rbsegment_relax

Bindings for protocols::rbsegment_relax namespace

class pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::rbsegment_relax::AutoRBMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover, : pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover) pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover

C++: protocols::rbsegment_relax::AutoRBMover::operator=(const class protocols::rbsegment_relax::AutoRBMover &) –> class protocols::rbsegment_relax::AutoRBMover &

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.rbsegment_relax.AutoRBMover) str

C++: protocols::rbsegment_relax::AutoRBMover::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

setup_topology(self: pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::rbsegment_relax::AutoRBMover::setup_topology(class core::pose::Pose &) –> 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.rbsegment_relax.FragInsertAndAlignMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Performs a rigid-body movement on a segment of a protein

Derived classes must implement ‘getCoordinateTransform’ and ‘apply’

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

insert one RB fragment + realign

C++: protocols::rbsegment_relax::FragInsertAndAlignMover::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, pose: pyrosetta.rosetta.core.pose.Pose, idx: int) -> None

  2. apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, pose: pyrosetta.rosetta.core.pose.Pose, idx: int, idealize: bool) -> None

insert one RB fragment + realign

C++: protocols::rbsegment_relax::FragInsertAndAlignMover::apply(class core::pose::Pose &, int, bool) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, : pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover) pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover

C++: protocols::rbsegment_relax::FragInsertAndAlignMover::operator=(const class protocols::rbsegment_relax::FragInsertAndAlignMover &) –> class protocols::rbsegment_relax::FragInsertAndAlignMover &

bootstrapCATrace(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, start_pose: pyrosetta.rosetta.core.pose.Pose) None

take a CA-only pose and insert idealized fragments close to the trace

C++: protocols::rbsegment_relax::FragInsertAndAlignMover::bootstrapCATrace(class core::pose::Pose &) –> 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.rbsegment_relax.FragInsertAndAlignMover) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::rbsegment_relax::FragInsertAndAlignMover::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.rbsegment_relax.FragInsertAndAlignMover) str

C++: protocols::rbsegment_relax::FragInsertAndAlignMover::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 &

class pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover

Bases: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

Generic random segment mover

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Randomly perturb the segment

C++: protocols::rbsegment_relax::GaussianRBSegmentMover::apply(class core::pose::Pose &) –> void

applyRotation(*args, **kwargs)

Overloaded function.

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None

Apply an arbitrary rotation specified by Euler angles (in degrees!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

Apply an arbitrary rotation specified by a rotation matrix

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void

applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None

Apply a spin of the specified angle (in degrees) about arbitrary axis

C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void

applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void

applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply an arbitrary translation

C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, : pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover

C++: protocols::rbsegment_relax::GaussianRBSegmentMover::operator=(const class protocols::rbsegment_relax::GaussianRBSegmentMover &) –> class protocols::rbsegment_relax::GaussianRBSegmentMover &

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.rbsegment_relax.GaussianRBSegmentMover) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::rbsegment_relax::GaussianRBSegmentMover::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>

getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None
Get the fragment center / matrix that rotates global coordinates into local fragment coordinates.

Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue

C++: protocols::rbsegment_relax::GaussianRBSegmentMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void

getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

Get the the starting and ending residues of transform

C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &

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.rbsegment_relax.GaussianRBSegmentMover) str

C++: protocols::rbsegment_relax::GaussianRBSegmentMover::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

print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

Print debugging info

C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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

setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

(re)set the starting and ending residues of this transform

C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)

Overloaded function.

  1. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover) -> None

  2. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float) -> None

  3. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float, sigAxisT: float) -> None

  4. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None

  5. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None

set movement parameters

sigR: the stdev of rotation

sigT: the stdev of movement

C++: protocols::rbsegment_relax::GaussianRBSegmentMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

Set the segment this mover is working on

C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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.rbsegment_relax.HelicalGaussianMover

Bases: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

Random movements wrt the helical axis

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply a +1 or -1 residue “shift” to this helix

C++: protocols::rbsegment_relax::HelicalGaussianMover::apply(class core::pose::Pose &) –> void

applyRotation(*args, **kwargs)

Overloaded function.

