sidechain_moves

Bindings for protocols::simple_moves::sidechain_moves namespace

class pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover

Bases: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover, rotamer_library: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover, arg0: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover) -> 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.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply a sidechain move to a Pose object

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

C++: protocols::canonical_sampling::ThermodynamicMover::operator=(const class protocols::canonical_sampling::ThermodynamicMover &) –> class protocols::canonical_sampling::ThermodynamicMover &

build_rotamer_list(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, : pyrosetta.rosetta.core.conformation.Residue, filter: bool, : pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(const class core::conformation::Residue &, bool, class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> > &) const –> void

change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::change_chi_without_replacing_residue() const –> bool

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.simple_moves.sidechain_moves.JumpRotamerSidechainMover) → pyrosetta.rosetta.protocols.moves.Mover

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

compute_proposal_density(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover, new_residue: pyrosetta.rosetta.core.conformation.Residue, resnum: int, old_res_type: pyrosetta.rosetta.core.chemical.ResidueType, old_chi: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density(const class core::conformation::Residue &, const unsigned long, const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &) const –> double

compute_rotdensities(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, : pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData, old_chi: pyrosetta.rosetta.utility.vector1_double, new_chi: pyrosetta.rosetta.utility.vector1_double, within_rot_density: float) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_rotdensities(const class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, double &) const –> void

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

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.simple_moves.sidechain_moves.JumpRotamerSidechainMover) → str

C++: protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::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

have_mutated_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

return true if your last move has mutated residue — make sure the residue is replaced entirely

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::have_mutated_residue() const –> bool

idealize_sidechains(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

idealize sidechains that might be altered

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(class core::pose::Pose &) –> void

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 > > &

init_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

initialize the packer task if necessary

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::init_task(const class core::pose::Pose &) –> void

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

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.simple_moves.sidechain_moves.SidechainMoverBase) → float

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio() –> double

make_chi_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover, residue: pyrosetta.rosetta.core.conformation.Residue, old_chi: pyrosetta.rosetta.utility.vector1_double, new_chi: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::make_chi_move(const class core::conformation::Residue &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

make_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_move(class std::shared_ptr<class core::conformation::Residue>) –> class std::shared_ptr<class core::conformation::Residue>

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::simple_moves::sidechain_moves::JumpRotamerSidechainMover::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

packed_residues(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_unsigned_long

get the residues that can be changed by this mover

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::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

residue_packed(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_bool

get a vector indicating whether each residue can be packed

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::residue_packed() const –> const class utility::vector1<bool, class std::allocator<bool> > &

rotamer_library(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

get the rotamer library

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library() const –> const class core::pack::dunbrack::RotamerLibrary &

set_change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_change_chi_without_replacing_residue(bool) –> 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.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_preserve_detailed_balance(bool) –> void

set_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

set the task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

set the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, setting: float) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_temperature(double) –> void

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

suggest_residue_number(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, : pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(const class core::pose::Pose &) const –> unsigned long

task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.PackerTask

get the packer task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.TaskFactory

get the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover) → float

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::temperature() const –> 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.simple_moves.sidechain_moves.SidechainMoverBase, 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::simple_moves::sidechain_moves::SidechainMoverBase::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.

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

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

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

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

class pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover

Bases: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover, rotamer_library: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover, arg0: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover) -> 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.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply a sidechain move to a Pose object

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

C++: protocols::canonical_sampling::ThermodynamicMover::operator=(const class protocols::canonical_sampling::ThermodynamicMover &) –> class protocols::canonical_sampling::ThermodynamicMover &

change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::change_chi_without_replacing_residue() const –> bool

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.simple_moves.sidechain_moves.PerturbChiSidechainMover) → pyrosetta.rosetta.protocols.moves.Mover

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

compute_proposal_density(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.chemical.ResidueType, : pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::compute_proposal_density(const class core::conformation::Residue &, const unsigned long, const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &) const –> double

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

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.simple_moves.sidechain_moves.PerturbChiSidechainMover) → str

C++: protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::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

have_mutated_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

return true if your last move has mutated residue — make sure the residue is replaced entirely

