kinematic_closure¶

Bindings for protocols::kinematic_closure namespace

class pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover¶

Bases: ThermodynamicMover

Make a kinematic closure move that obeys detailed balance.

This class is very conceptually similar to KicMover, so check out its documentation for a general overview of the kinematic closure algorithm. Here I will just highlight some details associated with making a balanced version of the move. Detailed balance is a useful property, because it allows a Monte Carlo simulation to recapitulate ensembles with correct equilibrium populations (so long as sampling is good, of course). There are a two reasons why the standard KicMover algorithm does not obey detailed balance. The first is that the geometry of the closure move itself introduces some inherent bias which has to be explicitly canceled out. The second is that care needs to be taken to perturb the non-pivot torsions in a way that also obeys detailed balance, as well.

The add_perturber() method works much like it does in KicMover. The only conceptual difference is that when the added perturbers are used internally within apply(), perturbers::Perturber::perturb_with_balance() is called instead of perturbers::Perturber::perturb(). This makes it easy to make variants of the perturber algorithms which obey detailed balance. The set_pivot_picker() method is no different from the KicMover version.

add_perturber(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, perturber: protocols::kinematic_closure::perturbers::Perturber) → None¶

KicMover::add_perturber

C++: protocols::kinematic_closure::BalancedKicMover::add_perturber(class std::shared_ptr<class protocols::kinematic_closure::perturbers::Perturber>) –> void

apply(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

KicMover::apply

C++: protocols::kinematic_closure::BalancedKicMover::apply(class core::pose::Pose &) –> void

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

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.kinematic_closure.BalancedKicMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::kinematic_closure::BalancedKicMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

static complex_type_generator_for_balancedKIC_mover(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::kinematic_closure::BalancedKicMover::complex_type_generator_for_balancedKIC_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.kinematic_closure.BalancedKicMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::kinematic_closure::BalancedKicMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

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

fpd

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

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

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

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover) → str¶

KicMover::get_name

C++: protocols::kinematic_closure::BalancedKicMover::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_t¶

non-const accessor

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

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

Callback executed before any Monte Carlo trials are attempted.

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

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

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

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

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

static is_solution_trivial(problem: protocols::kinematic_closure::ClosureProblem, solution: protocols::kinematic_closure::ClosureSolution, unperturbed_solutions: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t, perturbed_solutions: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t) → bool¶

Return true if the given solution is the same as the input pose.: This allows for a more accurate reporting of Monte Carlo statistics.

C++: protocols::kinematic_closure::BalancedKicMover::is_solution_trivial(class std::shared_ptr<const class protocols::kinematic_closure::ClosureProblem>, class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, const class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > > &, const class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > > &) –> 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.kinematic_closure.BalancedKicMover) → float¶

Right now the proposal probabilities are balanced internally, so: this ratio will always be unity. This could change eventually, though.

C++: protocols::kinematic_closure::BalancedKicMover::last_proposal_density_ratio() –> double

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

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

being used internally.

is_multi_trial()

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

static mover_name() → str¶: C++: protocols::kinematic_closure::BalancedKicMover::mover_name() –> std::string

static 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

parse_my_tag(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::kinematic_closure::BalancedKicMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static pick_solution(unperturbed_solutions: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t, perturbed_solutions: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t) → protocols::kinematic_closure::ClosureSolution¶

Pick a solution in a way that cancels out the geometrical bias of: the kinematic closure algorithm.

C++: protocols::kinematic_closure::BalancedKicMover::pick_solution(const class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > > &, const class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > > &) –> class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover) → bool¶

Return true, because this mover always obeys detailed balance.

C++: protocols::kinematic_closure::BalancedKicMover::preserve_detailed_balance() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::kinematic_closure::BalancedKicMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

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

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

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

residue_selector(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Get the residue selector that this mover uses

C++: protocols::kinematic_closure::BalancedKicMover::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

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

setter for poses contained for rms

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

set_loop(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, loop: pyrosetta.rosetta.protocols.loops.Loop) → None¶

KicMover::set_loop

C++: protocols::kinematic_closure::BalancedKicMover::set_loop(const class protocols::loops::Loop &) –> void

set_loops(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, loops: pyrosetta.rosetta.protocols.loops.Loops) → None¶

KicMover::set_loops

C++: protocols::kinematic_closure::BalancedKicMover::set_loops(const class std::shared_ptr<class protocols::loops::Loops>) –> 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_pivot_picker(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, picker: protocols::kinematic_closure::pivot_pickers::PivotPicker) → None¶

KicMover::set_pivot_picker

C++: protocols::kinematic_closure::BalancedKicMover::set_pivot_picker(class std::shared_ptr<class protocols::kinematic_closure::pivot_pickers::PivotPicker>) –> void

set_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, : bool) → None¶

This mover always obeys detailed balance, so this is a no-op.