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None

Apply an arbitrary rotation specified by Euler angles (in degrees!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

Apply an arbitrary rotation specified by a rotation matrix

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void

applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None

Apply a spin of the specified angle (in degrees) about arbitrary axis

C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void

applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void

applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply an arbitrary translation

C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, : pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover) pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover

C++: protocols::rbsegment_relax::HelicalGaussianMover::operator=(const class protocols::rbsegment_relax::HelicalGaussianMover &) –> class protocols::rbsegment_relax::HelicalGaussianMover &

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.rbsegment_relax.HelicalGaussianMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rbsegment_relax::HelicalGaussianMover::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>

getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None
Get the fragment center / matrix that rotates global coordinates into local fragment coordinates.

Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue

C++: protocols::rbsegment_relax::HelicalGaussianMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void

getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

Get the the starting and ending residues of transform

C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &

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.rbsegment_relax.HelicalGaussianMover) str

C++: protocols::rbsegment_relax::HelicalGaussianMover::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

print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

Print debugging info

C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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

setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

(re)set the starting and ending residues of this transform

C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)

Overloaded function.

  1. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover) -> None

  2. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float) -> None

  3. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float, sigAxisT: float) -> None

  4. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None

  5. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None

set movement parameters

sigAxisR: the stdev of rotation along the helical axis

sigAxisT: the stdev of movement along the helical axis

sigOffAxisR: the stdev of rotation normal to the helical axis

sigOffAxisT: the stdev of movement normal to the helical axis

C++: protocols::rbsegment_relax::HelicalGaussianMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

Set the segment this mover is working on

C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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.rbsegment_relax.IdealizeHelicesMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::rbsegment_relax::IdealizeHelicesMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover, : pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover) pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover

C++: protocols::rbsegment_relax::IdealizeHelicesMover::operator=(const class protocols::rbsegment_relax::IdealizeHelicesMover &) –> class protocols::rbsegment_relax::IdealizeHelicesMover &

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.rbsegment_relax.IdealizeHelicesMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rbsegment_relax::IdealizeHelicesMover::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.rbsegment_relax.IdealizeHelicesMover) str

C++: protocols::rbsegment_relax::IdealizeHelicesMover::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::rbsegment_relax::IdealizeHelicesMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::rbsegment_relax::IdealizeHelicesMover::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::rbsegment_relax::IdealizeHelicesMover::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.rbsegment_relax.IdealizeHelicesMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator, : pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator) pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator

C++: protocols::rbsegment_relax::IdealizeHelicesMoverCreator::operator=(const class protocols::rbsegment_relax::IdealizeHelicesMoverCreator &) –> class protocols::rbsegment_relax::IdealizeHelicesMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator) str

C++: protocols::rbsegment_relax::IdealizeHelicesMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::rbsegment_relax::MakeStarTopologyMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover, : pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover) pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover

C++: protocols::rbsegment_relax::MakeStarTopologyMover::operator=(const class protocols::rbsegment_relax::MakeStarTopologyMover &) –> class protocols::rbsegment_relax::MakeStarTopologyMover &

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.rbsegment_relax.MakeStarTopologyMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rbsegment_relax::MakeStarTopologyMover::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.rbsegment_relax.MakeStarTopologyMover) str

C++: protocols::rbsegment_relax::MakeStarTopologyMover::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::rbsegment_relax::MakeStarTopologyMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::rbsegment_relax::MakeStarTopologyMover::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::rbsegment_relax::MakeStarTopologyMover::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.rbsegment_relax.MakeStarTopologyMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator, : pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator) pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator

C++: protocols::rbsegment_relax::MakeStarTopologyMoverCreator::operator=(const class protocols::rbsegment_relax::MakeStarTopologyMoverCreator &) –> class protocols::rbsegment_relax::MakeStarTopologyMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator) str

C++: protocols::rbsegment_relax::MakeStarTopologyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::rbsegment_relax::OptimizeThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover, : pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover) pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover

C++: protocols::rbsegment_relax::OptimizeThreadingMover::operator=(const class protocols::rbsegment_relax::OptimizeThreadingMover &) –> class protocols::rbsegment_relax::OptimizeThreadingMover &