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::have_mutated_residue() const –> bool

idealize_sidechains(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

idealize sidechains that might be altered

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(class core::pose::Pose &) –> void

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 > > &

init_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

initialize the packer task if necessary

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::init_task(const class core::pose::Pose &) –> void

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

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.simple_moves.sidechain_moves.SidechainMoverBase) → float

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio() –> double

make_chi_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover, residue: pyrosetta.rosetta.core.conformation.Residue, old_chi: pyrosetta.rosetta.utility.vector1_double, new_chi: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::make_chi_move(const class core::conformation::Residue &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

make_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_move(class std::shared_ptr<class core::conformation::Residue>) –> class std::shared_ptr<class core::conformation::Residue>

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::simple_moves::sidechain_moves::PerturbChiSidechainMover::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

packed_residues(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_unsigned_long

get the residues that can be changed by this mover

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::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

residue_packed(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_bool

get a vector indicating whether each residue can be packed

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::residue_packed() const –> const class utility::vector1<bool, class std::allocator<bool> > &

rotamer_library(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

get the rotamer library

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library() const –> const class core::pack::dunbrack::RotamerLibrary &

set_change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_change_chi_without_replacing_residue(bool) –> 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_gaussian(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover, setting: bool) → None

C++: protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::set_gaussian(bool) –> void

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

setter for poses contained for rms

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

set_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover, setting: float) → None

C++: protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::set_magnitude(double) –> 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.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_preserve_detailed_balance(bool) –> void

set_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

set the task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

set the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

suggest_residue_number(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, : pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(const class core::pose::Pose &) const –> unsigned long

task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.PackerTask

get the packer task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.TaskFactory

get the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

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.simple_moves.sidechain_moves.SidechainMoverBase, 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::simple_moves::sidechain_moves::SidechainMoverBase::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.

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

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

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

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

class pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover

Bases: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, rotamer_library: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, arg0: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover) -> 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.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply a sidechain move to a Pose object

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

C++: protocols::canonical_sampling::ThermodynamicMover::operator=(const class protocols::canonical_sampling::ThermodynamicMover &) –> class protocols::canonical_sampling::ThermodynamicMover &

build_rotamer_list(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, : pyrosetta.rosetta.core.conformation.Residue, filter: bool, : pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(const class core::conformation::Residue &, bool, class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> > &) const –> void

change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::change_chi_without_replacing_residue() const –> bool

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.simple_moves.sidechain_moves.PerturbRotamerSidechainMover) → pyrosetta.rosetta.protocols.moves.Mover

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

compute_proposal_density(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, new_residue: pyrosetta.rosetta.core.conformation.Residue, resnum: int, old_res_type: pyrosetta.rosetta.core.chemical.ResidueType, old_chi: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density(const class core::conformation::Residue &, const unsigned long, const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &) const –> double

compute_rotdensities(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, : pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData, old_chi: pyrosetta.rosetta.utility.vector1_double, new_chi: pyrosetta.rosetta.utility.vector1_double, within_rot_density: float) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_rotdensities(const class utility::vector1<class core::pack::dunbrack::DunbrackRotamerSampleData, class std::allocator<class core::pack::dunbrack::DunbrackRotamerSampleData> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, double &) const –> void

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

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.simple_moves.sidechain_moves.PerturbRotamerSidechainMover) → str

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::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

have_mutated_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

return true if your last move has mutated residue — make sure the residue is replaced entirely

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::have_mutated_residue() const –> bool

idealize_sidechains(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

idealize sidechains that might be altered

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(class core::pose::Pose &) –> void

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 > > &

init_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

initialize the packer task if necessary

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::init_task(const class core::pose::Pose &) –> void

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

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.simple_moves.sidechain_moves.SidechainMoverBase) → float

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio() –> double

make_chi_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, residue: pyrosetta.rosetta.core.conformation.Residue, old_chi: pyrosetta.rosetta.utility.vector1_double, new_chi: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::make_chi_move(const class core::conformation::Residue &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

make_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_move(class std::shared_ptr<class core::conformation::Residue>) –> class std::shared_ptr<class core::conformation::Residue>