C++: protocols::kinematic_closure::BalancedKicMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the residue_selector to use

C++: protocols::kinematic_closure::BalancedKicMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

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

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

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

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

Indicate that each torsion in the loop may take on any value.

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator) → str¶: C++: protocols::kinematic_closure::BalancedKicMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::kinematic_closure::BalancedKicMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList¶

Bases: pybind11_object

Iterate sequentially through two solution lists.

This functionality is very important to the balanced solution picker. While it could be done without this class (basically by doubling the number of for-loops) I think that this class meaningfully improves the readability of the code.

class Iterator¶: Bases: pybind11_object

back(self: pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList) → pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution¶: C++: protocols::kinematic_closure::ChainedSolutionList::back() –> const class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>

begin(self: pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList) → protocols::kinematic_closure::ChainedSolutionList::Iterator¶: C++: protocols::kinematic_closure::ChainedSolutionList::begin() –> class protocols::kinematic_closure::ChainedSolutionList::Iterator

empty(self: pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList) → bool¶: C++: protocols::kinematic_closure::ChainedSolutionList::empty() –> bool

end(self: pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList) → protocols::kinematic_closure::ChainedSolutionList::Iterator¶: C++: protocols::kinematic_closure::ChainedSolutionList::end() –> class protocols::kinematic_closure::ChainedSolutionList::Iterator

front(self: pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList) → pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution¶: C++: protocols::kinematic_closure::ChainedSolutionList::front() –> const class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>

not_empty(self: pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList) → bool¶: C++: protocols::kinematic_closure::ChainedSolutionList::not_empty() –> bool

size(self: pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList) → bool¶: C++: protocols::kinematic_closure::ChainedSolutionList::size() –> bool

class pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem¶

Bases: pybind11_object

Represent and solve a kinematic closure problem.

A number of parameters are needed to define a kinematic closure problem. These parameters include a region of the protein backbone, a set of pivot residues, and a new set of torsion angles for the nonpivot residues. All of this can be specified using the frame() and methods. Once that has been done, the solve() method can be called to return the complete set of backbone conformations consistent with the given parameters. These conformations are represented by the ClosureSolution class. The restore() method can be used to undo a solution once it has been applied, which is useful in some Monte Carlo schemes.

class Memento¶

Bases: pybind11_object

Save the current state of the closure problem. This is meant to facilitate undoing rejected perturbations when necessary.

restore(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem.Memento) → None¶: C++: protocols::kinematic_closure::ClosureProblem::Memento::restore() const –> void

c_n(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int) → float¶

Return the current value of the given C-N bond length.

C++: protocols::kinematic_closure::ClosureProblem::c_n(unsigned long) const –> double

c_n_ca(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → float¶

Return the current value of the given C-N-CA bond angle.

C++: protocols::kinematic_closure::ClosureProblem::c_n_ca(unsigned long, enum numeric::conversions::AngleUnit) const –> double

ca_c(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int) → float¶

Return the current value of the given CA-C bond length.

C++: protocols::kinematic_closure::ClosureProblem::ca_c(unsigned long) const –> double

ca_c_n(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → float¶

Return the current value of the given CA-C-N bond angle.

C++: protocols::kinematic_closure::ClosureProblem::ca_c_n(unsigned long, enum numeric::conversions::AngleUnit) const –> double

cut_residue(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → int¶

Return the index of the second pivot residue.

C++: protocols::kinematic_closure::ClosureProblem::cut_residue() const –> unsigned long

first_residue(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → int¶

Return the index of the first pivot residue.