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.rbsegment_relax.OptimizeThreadingMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rbsegment_relax::OptimizeThreadingMover::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.rbsegment_relax.OptimizeThreadingMover) str

C++: protocols::rbsegment_relax::OptimizeThreadingMover::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::rbsegment_relax::OptimizeThreadingMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::rbsegment_relax::OptimizeThreadingMover::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::rbsegment_relax::OptimizeThreadingMover::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.rbsegment_relax.OptimizeThreadingMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator, : pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator) pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator

C++: protocols::rbsegment_relax::OptimizeThreadingMoverCreator::operator=(const class protocols::rbsegment_relax::OptimizeThreadingMoverCreator &) –> class protocols::rbsegment_relax::OptimizeThreadingMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator) str

C++: protocols::rbsegment_relax::OptimizeThreadingMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange

Bases: pybind11_builtins.pybind11_object

RB residue range

char_type(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) str

C++: protocols::rbsegment_relax::RBResidueRange::char_type() const –> char

end(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) int

C++: protocols::rbsegment_relax::RBResidueRange::end() const –> unsigned long

length(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) int

C++: protocols::rbsegment_relax::RBResidueRange::length() const –> unsigned long

set_end(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, E: int) None

C++: protocols::rbsegment_relax::RBResidueRange::set_end(unsigned long) –> void

set_start(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, S: int) None

C++: protocols::rbsegment_relax::RBResidueRange::set_start(unsigned long) –> void

start(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) int

C++: protocols::rbsegment_relax::RBResidueRange::start() const –> unsigned long

type(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType

C++: protocols::rbsegment_relax::RBResidueRange::type() const –> enum protocols::rbsegment_relax::RBSegmentType

class pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

Bases: pybind11_builtins.pybind11_object

Rigid-body segments in a protein

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, : pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

C++: protocols::rbsegment_relax::RBSegment::operator=(const class protocols::rbsegment_relax::RBSegment &) –> class protocols::rbsegment_relax::RBSegment &

getSigAxisR(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float

C++: protocols::rbsegment_relax::RBSegment::getSigAxisR() const –> double

getSigAxisT(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float

C++: protocols::rbsegment_relax::RBSegment::getSigAxisT() const –> double

getSigOffAxisR(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float

C++: protocols::rbsegment_relax::RBSegment::getSigOffAxisR() const –> double

getSigOffAxisT(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) float

C++: protocols::rbsegment_relax::RBSegment::getSigOffAxisT() const –> double

get_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) None

C++: protocols::rbsegment_relax::RBSegment::get_movement(double &, double &, double &, double &) const –> void

initialized(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool

C++: protocols::rbsegment_relax::RBSegment::initialized() const –> bool

isCompound(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool

C++: protocols::rbsegment_relax::RBSegment::isCompound() const –> bool

isEmpty(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool

C++: protocols::rbsegment_relax::RBSegment::isEmpty() const –> bool

isGenericRB(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool

C++: protocols::rbsegment_relax::RBSegment::isGenericRB() const –> bool

isHelix(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool

C++: protocols::rbsegment_relax::RBSegment::isHelix() const –> bool

isSheet(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool

C++: protocols::rbsegment_relax::RBSegment::isSheet() const –> bool

isSimple(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) bool

C++: protocols::rbsegment_relax::RBSegment::isSimple() const –> bool

nContinuousSegments(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) int

C++: protocols::rbsegment_relax::RBSegment::nContinuousSegments() const –> unsigned long

remap(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, mapping: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

C++: protocols::rbsegment_relax::RBSegment::remap(const class core::id::SequenceMapping &) const –> class protocols::rbsegment_relax::RBSegment

set_movement(*args, **kwargs)

Overloaded function.

  1. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float) -> None

  2. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None

  3. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None

C++: protocols::rbsegment_relax::RBSegment::set_movement(double, double, double, double) –> void

class pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Performs a rigid-body movement on a segment of a protein

Derived classes must implement ‘getCoordinateTransform’ and ‘apply’

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the rigid-body fragment mover to a pose. Must be defined by derived classes.