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::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::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

packed_residues(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_unsigned_long

get the residues that can be changed by this mover

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::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

residue_packed(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_bool

get a vector indicating whether each residue can be packed

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::residue_packed() const –> const class utility::vector1<bool, class std::allocator<bool> > &

rotamer_library(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

get the rotamer library

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library() const –> const class core::pack::dunbrack::RotamerLibrary &

set_change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_change_chi_without_replacing_residue(bool) –> 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.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_preserve_detailed_balance(bool) –> void

set_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

set the task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

set the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover, setting: float) → None

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_temperature(double) –> void

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

suggest_residue_number(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, : pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(const class core::pose::Pose &) const –> unsigned long

task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.PackerTask

get the packer task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.TaskFactory

get the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover) → float

C++: protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::temperature() const –> 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.simple_moves.sidechain_moves.SidechainMoverBase, 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::simple_moves::sidechain_moves::SidechainMoverBase::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.

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

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

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

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

class pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A mover to change one chi angle

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover, arg0: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover) -> 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).

angle(*args, **kwargs)

Overloaded function.

1. angle(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover) -> float

C++: protocols::simple_moves::sidechain_moves::SetChiMover::angle() const –> double

2. angle(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover, a: float) -> None

C++: protocols::simple_moves::sidechain_moves::SetChiMover::angle(const double) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::sidechain_moves::SetChiMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover, : pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover) → pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover

C++: protocols::simple_moves::sidechain_moves::SetChiMover::operator=(const class protocols::simple_moves::sidechain_moves::SetChiMover &) –> class protocols::simple_moves::sidechain_moves::SetChiMover &

chinum(*args, **kwargs)

Overloaded function.

1. chinum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover) -> int

C++: protocols::simple_moves::sidechain_moves::SetChiMover::chinum() const –> unsigned long

2. chinum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover, c: int) -> None

C++: protocols::simple_moves::sidechain_moves::SetChiMover::chinum(const unsigned long) –> 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.simple_moves.sidechain_moves.SetChiMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::sidechain_moves::SetChiMover::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.simple_moves.sidechain_moves.SetChiMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::sidechain_moves::SetChiMover::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.simple_moves.sidechain_moves.SetChiMover) → str

C++: protocols::simple_moves::sidechain_moves::SetChiMover::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::simple_moves::sidechain_moves::SetChiMover::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::simple_moves::sidechain_moves::SetChiMover::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

resnum(*args, **kwargs)

Overloaded function.

1. resnum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover) -> int

C++: protocols::simple_moves::sidechain_moves::SetChiMover::resnum() const –> unsigned long

2. resnum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover, r: int) -> None

C++: protocols::simple_moves::sidechain_moves::SetChiMover::resnum(const unsigned long) –> void

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

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

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

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

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

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

setter for poses contained for rms

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

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

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

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

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover

Bases: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, rotamer_library: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, arg0: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) -> 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.simple_moves.sidechain_moves.SidechainMCMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply a sidechain move to a Pose object

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

C++: protocols::canonical_sampling::ThermodynamicMover::operator=(const class protocols::canonical_sampling::ThermodynamicMover &) –> class protocols::canonical_sampling::ThermodynamicMover &

change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMover::change_chi_without_replacing_residue() const –> bool

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.simple_moves.sidechain_moves.SidechainMCMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::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

fresh_instance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::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.simple_moves.sidechain_moves.SidechainMCMover) → str

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::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

idealize_sidechains(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

idealize sidechains that might be altered

C++: protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(class core::pose::Pose &) –> void

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 > > &

inherit_scorefxn_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → bool

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::inherit_scorefxn_temperature() const –> bool

init_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

initialize the packer task if necessary

C++: protocols::simple_moves::sidechain_moves::SidechainMover::init_task(const class core::pose::Pose &) –> void

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

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

is_multi_trial(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → bool

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::last_inner_score_delta_over_temperature() –> double

last_mutation(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether the last move mutated the residue

