.rosetta.protocols.moves.VectorPoseMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::VectorPoseMover::apply(class core::pose::Pose &) –> void

apply_mpi(self: pyrosetta.rosetta.protocols.moves.VectorPoseMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Pure virtual method to apply this mover under MPI

C++: protocols::moves::VectorPoseMover::apply_mpi(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.VectorPoseMover, : pyrosetta.rosetta.protocols.moves.VectorPoseMover) → pyrosetta.rosetta.protocols.moves.VectorPoseMover¶: C++: protocols::moves::VectorPoseMover::operator=(const class protocols::moves::VectorPoseMover &) –> class protocols::moves::VectorPoseMover &

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.moves.VectorPoseMover) → str¶: C++: protocols::moves::VectorPoseMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static 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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_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_poses(self: pyrosetta.rosetta.protocols.moves.VectorPoseMover, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None¶

Set the vector of poses for the mover to act upon

C++: protocols::moves::VectorPoseMover::set_poses(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.WhileMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.moves.WhileMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::moves::WhileMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.WhileMover, : pyrosetta.rosetta.protocols.moves.WhileMover) → pyrosetta.rosetta.protocols.moves.WhileMover¶: C++: protocols::moves::WhileMover::operator=(const class protocols::moves::WhileMover &) –> class protocols::moves::WhileMover &

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.moves.WhileMover) → str¶: C++: protocols::moves::WhileMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static 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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.moves.X11Colors¶

Bases: pybind11_object

Members:

XC_first_color

XC_black

XC_AntiqueWhite

XC_BlanchedAlmond

XC_BlueViolet

XC_CadetBlue

XC_CornflowerBlue

XC_DarkBlue

XC_DarkCyan

XC_DarkGoldenrod

XC_DarkGray

XC_DarkGreen

XC_DarkGrey

XC_DarkKhaki

XC_DarkMagenta

XC_DarkOliveGreen

XC_DarkOrange

XC_DarkOrchid

XC_DarkRed

XC_DarkSalmon

XC_DarkSeaGreen

XC_DarkSlateBlue

XC_DarkSlateGray

XC_DarkSlateGrey

XC_DarkTurquoise

XC_DarkViolet

XC_DebianRed

XC_DeepPink

XC_DeepSkyBlue

XC_DimGray

XC_DimGrey

XC_DodgerBlue

XC_FloralWhite

XC_ForestGreen

XC_GhostWhite

XC_GreenYellow

XC_HotPink

XC_IndianRed

XC_LavenderBlush

XC_LawnGreen

XC_LemonChiffon

XC_LightBlue

XC_LightCoral

XC_LightCyan

XC_LightGoldenrod

XC_LightGoldenrodYellow

XC_LightGray

XC_LightGreen

XC_LightGrey

XC_LightPink

XC_LightSalmon

XC_LightSeaGreen

XC_LightSkyBlue

XC_LightSlateBlue

XC_LightSlateGray

XC_LightSlateGrey

XC_LightSteelBlue

XC_LightYellow

XC_LimeGreen

XC_MediumAquamarine

XC_MediumBlue

XC_MediumOrchid

XC_MediumPurple

XC_MediumSeaGreen

XC_MediumSlateBlue

XC_MediumSpringGreen

XC_MediumTurquoise

XC_MediumVioletRed

XC_MidnightBlue

XC_MintCream

XC_MistyRose

XC_NavajoWhite

XC_NavyBlue

XC_OldLace

XC_OliveDrab

XC_OrangeRed

XC_PaleGoldenrod

XC_PaleGreen

XC_PaleTurquoise

XC_PaleVioletRed

XC_PapayaWhip

XC_PeachPuff

XC_PowderBlue

XC_RosyBrown

XC_RoyalBlue

XC_SaddleBrown

XC_SandyBrown

XC_SeaGreen

XC_SkyBlue

XC_SlateBlue

XC_SlateGray

XC_SlateGrey

XC_SpringGreen

XC_SteelBlue

XC_VioletRed

XC_WhiteSmoke

XC_YellowGreen

XC_aquamarine

XC_azure

XC_beige

XC_bisque

XC_AliceBlue

XC_blue

XC_blue1

XC_blue2

XC_blue3

XC_blue4

XC_brown

XC_burlywood

XC_chartreuse

XC_chocolate

XC_coral

XC_cornsilk

XC_cyan

XC_firebrick

XC_gainsboro

XC_gold

XC_goldenrod

XC_gray

XC_gray0

XC_gray10

XC_gray100

XC_gray20

XC_gray30

XC_gray40

XC_gray50

XC_gray60

XC_gray70

XC_gray80

XC_gray90

XC_green

XC_green1

XC_green2

XC_green3

XC_green4

XC_honeydew

XC_ivory

XC_khaki

XC_lavender

XC_linen

XC_magenta

XC_maroon

XC_moccasin

XC_navy

XC_orange

XC_orchid

XC_peru

XC_pink

XC_plum

XC_purple

XC_red

XC_red1

XC_red2

XC_red3

XC_red4

XC_salmon

XC_seashell

XC_sienna

XC_snow

XC_snow1

XC_snow2

XC_snow3

XC_snow4

XC_tan

XC_thistle

XC_tomato

XC_turquoise

XC_violet

XC_wheat

XC_white

XC_yellow

XC_last_color

XC_AliceBlue = <X11Colors.XC_AliceBlue: 100>¶

XC_AntiqueWhite = <X11Colors.XC_AntiqueWhite: 1>¶

XC_BlanchedAlmond = <X11Colors.XC_BlanchedAlmond: 2>¶

XC_BlueViolet = <X11Colors.XC_BlueViolet: 3>¶

XC_CadetBlue = <X11Colors.XC_CadetBlue: 4>¶

XC_CornflowerBlue = <X11Colors.XC_CornflowerBlue: 5>¶

XC_DarkBlue = <X11Colors.XC_DarkBlue: 6>¶

XC_DarkCyan = <X11Colors.XC_DarkCyan: 7>¶

XC_DarkGoldenrod = <X11Colors.XC_DarkGoldenrod: 8>¶

XC_DarkGray = <X11Colors.XC_DarkGray: 9>¶

XC_DarkGreen = <X11Colors.XC_DarkGreen: 10>¶

XC_DarkGrey = <X11Colors.XC_DarkGrey: 11>¶

XC_DarkKhaki = <X11Colors.XC_DarkKhaki: 12>¶

XC_DarkMagenta = <X11Colors.XC_DarkMagenta: 13>¶

XC_DarkOliveGreen = <X11Colors.XC_DarkOliveGreen: 14>¶

XC_DarkOrange = <X11Colors.XC_DarkOrange: 15>¶

XC_DarkOrchid = <X11Colors.XC_DarkOrchid: 16>¶

XC_DarkRed = <X11Colors.XC_DarkRed: 17>¶

XC_DarkSalmon = <X11Colors.XC_DarkSalmon: 18>¶

XC_DarkSeaGreen = <X11Colors.XC_DarkSeaGreen: 19>¶

XC_DarkSlateBlue = <X11Colors.XC_DarkSlateBlue: 20>¶