C++: protocols::rbsegment_relax::RBSegmentMover::apply(class core::pose::Pose &) –> void

applyRotation(*args, **kwargs)

Overloaded function.

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None

Apply an arbitrary rotation specified by Euler angles (in degrees!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

Apply an arbitrary rotation specified by a rotation matrix

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void

applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None

Apply a spin of the specified angle (in degrees) about arbitrary axis

C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void

applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void

applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply an arbitrary translation

C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, : pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

C++: protocols::rbsegment_relax::RBSegmentMover::operator=(const class protocols::rbsegment_relax::RBSegmentMover &) –> class protocols::rbsegment_relax::RBSegmentMover &

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>

getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, : pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None
Returns: (a) the matrix that rotates global coordinates into local fragment coordinates and

(b) the center of rotation of the fragment. Default implementation sets them to global coords

C++: protocols::rbsegment_relax::RBSegmentMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void

getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

Get the the starting and ending residues of transform

C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &

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.rbsegment_relax.RBSegmentMover) str

C++: protocols::rbsegment_relax::RBSegmentMover::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

print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

Print debugging info

C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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

setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

(re)set the starting and ending residues of this transform

C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)

Overloaded function.

  1. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) -> None

  2. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float) -> None

  3. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float, p2: float) -> None

  4. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float, p2: float, p3: float) -> None

  5. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, p1: float, p2: float, p3: float, p4: float) -> None

Set mover-specific movement parameters. Do nothing by default.

C++: protocols::rbsegment_relax::RBSegmentMover::set_movement(double, double, double, double) –> void

  1. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, rb: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None

steal movement params from a segment definition

C++: protocols::rbsegment_relax::RBSegmentMover::set_movement(const class protocols::rbsegment_relax::RBSegment &) –> 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

Set the segment this mover is working on

C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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.rbsegment_relax.RBSegmentRelax

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_compositeSegmentMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

C++: protocols::rbsegment_relax::RBSegmentRelax::add_compositeSegmentMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void

add_genericRBMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

C++: protocols::rbsegment_relax::RBSegmentRelax::add_genericRBMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void

add_helixMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

C++: protocols::rbsegment_relax::RBSegmentRelax::add_helixMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void

add_strandMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

C++: protocols::rbsegment_relax::RBSegmentRelax::add_strandMover(class std::shared_ptr<class protocols::rbsegment_relax::RBSegmentMover>) –> void

add_wholeStructureMover(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, newMover: pyrosetta.rosetta.protocols.moves.Mover) None

C++: protocols::rbsegment_relax::RBSegmentRelax::add_wholeStructureMover(class std::shared_ptr<class protocols::moves::Mover>) –> void

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::rbsegment_relax::RBSegmentRelax::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, : pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax

C++: protocols::rbsegment_relax::RBSegmentRelax::operator=(const class protocols::rbsegment_relax::RBSegmentRelax &) –> class protocols::rbsegment_relax::RBSegmentRelax &

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

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

clear_info is called by jd2 before calling apply

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

clear_movesets(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax) None

C++: protocols::rbsegment_relax::RBSegmentRelax::clear_movesets() –> 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.rbsegment_relax.RBSegmentRelax) str

C++: protocols::rbsegment_relax::RBSegmentRelax::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

initialize(*args, **kwargs)

Overloaded function.

  1. initialize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, frag_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> None

  2. initialize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, frag_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t, rnd: float) -> None

C++: protocols::rbsegment_relax::RBSegmentRelax::initialize(const class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > > &, double) –> void

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

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

static name() str

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

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

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

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

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_bootstrap(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, boot: bool) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_bootstrap(bool) –> void

set_cst_weight(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, wt: float) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_cst_weight(double) –> void

set_cst_width(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, width: float) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_cst_width(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

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

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

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

set_fix_ligands(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, fix: bool) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_fix_ligands(bool) –> void

set_genericRBMoveStepsize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, trans: float, rot: float) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize(double, double) –> void

set_helicalMoveStepsize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, onAxisTrans: float, onAxisRot: float, offAxisTrans: float, offAxisRot: float) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_helicalMoveStepsize(double, double, double, double) –> void