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_mutation() const –> bool

last_nchi(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → int

get the number of chi angles sampled in the last move

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_nchi() const –> unsigned long

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::last_proposal_density_ratio() –> double

last_uniform(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether the last move used uniform chi sampling

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_uniform() const –> bool

last_withinrot(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether the last move sampled within the same rotamer

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_withinrot() const –> bool

make_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::simple_moves::sidechain_moves::SidechainMover::make_move(class std::shared_ptr<class core::conformation::Residue>) –> class std::shared_ptr<class core::conformation::Residue>

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

mover_name() → str

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::mover_name() –> std::string

name() → str

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

next_resnum(*args, **kwargs)

Overloaded function.

1. next_resnum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) -> int

get the next residue to be changed, 0 means a random will be chosen

C++: protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum() const –> unsigned long

2. next_resnum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, resnum: int) -> None

set the next residue to be changed, 0 means a random will be chosen

C++: protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum(unsigned long) –> void

ntrials(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → int

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::ntrials() –> unsigned long

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

packed_residues(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

get the residues that can be changed by this mover

C++: protocols::simple_moves::sidechain_moves::SidechainMover::packed_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMover::preserve_detailed_balance() const –> bool

prob_random_pert_current(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMover::prob_random_pert_current() const –> double

prob_uniform(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

get the probability of uniformly sampling chi angles

C++: protocols::simple_moves::sidechain_moves::SidechainMover::prob_uniform() const –> double

prob_withinrot(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

get the probability of sampling within the same rotamer

C++: protocols::simple_moves::sidechain_moves::SidechainMover::prob_withinrot() const –> double

proposal_density(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, proposed_residue: pyrosetta.rosetta.core.conformation.Residue, proposed_resnum: int, initial_residue_type: pyrosetta.rosetta.core.chemical.ResidueType, initial_chi_angles: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(const class core::conformation::Residue &, const unsigned long, const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &) const –> double

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::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

residue_packed(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.utility.vector1_bool

get a vector indicating whether each residue can be packed

C++: protocols::simple_moves::sidechain_moves::SidechainMover::residue_packed() const –> const class utility::vector1<bool, class std::allocator<bool> > &

rotamer_library(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

get the rotamer library

C++: protocols::simple_moves::sidechain_moves::SidechainMover::rotamer_library() const –> const class core::pack::dunbrack::RotamerLibrary &

sampling_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMover::sampling_temperature() –> double

scorefunction(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::scorefunction() –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, change_chi_without_replacing_residue: bool) → None

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_change_chi_without_replacing_residue(const bool) –> 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_inherit_scorefxn_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, inherit_scorefxn_temperature: bool) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::set_inherit_scorefxn_temperature(bool) –> void

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

setter for poses contained for rms

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

set_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::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_ntrials(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, ntrial: int) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::set_ntrials(unsigned long) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, preserve_detailed_balance: bool) → None

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_preserve_detailed_balance(bool) –> void

set_prob_random_pert_current(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, prob_pert: float) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_random_pert_current(double) –> void

set_prob_uniform(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, prob_uniform: float) → None

set the probability of uniformly sampling chi angles

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_uniform(double) –> void

set_prob_withinrot(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, prob_withinrot: float) → None

set the probability of sampling within the same rotamer

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_withinrot(double) –> void

set_sampling_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, temp: float) → None

set temperature for bias sampling at dunbrack distribution

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_sampling_temperature(double) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::set_scorefunction(const class core::scoring::ScoreFunction &) –> void

set_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

set the task

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

set the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, temp: float) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::set_temperature(double) –> 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

setup(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::setup(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

show_counters(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::show_counters(class std::basic_ostream<char> &) –> void

task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.core.pack.task.PackerTask

get the packer task

C++: protocols::simple_moves::sidechain_moves::SidechainMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.core.pack.task.TaskFactory

get the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

task_initialized(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

C++: protocols::simple_moves::sidechain_moves::SidechainMover::task_initialized() –> bool

temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMCMover::temperature() –> double

test_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, : pyrosetta.rosetta.core.pose.Pose) → None

test the backrub move

C++: protocols::simple_moves::sidechain_moves::SidechainMover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, 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::simple_moves::sidechain_moves::SidechainMover::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.