XC_DarkSlateGray = <X11Colors.XC_DarkSlateGray: 21>¶

XC_DarkSlateGrey = <X11Colors.XC_DarkSlateGrey: 22>¶

XC_DarkTurquoise = <X11Colors.XC_DarkTurquoise: 23>¶

XC_DarkViolet = <X11Colors.XC_DarkViolet: 24>¶

XC_DebianRed = <X11Colors.XC_DebianRed: 25>¶

XC_DeepPink = <X11Colors.XC_DeepPink: 26>¶

XC_DeepSkyBlue = <X11Colors.XC_DeepSkyBlue: 27>¶

XC_DimGray = <X11Colors.XC_DimGray: 28>¶

XC_DimGrey = <X11Colors.XC_DimGrey: 29>¶

XC_DodgerBlue = <X11Colors.XC_DodgerBlue: 30>¶

XC_FloralWhite = <X11Colors.XC_FloralWhite: 31>¶

XC_ForestGreen = <X11Colors.XC_ForestGreen: 32>¶

XC_GhostWhite = <X11Colors.XC_GhostWhite: 33>¶

XC_GreenYellow = <X11Colors.XC_GreenYellow: 34>¶

XC_HotPink = <X11Colors.XC_HotPink: 35>¶

XC_IndianRed = <X11Colors.XC_IndianRed: 36>¶

XC_LavenderBlush = <X11Colors.XC_LavenderBlush: 37>¶

XC_LawnGreen = <X11Colors.XC_LawnGreen: 38>¶

XC_LemonChiffon = <X11Colors.XC_LemonChiffon: 39>¶

XC_LightBlue = <X11Colors.XC_LightBlue: 40>¶

XC_LightCoral = <X11Colors.XC_LightCoral: 41>¶

XC_LightCyan = <X11Colors.XC_LightCyan: 42>¶

XC_LightGoldenrod = <X11Colors.XC_LightGoldenrod: 43>¶

XC_LightGoldenrodYellow = <X11Colors.XC_LightGoldenrodYellow: 44>¶

XC_LightGray = <X11Colors.XC_LightGray: 45>¶

XC_LightGreen = <X11Colors.XC_LightGreen: 46>¶

XC_LightGrey = <X11Colors.XC_LightGrey: 47>¶

XC_LightPink = <X11Colors.XC_LightPink: 48>¶

XC_LightSalmon = <X11Colors.XC_LightSalmon: 49>¶

XC_LightSeaGreen = <X11Colors.XC_LightSeaGreen: 50>¶

XC_LightSkyBlue = <X11Colors.XC_LightSkyBlue: 51>¶

XC_LightSlateBlue = <X11Colors.XC_LightSlateBlue: 52>¶

XC_LightSlateGray = <X11Colors.XC_LightSlateGray: 53>¶

XC_LightSlateGrey = <X11Colors.XC_LightSlateGrey: 54>¶

XC_LightSteelBlue = <X11Colors.XC_LightSteelBlue: 55>¶

XC_LightYellow = <X11Colors.XC_LightYellow: 56>¶

XC_LimeGreen = <X11Colors.XC_LimeGreen: 57>¶

XC_MediumAquamarine = <X11Colors.XC_MediumAquamarine: 58>¶

XC_MediumBlue = <X11Colors.XC_MediumBlue: 59>¶

XC_MediumOrchid = <X11Colors.XC_MediumOrchid: 60>¶

XC_MediumPurple = <X11Colors.XC_MediumPurple: 61>¶

XC_MediumSeaGreen = <X11Colors.XC_MediumSeaGreen: 62>¶

XC_MediumSlateBlue = <X11Colors.XC_MediumSlateBlue: 63>¶

XC_MediumSpringGreen = <X11Colors.XC_MediumSpringGreen: 64>¶

XC_MediumTurquoise = <X11Colors.XC_MediumTurquoise: 65>¶

XC_MediumVioletRed = <X11Colors.XC_MediumVioletRed: 66>¶

XC_MidnightBlue = <X11Colors.XC_MidnightBlue: 67>¶

XC_MintCream = <X11Colors.XC_MintCream: 68>¶

XC_MistyRose = <X11Colors.XC_MistyRose: 69>¶

XC_NavajoWhite = <X11Colors.XC_NavajoWhite: 70>¶

XC_NavyBlue = <X11Colors.XC_NavyBlue: 71>¶

XC_OldLace = <X11Colors.XC_OldLace: 72>¶

XC_OliveDrab = <X11Colors.XC_OliveDrab: 73>¶

XC_OrangeRed = <X11Colors.XC_OrangeRed: 74>¶

XC_PaleGoldenrod = <X11Colors.XC_PaleGoldenrod: 75>¶

XC_PaleGreen = <X11Colors.XC_PaleGreen: 76>¶

XC_PaleTurquoise = <X11Colors.XC_PaleTurquoise: 77>¶

XC_PaleVioletRed = <X11Colors.XC_PaleVioletRed: 78>¶

XC_PapayaWhip = <X11Colors.XC_PapayaWhip: 79>¶

XC_PeachPuff = <X11Colors.XC_PeachPuff: 80>¶

XC_PowderBlue = <X11Colors.XC_PowderBlue: 81>¶

XC_RosyBrown = <X11Colors.XC_RosyBrown: 82>¶

XC_RoyalBlue = <X11Colors.XC_RoyalBlue: 83>¶

XC_SaddleBrown = <X11Colors.XC_SaddleBrown: 84>¶

XC_SandyBrown = <X11Colors.XC_SandyBrown: 85>¶

XC_SeaGreen = <X11Colors.XC_SeaGreen: 86>¶

XC_SkyBlue = <X11Colors.XC_SkyBlue: 87>¶

XC_SlateBlue = <X11Colors.XC_SlateBlue: 88>¶

