rigid¶

Bindings for protocols::rigid namespace

class pyrosetta.rosetta.protocols.rigid.Direction¶

Bases: pybind11_builtins.pybind11_object

Direction, which direction

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.protocols.rigid.Direction, arg0: pyrosetta.rosetta.protocols.rigid.Direction) -> bool
__eq__(self: pyrosetta.rosetta.protocols.rigid.Direction, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.rigid.Direction) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.rigid.Direction) → int¶

__init__(self: pyrosetta.rosetta.protocols.rigid.Direction, 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.rigid.Direction) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.protocols.rigid.Direction, arg0: pyrosetta.rosetta.protocols.rigid.Direction) -> bool
__ne__(self: pyrosetta.rosetta.protocols.rigid.Direction, 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.rigid.Direction) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.rigid.Direction, 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.rigid.MembraneCenterPerturbationMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

perturb the pose along membrane normal

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover, trans_mag_in: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover, arg0: pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover) -> 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.rigid.MembraneCenterPerturbationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::MembraneCenterPerturbationMover::apply(class core::pose::Pose &) –> void

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

fpd

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

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.rigid.MembraneCenterPerturbationMover) → str¶: C++: protocols::rigid::MembraneCenterPerturbationMover::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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.

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

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

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.rigid.MembraneNormalPerturbationMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

rotation pose around membrane center, perturb the membrane normal vector relative to the pose

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover, rotation_mag_in: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover, arg0: pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover) -> 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.rigid.MembraneNormalPerturbationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::MembraneNormalPerturbationMover::apply(class core::pose::Pose &) –> void

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

fpd

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

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.rigid.MembraneNormalPerturbationMover) → str¶: C++: protocols::rigid::MembraneNormalPerturbationMover::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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.

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

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

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.rigid.MovePoseToMembraneCenterMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

move pose into a membrane

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover, arg0: pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover) -> 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.rigid.MovePoseToMembraneCenterMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::MovePoseToMembraneCenterMover::apply(class core::pose::Pose &) –> void

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

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>

estimate_membrane_center(self: pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(class core::pose::Pose &) –> class numeric::xyzVector<double>

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.rigid.MovePoseToMembraneCenterMover) → str¶: C++: protocols::rigid::MovePoseToMembraneCenterMover::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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.

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

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

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.rigid.Partner¶

Bases: pybind11_builtins.pybind11_object

Partner, which partner gets moved

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.protocols.rigid.Partner, arg0: pyrosetta.rosetta.protocols.rigid.Partner) -> bool
__eq__(self: pyrosetta.rosetta.protocols.rigid.Partner, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.rigid.Partner) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.rigid.Partner) → int¶

__init__(self: pyrosetta.rosetta.protocols.rigid.Partner, 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.rigid.Partner) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.protocols.rigid.Partner, arg0: pyrosetta.rosetta.protocols.rigid.Partner) -> bool
__ne__(self: pyrosetta.rosetta.protocols.rigid.Partner, 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.rigid.Partner) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.rigid.Partner, 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.rigid.RigidBodyDofPerturbMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

This Mover does a perturbation defined by the rotational and translational magnitudes. Allowed dofs are specified by a map. Can be defined through a move map or with rb_jump. A single jump is selected.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, arg0: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, arg0: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, arg1: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, rot_mag_in: float, trans_mag_in: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, arg0: int, arg1: pyrosetta.rosetta.core.conformation.symmetry.SymDof) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, arg0: int, arg1: pyrosetta.rosetta.core.conformation.symmetry.SymDof, arg2: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, rb_jump_in: int, dof: pyrosetta.rosetta.core.conformation.symmetry.SymDof, rot_mag_in: float, trans_mag_in: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover) -> 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.rigid.RigidBodyDofPerturbMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyDofPerturbMover::apply(class core::pose::Pose &) –> void

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

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>

dof(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, dof: pyrosetta.rosetta.core.conformation.symmetry.SymDof) → None¶: C++: protocols::rigid::RigidBodyDofPerturbMover::dof(class core::conformation::symmetry::SymDof) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> void

rot_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyDofPerturbMover::rot_magnitude(const double) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyDofPerturbMover::trans_magnitude(const double) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a randomly selected jump.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover) -> 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.rigid.RigidBodyDofRandomTransMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyDofRandomTransMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::show(class std::basic_ostream<char> &) const –> void

step_size(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover, step_size_in: float) → None¶: C++: protocols::rigid::RigidBodyDofRandomTransMover::step_size(double) –> void

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

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

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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_axis(*args, **kwargs)¶

Overloaded function.