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

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

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

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

update_type(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → None

update string describing the move type

C++: protocols::simple_moves::sidechain_moves::SidechainMover::update_type() –> void

class pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover

Bases: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, rotamer_library: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, arg0: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) -> 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.simple_moves.sidechain_moves.SidechainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply a sidechain move to a Pose object

C++: protocols::simple_moves::sidechain_moves::SidechainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

C++: protocols::canonical_sampling::ThermodynamicMover::operator=(const class protocols::canonical_sampling::ThermodynamicMover &) –> class protocols::canonical_sampling::ThermodynamicMover &

change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMover::change_chi_without_replacing_residue() const –> bool

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.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::sidechain_moves::SidechainMover::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

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.simple_moves.sidechain_moves.SidechainMover) → str

C++: protocols::simple_moves::sidechain_moves::SidechainMover::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

idealize_sidechains(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

idealize sidechains that might be altered

C++: protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(class core::pose::Pose &) –> void

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 > > &

init_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

initialize the packer task if necessary

C++: protocols::simple_moves::sidechain_moves::SidechainMover::init_task(const class core::pose::Pose &) –> void

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

C++: protocols::simple_moves::sidechain_moves::SidechainMover::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_mutation(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether the last move mutated the residue

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_mutation() const –> bool

last_nchi(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → int

get the number of chi angles sampled in the last move

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_nchi() const –> unsigned long

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_proposal_density_ratio() –> double

last_uniform(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether the last move used uniform chi sampling

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_uniform() const –> bool

last_withinrot(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether the last move sampled within the same rotamer

C++: protocols::simple_moves::sidechain_moves::SidechainMover::last_withinrot() const –> bool

make_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::simple_moves::sidechain_moves::SidechainMover::make_move(class std::shared_ptr<class core::conformation::Residue>) –> class std::shared_ptr<class core::conformation::Residue>

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::simple_moves::sidechain_moves::SidechainMover::mover_name() –> std::string

name() → str

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

next_resnum(*args, **kwargs)

Overloaded function.

1. next_resnum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) -> int

get the next residue to be changed, 0 means a random will be chosen

C++: protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum() const –> unsigned long

2. next_resnum(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, resnum: int) -> None

set the next residue to be changed, 0 means a random will be chosen

C++: protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum(unsigned long) –> void

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

packed_residues(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

get the residues that can be changed by this mover

C++: protocols::simple_moves::sidechain_moves::SidechainMover::packed_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMover::preserve_detailed_balance() const –> bool

prob_random_pert_current(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMover::prob_random_pert_current() const –> double

prob_uniform(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

get the probability of uniformly sampling chi angles

C++: protocols::simple_moves::sidechain_moves::SidechainMover::prob_uniform() const –> double

prob_withinrot(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

get the probability of sampling within the same rotamer

C++: protocols::simple_moves::sidechain_moves::SidechainMover::prob_withinrot() const –> double

proposal_density(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, proposed_residue: pyrosetta.rosetta.core.conformation.Residue, proposed_resnum: int, initial_residue_type: pyrosetta.rosetta.core.chemical.ResidueType, initial_chi_angles: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(const class core::conformation::Residue &, const unsigned long, const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &) const –> double

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMover::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

residue_packed(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.utility.vector1_bool

get a vector indicating whether each residue can be packed

C++: protocols::simple_moves::sidechain_moves::SidechainMover::residue_packed() const –> const class utility::vector1<bool, class std::allocator<bool> > &

rotamer_library(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

get the rotamer library

C++: protocols::simple_moves::sidechain_moves::SidechainMover::rotamer_library() const –> const class core::pack::dunbrack::RotamerLibrary &

sampling_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMover::sampling_temperature() –> double

set_change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, change_chi_without_replacing_residue: bool) → None

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_change_chi_without_replacing_residue(const bool) –> 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.simple_moves.sidechain_moves.SidechainMover, preserve_detailed_balance: bool) → None