XC_SlateGray = <X11Colors.XC_SlateGray: 89>¶

XC_SlateGrey = <X11Colors.XC_SlateGrey: 90>¶

XC_SpringGreen = <X11Colors.XC_SpringGreen: 91>¶

XC_SteelBlue = <X11Colors.XC_SteelBlue: 92>¶

XC_VioletRed = <X11Colors.XC_VioletRed: 93>¶

XC_WhiteSmoke = <X11Colors.XC_WhiteSmoke: 94>¶

XC_YellowGreen = <X11Colors.XC_YellowGreen: 95>¶

XC_aquamarine = <X11Colors.XC_aquamarine: 96>¶

XC_azure = <X11Colors.XC_azure: 97>¶

XC_beige = <X11Colors.XC_beige: 98>¶

XC_bisque = <X11Colors.XC_bisque: 99>¶

XC_black = <X11Colors.XC_first_color: 0>¶

XC_blue = <X11Colors.XC_blue: 101>¶

XC_blue1 = <X11Colors.XC_blue1: 102>¶

XC_blue2 = <X11Colors.XC_blue2: 103>¶

XC_blue3 = <X11Colors.XC_blue3: 104>¶

XC_blue4 = <X11Colors.XC_blue4: 105>¶

XC_brown = <X11Colors.XC_brown: 106>¶

XC_burlywood = <X11Colors.XC_burlywood: 107>¶

XC_chartreuse = <X11Colors.XC_chartreuse: 108>¶

XC_chocolate = <X11Colors.XC_chocolate: 109>¶

XC_coral = <X11Colors.XC_coral: 110>¶

XC_cornsilk = <X11Colors.XC_cornsilk: 111>¶

XC_cyan = <X11Colors.XC_cyan: 112>¶

XC_firebrick = <X11Colors.XC_firebrick: 113>¶

XC_first_color = <X11Colors.XC_first_color: 0>¶

XC_gainsboro = <X11Colors.XC_gainsboro: 114>¶

XC_gold = <X11Colors.XC_gold: 115>¶

XC_goldenrod = <X11Colors.XC_goldenrod: 116>¶

XC_gray = <X11Colors.XC_gray: 117>¶

XC_gray0 = <X11Colors.XC_gray0: 118>¶

XC_gray10 = <X11Colors.XC_gray10: 119>¶

XC_gray100 = <X11Colors.XC_gray100: 120>¶

XC_gray20 = <X11Colors.XC_gray20: 121>¶

XC_gray30 = <X11Colors.XC_gray30: 122>¶

XC_gray40 = <X11Colors.XC_gray40: 123>¶

XC_gray50 = <X11Colors.XC_gray50: 124>¶

XC_gray60 = <X11Colors.XC_gray60: 125>¶

XC_gray70 = <X11Colors.XC_gray70: 126>¶

XC_gray80 = <X11Colors.XC_gray80: 127>¶

XC_gray90 = <X11Colors.XC_gray90: 128>¶

XC_green = <X11Colors.XC_green: 129>¶

XC_green1 = <X11Colors.XC_green1: 130>¶

XC_green2 = <X11Colors.XC_green2: 131>¶

XC_green3 = <X11Colors.XC_green3: 132>¶

XC_green4 = <X11Colors.XC_green4: 133>¶

XC_honeydew = <X11Colors.XC_honeydew: 134>¶

XC_ivory = <X11Colors.XC_ivory: 135>¶

XC_khaki = <X11Colors.XC_khaki: 136>¶

XC_last_color = <X11Colors.XC_last_color: 170>¶

XC_lavender = <X11Colors.XC_lavender: 137>¶

XC_linen = <X11Colors.XC_linen: 138>¶

XC_magenta = <X11Colors.XC_magenta: 139>¶

XC_maroon = <X11Colors.XC_maroon: 140>¶

XC_moccasin = <X11Colors.XC_moccasin: 141>¶

XC_navy = <X11Colors.XC_navy: 142>¶

XC_orange = <X11Colors.XC_orange: 143>¶

XC_orchid = <X11Colors.XC_orchid: 144>¶

XC_peru = <X11Colors.XC_peru: 145>¶

XC_pink = <X11Colors.XC_pink: 146>¶

XC_plum = <X11Colors.XC_plum: 147>¶

XC_purple = <X11Colors.XC_purple: 148>¶

XC_red = <X11Colors.XC_red: 149>¶

XC_red1 = <X11Colors.XC_red1: 150>¶

XC_red2 = <X11Colors.XC_red2: 151>¶

XC_red3 = <X11Colors.XC_red3: 152>¶

XC_red4 = <X11Colors.XC_red4: 153>¶

XC_salmon = <X11Colors.XC_salmon: 154>¶

XC_seashell = <X11Colors.XC_seashell: 155>¶

XC_sienna = <X11Colors.XC_sienna: 156>¶

XC_snow = <X11Colors.XC_snow: 157>¶

XC_snow1 = <X11Colors.XC_snow1: 158>¶

XC_snow2 = <X11Colors.XC_snow2: 159>¶

XC_snow3 = <X11Colors.XC_snow3: 160>¶

XC_snow4 = <X11Colors.XC_snow4: 161>¶

XC_tan = <X11Colors.XC_tan: 162>¶

XC_thistle = <X11Colors.XC_thistle: 163>¶

XC_tomato = <X11Colors.XC_tomato: 164>¶

XC_turquoise = <X11Colors.XC_turquoise: 165>¶

XC_violet = <X11Colors.XC_violet: 166>¶

XC_wheat = <X11Colors.XC_wheat: 167>¶

XC_white = <X11Colors.XC_white: 168>¶