C++: protocols::kinematic_closure::ClosureProblem::first_residue() const –> unsigned long

frame(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop, pivot_picker: protocols::kinematic_closure::pivot_pickers::PivotPicker) → None¶

Choose pivots and copy coordinate information into the problem.

C++: protocols::kinematic_closure::ClosureProblem::frame(const class core::pose::Pose &, const class protocols::loops::Loop &, class std::shared_ptr<class protocols::kinematic_closure::pivot_pickers::PivotPicker>) –> void

is_nonpivot_residue(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int) → bool¶

Return true if the given residue is not a pivot.

C++: protocols::kinematic_closure::ClosureProblem::is_nonpivot_residue(unsigned long) const –> bool

is_pivot_residue(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int) → bool¶

Return true if the given residue is a pivot.

C++: protocols::kinematic_closure::ClosureProblem::is_pivot_residue(unsigned long) const –> bool

last_residue(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → int¶

Return the index of the third pivot residue.

C++: protocols::kinematic_closure::ClosureProblem::last_residue() const –> unsigned long

n_ca(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int) → float¶

Return the current value of the given N-CA bond length.

C++: protocols::kinematic_closure::ClosureProblem::n_ca(unsigned long) const –> double

n_ca_c(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → float¶

Return the current value of the given N-CA-C bond angle.

C++: protocols::kinematic_closure::ClosureProblem::n_ca_c(unsigned long, enum numeric::conversions::AngleUnit) const –> double

nonpivot_residues(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Return the indices of every nonpivot residue in the loop.

C++: protocols::kinematic_closure::ClosureProblem::nonpivot_residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

num_atoms(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → int¶

Return the number of atoms in the loop.

C++: protocols::kinematic_closure::ClosureProblem::num_atoms() const –> unsigned long

num_residues(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → int¶

Return the number of residues in the loop.

C++: protocols::kinematic_closure::ClosureProblem::num_residues() const –> unsigned long

omega(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → float¶

Return the current value of the given omega angle.

C++: protocols::kinematic_closure::ClosureProblem::omega(unsigned long, enum numeric::conversions::AngleUnit) const –> double

perturb_angles(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_double¶

Provide non-const access to the raw bond angle list.

C++: protocols::kinematic_closure::ClosureProblem::perturb_angles() –> class utility::vector1<double, class std::allocator<double> > &

perturb_c_n(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float) → None¶

Perturb the C-N bond length in the given residue.

C++: protocols::kinematic_closure::ClosureProblem::perturb_c_n(unsigned long, double) –> void

perturb_c_n_ca(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → None¶

Perturb the C-N-CA bond angle in the given residue.

C++: protocols::kinematic_closure::ClosureProblem::perturb_c_n_ca(unsigned long, double, enum numeric::conversions::AngleUnit) –> void

perturb_ca_c(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float) → None¶

Perturb the CA-C bond length in the given residue.

C++: protocols::kinematic_closure::ClosureProblem::perturb_ca_c(unsigned long, double) –> void

perturb_ca_c_n(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → None¶

Perturb the CA-C-N bond angle in the given residue.

C++: protocols::kinematic_closure::ClosureProblem::perturb_ca_c_n(unsigned long, double, enum numeric::conversions::AngleUnit) –> void

perturb_lengths(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_double¶

Provide non-const access to the raw bond length list.

C++: protocols::kinematic_closure::ClosureProblem::perturb_lengths() –> class utility::vector1<double, class std::allocator<double> > &

perturb_n_ca(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float) → None¶

Perturb the N-CA bond length in the given residue.

C++: protocols::kinematic_closure::ClosureProblem::perturb_n_ca(unsigned long, double) –> void

perturb_n_ca_c(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → None¶

Perturb the N-CA-C bond angle in the given residue.

C++: protocols::kinematic_closure::ClosureProblem::perturb_n_ca_c(unsigned long, double, enum numeric::conversions::AngleUnit) –> void

perturb_omega(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → None¶

Perturb the given omega angle.

C++: protocols::kinematic_closure::ClosureProblem::perturb_omega(unsigned long, double, enum numeric::conversions::AngleUnit) –> void

perturb_phi(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → None¶

Perturb the given phi angle.

C++: protocols::kinematic_closure::ClosureProblem::perturb_phi(unsigned long, double, enum numeric::conversions::AngleUnit) –> void

perturb_psi(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, value: float, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → None¶

Perturb the given psi angle.

