rbsegment_relax

Bindings for protocols::rbsegment_relax namespace

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’

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, arg0: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, arg1: pyrosetta.rosetta.core.pose.Pose) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, rbsegs: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment, ref_pose: pyrosetta.rosetta.core.pose.Pose, randomness: float) -> None
4. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

2. apply(self: pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover, pose: pyrosetta.rosetta.core.pose.Pose, idx: int) -> None
3. 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.

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

name() → str

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover

Bases: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

Generic random segment mover

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg1: float) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, sigR: float, sigT: float) -> None
4. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover) -> None

doc

5. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, arg0: float) -> None

doc

6. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, sigR: float, sigT: float) -> None
7. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

2. 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.

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

name() → str

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

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

Print debugging info

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover

Bases: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

Random movements wrt the helical axis

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg1: float) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg1: float, arg2: float) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg1: float, arg2: float, arg3: float) -> None

doc

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

doc

7. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: float) -> None

doc

8. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: float, arg1: float) -> None

doc

9. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: float, arg1: float, arg2: float) -> None

doc

10. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None
11. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

2. 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.

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

name() → str

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

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

Print debugging info

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange

Bases: pybind11_builtins.pybind11_object

RB residue range

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) -> None
2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, arg0: int, arg1: int) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, begin: int, end: int, type: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) -> None
4. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, i: int) → pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange

C++: protocols::rbsegment_relax::RBSegment::operator[](int) –> class protocols::rbsegment_relax::RBResidueRange &

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None
2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, seg_begin: int, seg_end: int, seg_type: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) -> None
3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, range_in: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) -> None
4. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, seg_begin: int, seg_end: int, type: str) -> None
5. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, segs_in: pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment) -> None
6. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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’

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None
3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

2. 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.

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

name() → str

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

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

Print debugging info

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

6. 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType

Bases: pybind11_builtins.pybind11_object

Enumeration of RB types

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) → int

__init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType, arg0: int) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType, arg0: int) -> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType, arg0: tuple) → None

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

class pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt

Bases: pyrosetta.rosetta.std.binary_function_double_double_bool_t

__call__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt, x: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, y: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) → bool

C++: protocols::rbsegment_relax::RB_lt::operator()(class protocols::rbsegment_relax::RBSegment, class protocols::rbsegment_relax::RBSegment) –> bool

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, magnitude: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, pose_in: pyrosetta.rosetta.core.pose.Pose, seg: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, magnitude: int) -> None
5. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange) -> None

doc

6. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, rb: pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange, magnitude: int) -> None
7. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) -> None
8. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

2. 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

2. 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.

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

name() → str

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

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

Print debugging info

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover

Bases: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover

Strand Twisting

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg1: float) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg1: float, arg2: float) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment, arg1: float, arg2: float, arg3: float) -> None

doc

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

doc

7. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: float) -> None

doc

8. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: float, arg1: float) -> None

doc

9. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: float, arg1: float, arg2: float) -> None

doc

10. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, sigAxisR: float, sigAxisT: float, sigOffAxisR: float, sigOffAxisT: float) -> None
11. __init__(self: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover, arg0: pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

2. 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.

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

name() → str

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

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

Print debugging info

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

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 &, class std::basic_string<char>, 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