local_backbone_mover¶

Bindings for protocols::backbone_moves::local_backbone_mover namespace

class pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide¶

Bases: pybind11_builtins.pybind11_object

FreePeptide represents a free peptide

__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.backbone_moves.local_backbone_mover.FreePeptide, pose: pyrosetta.rosetta.core.pose.Pose, pivot1: int, pivot2: int) -> None
__init__(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, arg0: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) -> 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).

align(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → None¶

Align the stubs to the old stubs.

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::align() –> void

apply_to_pose(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the coordinates of the free peptide to a pose.

The internal coordinates from pivot1 - 1 to pivot2 + 1 will be apply to the pose. Torsions in the two gaps should be further reset to close the segment.

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::apply_to_pose(class core::pose::Pose &) –> void

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

c_n_bond(*args, **kwargs)¶

Overloaded function.

c_n_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the c_n_bond

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_bond(unsigned long) –> double

c_n_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the c_n_bond

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_bond(unsigned long, double) –> void

c_n_ca_angle(*args, **kwargs)¶

Overloaded function.

c_n_ca_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the c_n_ca_angle

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_ca_angle(unsigned long) –> double

c_n_ca_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the c_n_ca_angle

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::c_n_ca_angle(unsigned long, double) –> void

c_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Getter of the xyz coordinates of C

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::c_xyz(unsigned long) –> class numeric::xyzVector<double>

ca_c_bond(*args, **kwargs)¶

Overloaded function.

ca_c_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the ca_c_bond

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_bond(unsigned long) –> double

ca_c_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the ca_c_bond

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_bond(unsigned long, double) –> void

ca_c_n_angle(*args, **kwargs)¶

Overloaded function.

ca_c_n_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the ca_c_n_angle

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_n_angle(unsigned long) –> double

ca_c_n_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the ca_c_n_angle

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_c_n_angle(unsigned long, double) –> void

ca_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Getter of the xyz coordinates of CA

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::ca_xyz(unsigned long) –> class numeric::xyzVector<double>

clone(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide¶: C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::clone() const –> class std::shared_ptr<class protocols::backbone_moves::local_backbone_mover::FreePeptide>

n_ca_bond(*args, **kwargs)¶

Overloaded function.

n_ca_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the n_ca_bond

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_bond(unsigned long) –> double

n_ca_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the n_ca_bond

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_bond(unsigned long, double) –> void

n_ca_c_angle(*args, **kwargs)¶

Overloaded function.

n_ca_c_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the n_ca_c_angle

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_c_angle(unsigned long) –> double

n_ca_c_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the n_ca_c_angle

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::n_ca_c_angle(unsigned long, double) –> void

n_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Getter of the xyz coordinates of N

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::n_xyz(unsigned long) –> class numeric::xyzVector<double>

number_of_atoms(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → int¶

Total number of atoms

Only consider atoms in the free peptide, The N of the first residue and C of the last residue are excluded

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::number_of_atoms() –> unsigned long

number_of_residues(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → int¶

Total number of free peptide residues.

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::number_of_residues() –> unsigned long

omega(*args, **kwargs)¶

Overloaded function.

omega(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the omega

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::omega(unsigned long) –> double

omega(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the omega

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::omega(unsigned long, double) –> void

phi(*args, **kwargs)¶

Overloaded function.

phi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the phi

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::phi(unsigned long) –> double

phi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the phi

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::phi(unsigned long, double) –> void

pivot1(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → int¶

Getter of the first pivot

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot1() –> unsigned long

pivot2(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → int¶

Getter of the second pivot

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::pivot2() –> unsigned long

psi(*args, **kwargs)¶

Overloaded function.

psi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int) -> float

Getter of the psi

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::psi(unsigned long) –> double

psi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, seqpos: int, value: float) -> None

Setter of the psi

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::psi(unsigned long, double) –> void

rotate(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, M: pyrosetta.rosetta.numeric.xyzMatrix_double_t) → None¶

Rotate the free peptide by the rotation matrix M

The center of rotation is the CA atom of the first residue of the free peptide

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::rotate(class numeric::xyzMatrix<double>) –> void

translate(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide, v: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Translate the free peptide by the vector v

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::translate(class numeric::xyzVector<double>) –> void

update_xyz_coords(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → None¶

Update the xyz coordinates of the residues

C++: protocols::backbone_moves::local_backbone_mover::FreePeptide::update_xyz_coords() –> void

class pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser¶

Bases: pybind11_builtins.pybind11_object

GapCloser closes the gaps after moving the free peptide.

