loop_build

Bindings for protocols::loop_build namespace

class pyrosetta.rosetta.protocols.loop_build.LoopBuildMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.loop_build.LoopBuildMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::loop_build::LoopBuildMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loop_build.LoopBuildMover, : pyrosetta.rosetta.protocols.loop_build.LoopBuildMover) pyrosetta.rosetta.protocols.loop_build.LoopBuildMover

C++: protocols::loop_build::LoopBuildMover::operator=(const class protocols::loop_build::LoopBuildMover &) –> class protocols::loop_build::LoopBuildMover &

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.loop_build.LoopBuildMover) str

C++: protocols::loop_build::LoopBuildMover::get_name() const –> std::string

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

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

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

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

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

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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

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

Outputs details about the Mover, including current settings.

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

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

pyrosetta.rosetta.protocols.loop_build.LoopBuild_main(boinc_mode: bool) int

C++: protocols::loop_build::LoopBuild_main(bool) –> int

class pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow

Bases: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover

LoopMover utilizing fragment insertion, ccd loop closure, and minimization

add_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, fragset: pyrosetta.rosetta.core.fragment.FragSet) None

add a fragment set

C++: protocols::loops::loop_mover::LoopMover::add_fragments(class std::shared_ptr<class core::fragment::FragSet>) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the loop-build protocol to the input pose

C++: protocols::loops::loop_mover::IndependentLoopMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow, : pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow) pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow

C++: protocols::loop_build::LoopMover_SlidingWindow::operator=(const class protocols::loop_build::LoopMover_SlidingWindow &) –> class protocols::loop_build::LoopMover_SlidingWindow &

clear_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) None

clear the list of fragment sets

C++: protocols::loops::loop_mover::LoopMover::clear_fragments() –> 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.loop_build.LoopMover_SlidingWindow) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::loop_build::LoopMover_SlidingWindow::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>

false_movemap(*args, **kwargs)

Overloaded function.

  1. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap() const –> const class std::shared_ptr<class core::kinematics::MoveMap> &

  1. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap(const class std::shared_ptr<class core::kinematics::MoveMap> &) –> void

frag_libs(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t

C++: protocols::loops::loop_mover::LoopMover::frag_libs() const –> const class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > > &

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_accept_aborted_loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) bool

C++: protocols::loops::loop_mover::IndependentLoopMover::get_accept_aborted_loops() const –> bool

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_all_loops_closed(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) bool

C++: protocols::loops::loop_mover::IndependentLoopMover::get_all_loops_closed() const –> bool

get_build_all_loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) bool

C++: protocols::loops::loop_mover::IndependentLoopMover::get_build_all_loops() const –> bool

get_build_attempts(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) int

C++: protocols::loops::loop_mover::IndependentLoopMover::get_build_attempts() const –> int

get_checkpoints(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::loops::loop_mover::LoopMover::get_checkpoints() –> class std::shared_ptr<class protocols::checkpoint::CheckPointer> &

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_grow_attempts(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) int

C++: protocols::loops::loop_mover::IndependentLoopMover::get_grow_attempts() const –> int

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_LoopResult(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) pyrosetta.rosetta.protocols.loops.loop_mover.LoopResult

C++: protocols::loops::loop_mover::IndependentLoopMover::get_last_LoopResult() const –> enum protocols::loops::loop_mover::LoopResult

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_loop_combine_rate(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) bool

C++: protocols::loops::loop_mover::IndependentLoopMover::get_loop_combine_rate() const –> bool

get_name(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow) str

C++: protocols::loop_build::LoopMover_SlidingWindow::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_random_order(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) bool

C++: protocols::loops::loop_mover::IndependentLoopMover::get_random_order() const –> bool

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_strict_loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) bool

C++: protocols::loops::loop_mover::IndependentLoopMover::get_strict_loops() const –> bool

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

loops(*args, **kwargs)

Overloaded function.

  1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, lptr: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets

the GuardedLoopsFromFile object into a “not in charge” state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data.

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

  1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data: protocols::loops::LoopsFileData) -> None

Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).

C++: protocols::loops::loop_mover::LoopMover::loops(const class protocols::loops::LoopsFileData &) –> void

  1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, setting: protocols::loops::loops_definers::LoopsDefiner) -> None

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>) –> void

  1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops: protocols::loops::GuardedLoopsFromFile) -> None

Set the guarded_loops pointer

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::GuardedLoopsFromFile>) –> void

  1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.protocols.loops.Loops

non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this

before apply() has been called.

C++: protocols::loops::loop_mover::LoopMover::loops() –> class std::shared_ptr<class protocols::loops::Loops>

static mover_name() str

C++: protocols::loop_build::LoopMover_SlidingWindow::mover_name() –> std::string

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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::loop_build::LoopMover_SlidingWindow::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_loop(*args, **kwargs)

Overloaded function.