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

setter for poses contained for rms

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

set_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_ncycles(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, ncycles: int) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_ncycles(int) –> void

set_randomize(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, rand: int) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_randomize(unsigned long) –> void

set_skip_lr(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, skip: bool) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_skip_lr(bool) –> void

set_temperature(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax, start: float, final: float) None

C++: protocols::rbsegment_relax::RBSegmentRelax::set_temperature(double, double) –> 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.rbsegment_relax.RBSegmentType

Bases: pybind11_builtins.pybind11_object

Enumeration of RB types

Members:

RB_HELIX

RB_SHEET

RB_DEFAULT

RB_DEFAULT = <RBSegmentType.RB_DEFAULT: 3>
RB_HELIX = <RBSegmentType.RB_HELIX: 1>
RB_SHEET = <RBSegmentType.RB_SHEET: 2>
property name
class pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt

Bases: pyrosetta.rosetta.std.binary_function_double_double_bool_t

assign(self: pyrosetta.rosetta.std.binary_function_double_double_bool_t, : pyrosetta.rosetta.std.binary_function_double_double_bool_t) pyrosetta.rosetta.std.binary_function_double_double_bool_t

C++: std::binary_function<double, double, bool>::operator=(const struct std::binary_function<double, double, bool> &) –> struct std::binary_function<double, double, bool> &

class pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover

Bases: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

“Register shift” a segment by one amino-acid Works in both centroid and all-atom

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Apply a + or - residue “shift” to this helix

C++: protocols::rbsegment_relax::SequenceShiftMover::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, pose: pyrosetta.rosetta.core.pose.Pose, shift: int) -> None

Apply a + or - residue “shift” to this helix

C++: protocols::rbsegment_relax::SequenceShiftMover::apply(class core::pose::Pose &, int) –> void

applyRotation(*args, **kwargs)

Overloaded function.

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None

Apply an arbitrary rotation specified by Euler angles (in degrees!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

Apply an arbitrary rotation specified by a rotation matrix

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void

applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None

Apply a spin of the specified angle (in degrees) about arbitrary axis

C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void

applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void

applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply an arbitrary translation

C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, : pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover

C++: protocols::rbsegment_relax::SequenceShiftMover::operator=(const class protocols::rbsegment_relax::SequenceShiftMover &) –> class protocols::rbsegment_relax::SequenceShiftMover &

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.rbsegment_relax.SequenceShiftMover) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::rbsegment_relax::SequenceShiftMover::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>

getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, : pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None
Returns: (a) the matrix that rotates global coordinates into local fragment coordinates and

(b) the center of rotation of the fragment. Default implementation sets them to global coords

C++: protocols::rbsegment_relax::RBSegmentMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void

getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

Get the the starting and ending residues of transform

C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &

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.rbsegment_relax.RBSegmentMover) str

C++: protocols::rbsegment_relax::RBSegmentMover::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_residues_to_rebuild(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) pyrosetta.rosetta.protocols.loops.Loops

IF ref_pose is given, get a list of residues to rebuild via fragment insertion

C++: protocols::rbsegment_relax::SequenceShiftMover::get_residues_to_rebuild() –> class std::shared_ptr<class protocols::loops::Loops>

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

print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

Print debugging info

C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) -> int

  2. score(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, step_fn: bool) -> int

Return a score: the minimum number of block shifts accumulated

C++: protocols::rbsegment_relax::SequenceShiftMover::score(bool) –> int

setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

(re)set the starting and ending residues of this transform

C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_extra_penalty(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, penalty_res: pyrosetta.rosetta.utility.vector1_bool) None

Set an extra block-shift penalty at certain residues

C++: protocols::rbsegment_relax::SequenceShiftMover::set_extra_penalty(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

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

setter for poses contained for rms

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

set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, : float, : float, : float, : float) None

set movement parameters. ignore all input args

C++: protocols::rbsegment_relax::SequenceShiftMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

Set the segment this mover is working on

C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> void

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

Set the ‘type’ string

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

set_verbose(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, inval: bool) None

C++: protocols::rbsegment_relax::SequenceShiftMover::set_verbose(bool) –> 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

trigger_accept(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) None

Last move accepted; update offsets_

C++: protocols::rbsegment_relax::SequenceShiftMover::trigger_accept() –> 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.rbsegment_relax.StrandTwistingMover

Bases: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

Strand Twisting

apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply a +1 or -1 residue “shift” to this helix

C++: protocols::rbsegment_relax::StrandTwistingMover::apply(class core::pose::Pose &) –> void

applyRotation(*args, **kwargs)

Overloaded function.