__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.backbone_moves.local_backbone_mover.GapCloser) -> None
__init__(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser, arg0: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser) -> 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_closure(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser, pose: pyrosetta.rosetta.core.pose.Pose, free_peptide: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → None¶

Apply closure to a pose

Exception will be raised if the closure problems haven’t been solved

C++: protocols::backbone_moves::local_backbone_mover::GapCloser::apply_closure(class core::pose::Pose &, class protocols::backbone_moves::local_backbone_mover::FreePeptide &) –> void

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

clone(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser) → pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser¶: C++: protocols::backbone_moves::local_backbone_mover::GapCloser::clone() const –> class std::shared_ptr<class protocols::backbone_moves::local_backbone_mover::GapCloser>

gap_solved(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser) → bool¶

Return true if the gap problem is solved

C++: protocols::backbone_moves::local_backbone_mover::GapCloser::gap_solved() –> bool

set_solution_picker(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser, solution_picker: protocols::backbone_moves::local_backbone_mover::gap_solution_pickers::GapSolutionPicker) → None¶

Set the solution picker

C++: protocols::backbone_moves::local_backbone_mover::GapCloser::set_solution_picker(class std::shared_ptr<class protocols::backbone_moves::local_backbone_mover::gap_solution_pickers::GapSolutionPicker>) –> void

solve_gaps(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser, free_peptide: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide) → None¶

Find solutions for the two gaps

C++: protocols::backbone_moves::local_backbone_mover::GapCloser::solve_gaps(class protocols::backbone_moves::local_backbone_mover::FreePeptide &) –> void

class pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

LocalBackboneMover moves a stretch of backbone locally.

__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.backbone_moves.local_backbone_mover.LocalBackboneMover) -> None
__init__(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover, arg0: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover) -> 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.backbone_moves.local_backbone_mover.LocalBackboneMover) → 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).

add_free_peptide_mover(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover, free_peptide_mover: protocols::backbone_moves::local_backbone_mover::free_peptide_movers::FreePeptideMover) → None¶

Add a free peptide mover

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::add_free_peptide_mover(class std::shared_ptr<class protocols::backbone_moves::local_backbone_mover::free_peptide_movers::FreePeptideMover>) –> void

apply(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::apply(class core::pose::Pose &) –> void

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

clear_free_peptide_movers(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover) → None¶

Clear all free peptide movers

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::clear_free_peptide_movers() –> void

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

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

clear_info is called by jd2 before calling apply

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

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

required in the context of the parser/scripting scheme

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::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.backbone_moves.local_backbone_mover.LocalBackboneMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::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.backbone_moves.local_backbone_mover.LocalBackboneMover) → str¶: C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::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

mover_name() → str¶: C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::mover_name() –> std::string

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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

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_free_peptide(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover, pose: pyrosetta.rosetta.core.pose.Pose, pivot1: int, pivot2: int) → None¶

Set the free peptide

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::set_free_peptide(class core::pose::Pose &, unsigned long, unsigned long) –> 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_max_trial_num(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover, max_trial_num: int) → None¶

Set the maximum number of move trials

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::set_max_trial_num(unsigned long) –> 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.backbone_moves.local_backbone_mover.LocalBackboneMover) -> None
show(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::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.backbone_moves.local_backbone_mover.Residue¶