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::rigid::RigidBodyDofRandomTransMover::trans_axis() –> class numeric::xyzVector<double> &

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover, trans_axis_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::rigid::RigidBodyDofRandomTransMover::trans_axis(class numeric::xyzVector<double>) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover, rb_jump_in: int, : pyrosetta.rosetta.core.conformation.symmetry.SymDof) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover) -> 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.rigid.RigidBodyDofRandomizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyDofRandomizeMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

This Mover does a perturbation defined by the rotational and translational magnitudes. Allowed dofs are specified by a map. Can be defined through a move map or with rb_jump. All jumps are selected in random order.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover, arg0: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover, arg0: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, arg1: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, rot_mag_in: float, trans_mag_in: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover) -> 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.rigid.RigidBodyDofSeqPerturbMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyDofSeqPerturbMover::apply(class core::pose::Pose &) –> void

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

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>

dofs(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) → None¶: C++: protocols::rigid::RigidBodyDofSeqPerturbMover::dofs(class std::map<unsigned long, class core::conformation::symmetry::SymDof, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class core::conformation::symmetry::SymDof> > >) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> void

rot_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyDofSeqPerturbMover::rot_magnitude(const double) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyDofSeqPerturbMover::trans_magnitude(const double) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover) -> 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.rigid.RigidBodyDofSeqRandomizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyDofSeqRandomizeMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump. Jumps are visited in random order

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover) -> 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.rigid.RigidBodyDofSeqTransMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyDofSeqTransMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::show(class std::basic_ostream<char> &) const –> void

step_size(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover, step_size_in: float) → None¶: C++: protocols::rigid::RigidBodyDofSeqTransMover::step_size(double) –> void

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

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

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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_axis(*args, **kwargs)¶

Overloaded function.

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::rigid::RigidBodyDofSeqTransMover::trans_axis() –> class numeric::xyzVector<double> &

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover, trans_axis_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::rigid::RigidBodyDofSeqTransMover::trans_axis(class numeric::xyzVector<double>) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover, dof: pyrosetta.rosetta.core.conformation.symmetry.SymDof, rb_jump_in: int, step_size: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover) -> 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.rigid.RigidBodyDofTransMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyDofTransMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

last_slide_good(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover) → bool¶: C++: protocols::rigid::RigidBodyDofTransMover::last_slide_good() –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::show(class std::basic_ostream<char> &) const –> void

step_size(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover, step_size_in: float) → None¶: C++: protocols::rigid::RigidBodyDofTransMover::step_size(double) –> void

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

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

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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_axis(*args, **kwargs)¶

Overloaded function.

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::rigid::RigidBodyDofTransMover::trans_axis() –> class numeric::xyzVector<double> &

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover, trans_axis_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::rigid::RigidBodyDofTransMover::trans_axis(class numeric::xyzVector<double>) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyMover¶

Bases: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

Rigid-body random translate/rotate around centroid of downstream side of a jump.

We operate on a single jump rather than e.g. a randomly selected jump from the mobile jumps in a MoveMap. If you want a random choice among jumps, put multiple RigidBodyMovers into a RandomMover (which will give you more control, anyway).

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, arg0: int) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rb_jump_in: int, dir_in: pyrosetta.rosetta.protocols.rigid.Direction) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> 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.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

This Mover does a perturbation defined by the rotational and translational magnitudes.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, arg0: int, arg1: float, arg2: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, arg0: int, arg1: float, arg2: float, arg3: pyrosetta.rosetta.protocols.rigid.Partner) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, rb_jump_in: int, rot_mag_in: float, trans_mag_in: float, partner_in: pyrosetta.rosetta.protocols.rigid.Partner, interface_in: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, rb_jump_in: int, rot_mag_in: float, trans_mag_in: float, partner_in: pyrosetta.rosetta.protocols.rigid.Partner, ok_for_centroid_calculation: pyrosetta.rosetta.utility.vector1_bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: pyrosetta.rosetta.core.kinematics.MoveMap, arg2: float, arg3: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: pyrosetta.rosetta.core.kinematics.MoveMap, arg2: float, arg3: float, arg4: pyrosetta.rosetta.protocols.rigid.Partner) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, pose_in: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, rot_mag_in: float, trans_mag_in: float, partner_in: pyrosetta.rosetta.protocols.rigid.Partner, interface_in: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, arg0: float, arg1: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, arg0: float, arg1: float, arg2: pyrosetta.rosetta.protocols.rigid.Partner) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, rot_mag_in: float, trans_mag_in: float, partner_in: pyrosetta.rosetta.protocols.rigid.Partner, interface_in: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover) -> 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__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover) → str¶