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, alpha: float, beta: float, gamma: float) -> None

Apply an arbitrary rotation specified by Euler angles (in degrees!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, double, double, double) –> void

  1. applyRotation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

Apply an arbitrary rotation specified by a rotation matrix

C++: protocols::rbsegment_relax::RBSegmentMover::applyRotation(class core::pose::Pose &, class numeric::xyzMatrix<double>) –> void

applySpin(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationAxis: pyrosetta.rosetta.numeric.xyzVector_double_t, degrees: float) None

Apply a spin of the specified angle (in degrees) about arbitrary axis

C++: protocols::rbsegment_relax::RBSegmentMover::applySpin(class core::pose::Pose &, class numeric::xyzVector<double>, double) –> void

applyTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)

C++: protocols::rbsegment_relax::RBSegmentMover::applyTransformation(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void

applyTranslation(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Apply an arbitrary translation

C++: protocols::rbsegment_relax::RBSegmentMover::applyTranslation(class core::pose::Pose &, class numeric::xyzVector<double>) –> void

assign(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, : pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover) pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover

C++: protocols::rbsegment_relax::StrandTwistingMover::operator=(const class protocols::rbsegment_relax::StrandTwistingMover &) –> class protocols::rbsegment_relax::StrandTwistingMover &

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.rbsegment_relax.StrandTwistingMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rbsegment_relax::StrandTwistingMover::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>

getCoordinateTransformation(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, pose: pyrosetta.rosetta.core.pose.Pose, rotationCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, coordinateTransform: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None
Get the fragment center / matrix that rotates global coordinates into local fragment coordinates.

Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue

C++: protocols::rbsegment_relax::StrandTwistingMover::getCoordinateTransformation(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzMatrix<double> &) –> void

getResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment

Get the the starting and ending residues of transform

C++: protocols::rbsegment_relax::RBSegmentMover::getResidueRange() –> const class protocols::rbsegment_relax::RBSegment &

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.rbsegment_relax.StrandTwistingMover) str

C++: protocols::rbsegment_relax::StrandTwistingMover::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

print(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) None

Print debugging info

C++: protocols::rbsegment_relax::RBSegmentMover::print() –> 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

setResidueRange(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

(re)set the starting and ending residues of this transform

C++: protocols::rbsegment_relax::RBSegmentMover::setResidueRange(const class protocols::rbsegment_relax::RBSegment &) –> 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_movement(*args, **kwargs)

Overloaded function.

  1. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover) -> None

  2. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float) -> None

  3. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float, sigAxisT: float) -> None

  4. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float) -> None

  5. set_movement(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None

set movement parameters

sigAxisR: the stdev of rotation along the helical axis

sigAxisT: the stdev of movement along the helical axis

sigOffAxisR: the stdev of rotation normal to the helical axis

sigOffAxisT: the stdev of movement normal to the helical axis

C++: protocols::rbsegment_relax::StrandTwistingMover::set_movement(double, double, double, 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_segment(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) None

Set the segment this mover is working on

C++: protocols::rbsegment_relax::RBSegmentMover::set_segment(const class protocols::rbsegment_relax::RBSegment &) –> 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.rbsegment_relax.guess_rbsegs_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, rigid_segs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, rb_chunks: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops) None

use DSSP and simple rules to guess the asignment of rigid-body segments

C++: protocols::rbsegment_relax::guess_rbsegs_from_pose(const class core::pose::Pose &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class protocols::loops::Loops &) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.read_RBSegment_file(*args, **kwargs)

Overloaded function.