XC_yellow = <X11Colors.XC_yellow: 169>¶

property name¶

property value¶

pyrosetta.rosetta.protocols.moves.complex_type_name_for_mover(mover_name: str) → str¶: C++: protocols::moves::complex_type_name_for_mover(const std::string &) –> std::string

pyrosetta.rosetta.protocols.moves.find_filter_or_die(filter_name: str, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.filters.Filter¶

Searches <filters> for the named filter, returning it if it exists,: otherwise halts execution with an error message. Now parses logic to create a CompoundFilter if string is more than one word.

C++: protocols::moves::find_filter_or_die(const std::string &, class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::filters::Filter>

pyrosetta.rosetta.protocols.moves.find_mover_or_die(mover_name: str, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.moves.Mover¶

Searches <movers> for the named mover, returning it if it exists,: otherwise halts execution with an error message.

C++: protocols::moves::find_mover_or_die(const std::string &, class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::moves::Mover>

pyrosetta.rosetta.protocols.moves.get_pymol_observer(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.moves.PyMOLObserver¶

(Internal) helper function to create a PyMOLObserver and add it to the given pose: NOTE: You NEED to adjust the observer type and call attach() on the return - by default a new PyMOLObserver isn’t attached/observing.

C++: protocols::moves::get_pymol_observer(class core::pose::Pose &) –> class std::shared_ptr<class protocols::moves::PyMOLObserver>

pyrosetta.rosetta.protocols.moves.mstype_from_name(name: str) → pyrosetta.rosetta.protocols.moves.MoverStatus¶: C++: protocols::moves::mstype_from_name(const std::string &) –> enum protocols::moves::MoverStatus

pyrosetta.rosetta.protocols.moves.to_string(mc_accepted: pyrosetta.rosetta.protocols.moves.MCA) → str¶: C++: protocols::moves::to_string(const enum protocols::moves::MCA &) –> std::string

pyrosetta.rosetta.protocols.moves.xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, mover_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶

Define the XML schema definition for a Mover that: contains no subtags but may contain any number of attributes (aka options).

C++: protocols::moves::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.moves.xsd_type_definition_w_attributes_and_repeatable_subelements(xsd: utility::tag::XMLSchemaDefinition, mover_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, subelements: utility::tag::XMLSchemaSimpleSubelementList) → None¶

Define the XML schema definition for a Mover that: contains subtags attributes (aka options).

C++: protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const class utility::tag::XMLSchemaSimpleSubelementList &) –> void

pyrosetta.rosetta.protocols.moves.xsd_type_definition_w_attributes_and_single_subelement(xsd: utility::tag::XMLSchemaDefinition, mover_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, subelement: utility::tag::XMLSchemaSimpleSubelementList) → None¶

Define the XML schema definition for a Mover that: contains subtags attributes (aka options).

C++: protocols::moves::xsd_type_definition_w_attributes_and_single_subelement(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const class utility::tag::XMLSchemaSimpleSubelementList &) –> void