  1. randomize_loop(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow) -> bool

randomize loops prior to loop modeling?

C++: protocols::loop_build::LoopMover_SlidingWindow::randomize_loop() const –> bool

  1. randomize_loop(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow, flag: bool) -> None

indicate whether loops should be randomized prior to modeling

C++: protocols::loop_build::LoopMover_SlidingWindow::randomize_loop(const bool) –> void

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::LoopMover::scorefxn() const –> const class std::shared_ptr<class core::scoring::ScoreFunction> &

set_accept_aborted_loops_(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, value: bool) None

C++: protocols::loops::loop_mover::IndependentLoopMover::set_accept_aborted_loops_(bool) –> void

set_build_all_loops_(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, value: bool) None

C++: protocols::loops::loop_mover::IndependentLoopMover::set_build_all_loops_(bool) –> void

set_build_attempts_(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, value: int) None

Accessors:

C++: protocols::loops::loop_mover::IndependentLoopMover::set_build_attempts_(int) –> 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_default_settings(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow) None

set default settings

default settings are as follows:

randomize_loop() = true

C++: protocols::loop_build::LoopMover_SlidingWindow::set_default_settings() –> void

set_defaults(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover) None

C++: protocols::loops::loop_mover::IndependentLoopMover::set_defaults() –> void

set_extended_torsions(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) None

Extend a loop

C++: protocols::loops::loop_mover::LoopMover::set_extended_torsions(class core::pose::Pose &, const class protocols::loops::Loop &) –> void

set_grow_attempts_(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, value: int) None

C++: protocols::loops::loop_mover::IndependentLoopMover::set_grow_attempts_(int) –> void

set_guarded_loops_not_in_charge(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) None
Inform the GuardedLoopsFromFile object that it is not in charge of

updating its Loops object at the beginning of apply()

C++: protocols::loops::loop_mover::LoopMover::set_guarded_loops_not_in_charge() –> 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_loop_combine_rate_(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, value: float) None

C++: protocols::loops::loop_mover::IndependentLoopMover::set_loop_combine_rate_(double) –> 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_random_order_(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, value: bool) None

C++: protocols::loops::loop_mover::IndependentLoopMover::set_random_order_(bool) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, score_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::loops::loop_mover::LoopMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_strict_loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover, value: bool) None

C++: protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(bool) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

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

Outputs details about the Mover, including current settings.

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

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

torsion_features_string(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin
create a string representing the torsion bins (ABEGX) for the loops defined in the

guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there’s only one Loop object in the guarded_loops_ object).

C++: protocols::loops::loop_mover::LoopMover::torsion_features_string(const class core::pose::Pose &) const –> class utility::vector0<enum core::conformation::ppo_torsion_bin, class std::allocator<enum core::conformation::ppo_torsion_bin> >

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

creator for the LoopMover_SlidingWindowCreator class

assign(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator, : pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator) pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator

C++: protocols::loop_build::LoopMover_SlidingWindowCreator::operator=(const class protocols::loop_build::LoopMover_SlidingWindowCreator &) –> class protocols::loop_build::LoopMover_SlidingWindowCreator &

create_mover(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loop_build::LoopMover_SlidingWindowCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator) str

C++: protocols::loop_build::LoopMover_SlidingWindowCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::loop_build::LoopMover_SlidingWindowCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper, pose: pyrosetta.rosetta.core.pose.Pose) None

Invoke the loopmodel app.

This mover is a very thin wrapper around the command-line loopmodel app. The purpose of this mover is exclusively to add support for the loopmodel application in rosetta scripts. The behavior of loop modeling cannot be controlled at all from this mover and must instead be controlled using the usual command-line flags.

C++: protocols::loop_build::LoopmodelWrapper::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper, : pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper) pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper

C++: protocols::loop_build::LoopmodelWrapper::operator=(const class protocols::loop_build::LoopmodelWrapper &) –> class protocols::loop_build::LoopmodelWrapper &

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.loop_build.LoopmodelWrapper) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loop_build::LoopmodelWrapper::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.loop_build.LoopmodelWrapper) str

C++: protocols::loop_build::LoopmodelWrapper::get_name() const –> std::string

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

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

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

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

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

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::loop_build::LoopmodelWrapper::mover_name() –> std::string

static name() str

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

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

{parent}::parse_my_tag

C++: protocols::loop_build::LoopmodelWrapper::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::loop_build::LoopmodelWrapper::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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

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

Outputs details about the Mover, including current settings.

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

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator, : pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator) pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator

C++: protocols::loop_build::LoopmodelWrapperCreator::operator=(const class protocols::loop_build::LoopmodelWrapperCreator &) –> class protocols::loop_build::LoopmodelWrapperCreator &

create_mover(self: pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loop_build::LoopmodelWrapperCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator) str

C++: protocols::loop_build::LoopmodelWrapperCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::loop_build::LoopmodelWrapperCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void