__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.rigid.RigidBodyPerturbMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyPerturbMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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.rigid.RigidBodyPerturbMover) → str¶: C++: protocols::rigid::RigidBodyPerturbMover::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_rot_mag(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover) → float¶: C++: protocols::rigid::RigidBodyPerturbMover::get_rot_mag() const –> double

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_trans_mag(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover) → float¶: C++: protocols::rigid::RigidBodyPerturbMover::get_trans_mag() const –> double

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, : pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyPerturbMover::rot_center(const class numeric::xyzVector<double> &) –> void

rot_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyPerturbMover::rot_magnitude(const double) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyPerturbMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyPerturbMover::trans_magnitude(const double) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

does a perturbation defined by the rotational and translational magnitudes without setting up the center Can be defined through a move map or with rb_jump Defining through a movemap with multiple jumps leads to a random jump being chosen at apply time, NOT at construction time! This is done to simplify docking with more than one active jump.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover, rb_jump_in: int, rot_mag_in: float, trans_mag_in: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover, pose_in: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, rot_mag_in: float, trans_mag_in: float, dir_in: pyrosetta.rosetta.protocols.rigid.Direction) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover) -> 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).

add_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover, : int) → None¶: C++: protocols::rigid::RigidBodyPerturbNoCenterMover::add_jump(unsigned long) –> void

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

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

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

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

clear_info is called by jd2 before calling apply

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

clear_jumps(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover) → None¶: C++: protocols::rigid::RigidBodyPerturbNoCenterMover::clear_jumps() –> void

clone(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::rigid::RigidBodyPerturbNoCenterMover::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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

mover_name() → str¶: C++: protocols::rigid::RigidBodyPerturbNoCenterMover::mover_name() –> std::string

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::rigid::RigidBodyPerturbNoCenterMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> void

rot_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyPerturbNoCenterMover::rot_magnitude(const double) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_magnitude(self: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover, magnitude: float) → None¶: C++: protocols::rigid::RigidBodyPerturbNoCenterMover::trans_magnitude(const double) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

A Mover that spins about a random 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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover, rb_jump_in: int) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover) -> 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.rigid.RigidBodySpinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodySpinMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::rigid::RigidBodySpinMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::show(class std::basic_ostream<char> &) const –> void

spin_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover, spin_axis_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::rigid::RigidBodySpinMover::spin_axis(class numeric::xyzVector<double>) –> void

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

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

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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

A Mover that tilts around the spin 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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover, rb_jump_in: int, tilt1_mag_in: float, tilt2_mag_in: float, tilt1_center_in: int, tilt2_center_in: int) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover) -> 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.rigid.RigidBodyTiltMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyTiltMover::apply(class core::pose::Pose &) –> void

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

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

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

mover_name() → str¶: C++: protocols::rigid::RigidBodyTiltMover::mover_name() –> std::string

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::rigid::RigidBodyTiltMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::show(class std::basic_ostream<char> &) const –> void

spin_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover, spin_axis_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::rigid::RigidBodyTiltMover::spin_axis(const class numeric::xyzVector<double> &) –> void

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

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

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

tilt1_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover, tilt1_center_in: int) → None¶: C++: protocols::rigid::RigidBodyTiltMover::tilt1_center(const unsigned long) –> void

tilt1_mag(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover, tilt1_mag_in: float) → None¶: C++: protocols::rigid::RigidBodyTiltMover::tilt1_mag(const double) –> void

tilt2_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover, tilt2_center_in: int) → None¶: C++: protocols::rigid::RigidBodyTiltMover::tilt2_center(const unsigned long) –> void

tilt2_mag(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover, tilt2_mag_in: float) → None¶: C++: protocols::rigid::RigidBodyTiltMover::tilt2_mag(const double) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

This Mover translate down an 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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, vary_stepsize: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, arg0: pyrosetta.rosetta.core.pose.Pose) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: int) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, pose_in: pyrosetta.rosetta.core.pose.Pose, rb_jump_in: int, vary_stepsize: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t, arg1: int) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, trans_axis: pyrosetta.rosetta.numeric.xyzVector_double_t, rb_jump_in: int, vary_stepsize: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, arg0: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover) -> 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.rigid.RigidBodyTransMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RigidBodyTransMover::apply(class core::pose::Pose &) –> void

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

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

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

mover_name() → str¶: C++: protocols::rigid::RigidBodyTransMover::mover_name() –> std::string

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::rigid::RigidBodyTransMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::show(class std::basic_ostream<char> &) const –> void

step_size(*args, **kwargs)¶

Overloaded function.

step_size(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, step_size_in: float) -> None

C++: protocols::rigid::RigidBodyTransMover::step_size(double) –> void

step_size(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover) -> float

C++: protocols::rigid::RigidBodyTransMover::step_size() –> double

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

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

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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

trans_axis(*args, **kwargs)¶

Overloaded function.