  1. read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str) -> None

  2. read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str, autoGenerateLoops: bool) -> None

  3. read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str, autoGenerateLoops: bool, nres: int) -> None

  4. read_RBSegment_file(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, filename: str, autoGenerateLoops: bool, nres: int, cutpts: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Parses an RB segment file into a vector of RBsegments

C++: protocols::rbsegment_relax::read_RBSegment_file(class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class protocols::loops::Loops &, std::string, bool, int, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.remap_rb_segments(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, rbsegs_remap: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, resmap: pyrosetta.rosetta.core.id.SequenceMapping) None

res mapping to rbsegments

C++: protocols::rbsegment_relax::remap_rb_segments(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::id::SequenceMapping &) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.restore_pose_from_rbsegs(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, pose_in: pyrosetta.rosetta.core.pose.Pose, pose_out: pyrosetta.rosetta.core.pose.Pose) None

restore loops from pose

C++: protocols::rbsegment_relax::restore_pose_from_rbsegs(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::pose::Pose &, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.select_RBsegments(rbsegs_in: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops_in: pyrosetta.rosetta.protocols.loops.Loops, rbsegs_selected: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops_selected: pyrosetta.rosetta.protocols.loops.Loops) None

C++: protocols::rbsegment_relax::select_RBsegments(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class protocols::loops::Loops &, class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, class protocols::loops::Loops &) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.set_constraints(pose: pyrosetta.rosetta.core.pose.Pose, cst_pose: pyrosetta.rosetta.core.pose.Pose, cst_width: float, cst_stdev: float, cst_seqwidth: int) None

set up constraints accounting for missing density in start pose

C++: protocols::rbsegment_relax::set_constraints(class core::pose::Pose &, const class core::pose::Pose &, double, double, unsigned long) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.set_rb_constraints(pose: pyrosetta.rosetta.core.pose.Pose, cst_pose: pyrosetta.rosetta.core.pose.Pose, rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, resmap: pyrosetta.rosetta.core.id.SequenceMapping, cst_width: float, cst_stdev: float, cst_seqwidth: int) None

set up constraints over RB segments only; allow ambiguity in sequence threading

C++: protocols::rbsegment_relax::set_rb_constraints(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::id::SequenceMapping &, double, double, unsigned long) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.setup_disconnected(pose: pyrosetta.rosetta.core.pose.Pose) None

build a pose where every residue is connected by jumps to vrt

C++: protocols::rbsegment_relax::setup_disconnected(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.setup_pose_from_rbsegs(*args, **kwargs)

Overloaded function.

  1. setup_pose_from_rbsegs(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, pose_in: pyrosetta.rosetta.core.pose.Pose, pose_out: pyrosetta.rosetta.core.pose.Pose, resmap: pyrosetta.rosetta.core.id.SequenceMapping, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

  2. setup_pose_from_rbsegs(rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, pose_in: pyrosetta.rosetta.core.pose.Pose, pose_out: pyrosetta.rosetta.core.pose.Pose, resmap: pyrosetta.rosetta.core.id.SequenceMapping, mm: pyrosetta.rosetta.core.kinematics.MoveMap, fixligs: bool) -> None

remove loops from pose

C++: protocols::rbsegment_relax::setup_pose_from_rbsegs(const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class core::pose::Pose &, class core::pose::Pose &, class core::id::SequenceMapping &, class core::kinematics::MoveMap &, bool) –> void

pyrosetta.rosetta.protocols.rbsegment_relax.setup_pose_rbsegs_keep_loops(pose: pyrosetta.rosetta.core.pose.Pose, rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, loops: pyrosetta.rosetta.protocols.loops.Loops, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(class core::pose::Pose &, const class utility::vector1<class protocols::rbsegment_relax::RBSegment, class std::allocator<class protocols::rbsegment_relax::RBSegment> > &, const class protocols::loops::Loops &, class std::shared_ptr<class core::kinematics::MoveMap>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.rbsegment_relax.setup_star_topology(pose: pyrosetta.rosetta.core.pose.Pose) None

setup star-topology fold tree

C++: protocols::rbsegment_relax::setup_star_topology(class core::pose::Pose &) –> void