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_preserve_detailed_balance(bool) –> void

set_prob_random_pert_current(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, prob_pert: float) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_random_pert_current(double) –> void

set_prob_uniform(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, prob_uniform: float) → None

set the probability of uniformly sampling chi angles

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_uniform(double) –> void

set_prob_withinrot(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, prob_withinrot: float) → None

set the probability of sampling within the same rotamer

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_withinrot(double) –> void

set_sampling_temperature(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, temp: float) → None

set temperature for bias sampling at dunbrack distribution

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_sampling_temperature(double) –> void

set_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

set the task

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

set the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMover::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.core.pack.task.PackerTask

get the packer task

C++: protocols::simple_moves::sidechain_moves::SidechainMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → pyrosetta.rosetta.core.pack.task.TaskFactory

get the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

task_initialized(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → bool

C++: protocols::simple_moves::sidechain_moves::SidechainMover::task_initialized() –> bool

test_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, : pyrosetta.rosetta.core.pose.Pose) → None

test the backrub move

C++: protocols::simple_moves::sidechain_moves::SidechainMover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover, 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::simple_moves::sidechain_moves::SidechainMover::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.

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

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

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

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

update_type(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover) → None

update string describing the move type

C++: protocols::simple_moves::sidechain_moves::SidechainMover::update_type() –> void

class pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase

Bases: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, rotamer_library: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, arg0: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) -> 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.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply a sidechain move to a Pose object

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, : pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

C++: protocols::canonical_sampling::ThermodynamicMover::operator=(const class protocols::canonical_sampling::ThermodynamicMover &) –> class protocols::canonical_sampling::ThermodynamicMover &

change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::change_chi_without_replacing_residue() const –> bool

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>

compute_proposal_density(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, new_residue: pyrosetta.rosetta.core.conformation.Residue, resnum: int, old_res_type: pyrosetta.rosetta.core.chemical.ResidueType, old_chi: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::compute_proposal_density(const class core::conformation::Residue &, const unsigned long, const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &) const –> double

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

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.simple_moves.sidechain_moves.SidechainMoverBase) → str

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::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

have_mutated_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

return true if your last move has mutated residue — make sure the residue is replaced entirely

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::have_mutated_residue() const –> bool

idealize_sidechains(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

idealize sidechains that might be altered

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(class core::pose::Pose &) –> void

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 > > &

init_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

initialize the packer task if necessary

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::init_task(const class core::pose::Pose &) –> void

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

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.simple_moves.sidechain_moves.SidechainMoverBase) → float

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio() –> double

make_chi_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, residue: pyrosetta.rosetta.core.conformation.Residue, old_chi: pyrosetta.rosetta.utility.vector1_double, new_chi: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_chi_move(const class core::conformation::Residue &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

make_move(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::make_move(class std::shared_ptr<class core::conformation::Residue>) –> class std::shared_ptr<class core::conformation::Residue>

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

packed_residues(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_unsigned_long

get the residues that can be changed by this mover

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::packed_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → bool

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance() const –> bool

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

residue_packed(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.utility.vector1_bool

get a vector indicating whether each residue can be packed

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::residue_packed() const –> const class utility::vector1<bool, class std::allocator<bool> > &

rotamer_library(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

get the rotamer library

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library() const –> const class core::pack::dunbrack::RotamerLibrary &

set_change_chi_without_replacing_residue(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_change_chi_without_replacing_residue(bool) –> 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.simple_moves.sidechain_moves.SidechainMoverBase, setting: bool) → None

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_preserve_detailed_balance(bool) –> void

set_task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

set the task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

set the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

suggest_residue_number(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase, : pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(const class core::pose::Pose &) const –> unsigned long

task(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.PackerTask

get the packer task

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase) → pyrosetta.rosetta.core.pack.task.TaskFactory

get the task factory

C++: protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

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.simple_moves.sidechain_moves.SidechainMoverBase, 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::simple_moves::sidechain_moves::SidechainMoverBase::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.

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

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

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

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