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::rigid::RigidBodyTransMover::trans_axis() –> class numeric::xyzVector<double> &

trans_axis(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, trans_axis_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::rigid::RigidBodyTransMover::trans_axis(class numeric::xyzVector<double>) –> void

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

vary_stepsize(self: pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover, vary: bool) → None¶: C++: protocols::rigid::RigidBodyTransMover::vary_stepsize(bool) –> void

class pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover rotates a jump transform. Its original use was to rotate a freely rotateable zinc-histidine bond as emulated by an atom-to-atom fixed-length jump. It recalculates the Stubs for the jump and applies the new jump, resulting in an N degree rotation of one partner about the axis between the histidine nitrogen and the zinc. It will work for any jump but is intended for atom-atom jumps (not residue-residue jumps). It will choose an angle from the uniform random distribution bounded by inputs (defaults to (-180,180]); if you want a particular value then set the limits equal.

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover, rb_jump_num: int) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover, rb_jump_num: int, upper: float, lower: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover, rb_jump_num: int, angle: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover, arg0: pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover) -> 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.rigid.RotateJumpAxisMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::RotateJumpAxisMover::apply(class core::pose::Pose &) –> void

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

fpd

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

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.rigid.RotateJumpAxisMover) → str¶: C++: protocols::rigid::RotateJumpAxisMover::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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.

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

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

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.rigid.UniformSphereTransMover¶

Bases: pyrosetta.rosetta.protocols.rigid.RigidBodyMover

Rigid-body move that evenly samples the space within a sphere

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover, rb_jump_in: int, step_size_in: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover, arg0: pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover) -> 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.rigid.UniformSphereTransMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::UniformSphereTransMover::apply(class core::pose::Pose &) –> void

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

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

freeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::freeze() –> void

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

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

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

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

fpd

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

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

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

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

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

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

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

non-const accessor

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

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None¶

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool¶

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float¶

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t¶

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None¶

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → bool¶: C++: protocols::rigid::RigidBodyMover::preserve_detailed_balance() const –> bool

rb_jump(*args, **kwargs)¶

Overloaded function.

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) -> int

C++: protocols::rigid::RigidBodyMover::rb_jump() const –> int

rb_jump(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, jump_id: int) -> None

C++: protocols::rigid::RigidBodyMover::rb_jump(int) –> 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

rot_center(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, rot_center_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Manual override of rotation center.

C++: protocols::rigid::RigidBodyMover::rot_center(const class numeric::xyzVector<double> &) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None¶

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, : bool) → None¶

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

C++: protocols::rigid::RigidBodyMover::set_preserve_detailed_balance(bool) –> 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.

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

C++: protocols::rigid::RigidBodyMover::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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range¶

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::rigid::RigidBodyMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

unfreeze(self: pyrosetta.rosetta.protocols.rigid.RigidBodyMover) → None¶: C++: protocols::rigid::RigidBodyMover::unfreeze() –> void

class pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

rotate the whole pose

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover, axis: pyrosetta.rosetta.numeric.xyzVector_double_t, center: pyrosetta.rosetta.numeric.xyzVector_double_t, alpha: float) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover, arg0: pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover) -> 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.rigid.WholeBodyRotationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::WholeBodyRotationMover::apply(class core::pose::Pose &) –> void

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

fpd

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

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.rigid.WholeBodyRotationMover) → str¶: C++: protocols::rigid::WholeBodyRotationMover::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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.

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

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

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.rigid.WholeBodyTranslationMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

translate the whole pose

__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.

__init__(self: pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover, trans_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None
__init__(self: pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover, arg0: pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover) -> 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.rigid.WholeBodyTranslationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rigid::WholeBodyTranslationMover::apply(class core::pose::Pose &) –> void

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

fpd

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

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.rigid.WholeBodyTranslationMover) → str¶: C++: protocols::rigid::WholeBodyTranslationMover::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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.

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

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

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.rigid.gaussian_jump_move(*args, **kwargs)¶

Overloaded function.

gaussian_jump_move(pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, translation_magnitude: float, rotation_magnitude: float) -> int
gaussian_jump_move(pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, translation_magnitude: float, rotation_magnitude: float, dir: int) -> int

C++: protocols::rigid::gaussian_jump_move(class core::pose::Pose &, const class core::kinematics::MoveMap &, const double, const double, const int) –> int

gaussian_jump_move(pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int, translation_magnitude: float, rotation_magnitude: float) -> None
gaussian_jump_move(pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int, translation_magnitude: float, rotation_magnitude: float, dir: int) -> None

C++: protocols::rigid::gaussian_jump_move(class core::pose::Pose &, const int, const double, const double, int) –> void