Bases: pybind11_builtins.pybind11_object

Residue is a helper class for FreePeptide

__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.backbone_moves.local_backbone_mover.Residue, seqpos: int, n_ca_bond: float, ca_c_bond: float, c_n_bond: float, n_ca_c_angle: float, ca_c_n_angle: float, c_n_ca_angle: float, phi: float, psi: float, omega: float) -> None
__init__(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose) -> 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_to_pose(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::backbone_moves::local_backbone_mover::Residue::apply_to_pose(class core::pose::Pose &) –> void

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

c_n_bond(*args, **kwargs)¶

Overloaded function.

c_n_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, c_n_bond: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::c_n_bond(double) –> void

c_n_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::c_n_bond() –> double

c_n_ca_angle(*args, **kwargs)¶

Overloaded function.

c_n_ca_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, c_n_ca_angle: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::c_n_ca_angle(double) –> void

c_n_ca_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::c_n_ca_angle() –> double

c_xyz(*args, **kwargs)¶

Overloaded function.

c_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, c_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::c_xyz(class numeric::xyzVector<double>) –> void

c_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::backbone_moves::local_backbone_mover::Residue::c_xyz() –> class numeric::xyzVector<double>

ca_c_bond(*args, **kwargs)¶

Overloaded function.

ca_c_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, ca_c_bond: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::ca_c_bond(double) –> void

ca_c_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::ca_c_bond() –> double

ca_c_n_angle(*args, **kwargs)¶

Overloaded function.

ca_c_n_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, ca_c_n_angle: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::ca_c_n_angle(double) –> void

ca_c_n_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::ca_c_n_angle() –> double

ca_xyz(*args, **kwargs)¶

Overloaded function.

ca_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, ca_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::ca_xyz(class numeric::xyzVector<double>) –> void

ca_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::backbone_moves::local_backbone_mover::Residue::ca_xyz() –> class numeric::xyzVector<double>

n_ca_bond(*args, **kwargs)¶

Overloaded function.

n_ca_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, n_ca_bond: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::n_ca_bond(double) –> void

n_ca_bond(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::n_ca_bond() –> double

n_ca_c_angle(*args, **kwargs)¶

Overloaded function.

n_ca_c_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, n_ca_c_angle: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::n_ca_c_angle(double) –> void

n_ca_c_angle(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::n_ca_c_angle() –> double

n_xyz(*args, **kwargs)¶

Overloaded function.

n_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, n_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::n_xyz(class numeric::xyzVector<double>) –> void

n_xyz(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::backbone_moves::local_backbone_mover::Residue::n_xyz() –> class numeric::xyzVector<double>

omega(*args, **kwargs)¶

Overloaded function.

omega(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, omega: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::omega(double) –> void

omega(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::omega() –> double

phi(*args, **kwargs)¶

Overloaded function.

phi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, phi: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::phi(double) –> void

phi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::phi() –> double

psi(*args, **kwargs)¶

Overloaded function.

psi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, psi: float) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::psi(double) –> void

psi(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> float

C++: protocols::backbone_moves::local_backbone_mover::Residue::psi() –> double

seqpos(*args, **kwargs)¶

Overloaded function.

seqpos(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue, seqpos: int) -> None

C++: protocols::backbone_moves::local_backbone_mover::Residue::seqpos(unsigned long) –> void

seqpos(self: pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue) -> int

C++: protocols::backbone_moves::local_backbone_mover::Residue::seqpos() –> unsigned long

pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.xyz_from_internal_coords(atom1_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, atom2_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, atom3_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, phi: float, theta: float, d: float) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Get the coordinate of an atom given three: preceeding atoms and the torsion phi, angle theta and distance d. Note that phi and theta should be in radians.

C++: protocols::backbone_moves::local_backbone_mover::xyz_from_internal_coords(class numeric::xyzVector<double>, class numeric::xyzVector<double>, class numeric::xyzVector<double>, double, double, double) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.xyz_to_vec1(vec_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, vec1: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) → None¶

covert an xyzVector to a vector of 3 real numbers

C++: protocols::backbone_moves::local_backbone_mover::xyz_to_vec1(const class numeric::xyzVector<double> &, class utility::fixedsizearray1<double, 3> &) –> void