C++: protocols::kinematic_closure::ClosureProblem::perturb_psi(unsigned long, double, enum numeric::conversions::AngleUnit) –> void

perturb_torsions(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_double¶

Provide non-const access to the raw torsion angle list.

C++: protocols::kinematic_closure::ClosureProblem::perturb_torsions() –> class utility::vector1<double, class std::allocator<double> > &

perturbed_sequence(*args, **kwargs)¶

Overloaded function.

perturbed_sequence(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, values: pyrosetta.rosetta.utility.vector1_std_string) -> None

Set AA sequence from left pivot to the right pivot (including the pivots)

C++: protocols::kinematic_closure::ClosureProblem::perturbed_sequence(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

perturbed_sequence(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) -> pyrosetta.rosetta.utility.vector1_std_string

Get perturbed AA sequence from left pivot to the right pivot (including the pivots)

C++: protocols::kinematic_closure::ClosureProblem::perturbed_sequence() const –> class utility::vector1<std::string, class std::allocator<std::string > >

phi(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → float¶

Return the current value of the given phi angle.

C++: protocols::kinematic_closure::ClosureProblem::phi(unsigned long, enum numeric::conversions::AngleUnit) const –> double

pivot_atoms(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Return the indices of all three pivot atoms.

C++: protocols::kinematic_closure::ClosureProblem::pivot_atoms() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pivot_loop(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.protocols.loops.Loop¶

Return a loop specifying the three pivot residues.

C++: protocols::kinematic_closure::ClosureProblem::pivot_loop() const –> class protocols::loops::Loop

pivot_residues(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Return the indices of all three pivot residues.

C++: protocols::kinematic_closure::ClosureProblem::pivot_residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

psi(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, residue: int, unit: pyrosetta.rosetta.numeric.conversions.AngleUnit) → float¶

Return the current value of the given psi angle.

C++: protocols::kinematic_closure::ClosureProblem::psi(unsigned long, enum numeric::conversions::AngleUnit) const –> double

residues(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Return the indices of every residue in the loop.

C++: protocols::kinematic_closure::ClosureProblem::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

restore(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Undo any changes made to the pose during the last move.

C++: protocols::kinematic_closure::ClosureProblem::restore(class core::pose::Pose &) const –> void

sequence_mutated(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → bool¶

Return if mutations have been made to the sequence

C++: protocols::kinematic_closure::ClosureProblem::sequence_mutated() const –> bool

solve(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t¶

Return every possible solution to this problem.

C++: protocols::kinematic_closure::ClosureProblem::solve() const –> class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > >

unperturbed_sequence(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → pyrosetta.rosetta.utility.vector1_std_string¶

Get unperturbed AA sequence from left pivot to the right pivot (including the pivots)

C++: protocols::kinematic_closure::ClosureProblem::unperturbed_sequence() const –> class utility::vector1<std::string, class std::allocator<std::string > >

class pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution¶

Bases: pybind11_object

Represent a single solution to a kinematic closure problem.

The ClosureSolution class represents the solutions returned by ClosureProblem.solve(). The most important methods of this class are apply() and apply_if_reasonable(). The former unconditionally applies the solution to the given pose, while the latter does so only if the solution passes a rama and bump check.

apply(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply this solution to the given pose.

C++: protocols::kinematic_closure::ClosureSolution::apply(class core::pose::Pose &) const –> void

apply_if_reasonable(*args, **kwargs)¶

Overloaded function.

apply_if_reasonable(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
apply_if_reasonable(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution, pose: pyrosetta.rosetta.core.pose.Pose, rama_on: bool) -> bool
apply_if_reasonable(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution, pose: pyrosetta.rosetta.core.pose.Pose, rama_on: bool, bump_on: bool) -> bool
apply_if_reasonable(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution, pose: pyrosetta.rosetta.core.pose.Pose, rama_on: bool, bump_on: bool, be_lenient: bool) -> bool

If this solution passes rama and bump checks, apply it to the: given pose. Return whether or not the filters were passed.

C++: protocols::kinematic_closure::ClosureSolution::apply_if_reasonable(class core::pose::Pose &, bool, bool, bool) const –> bool

get_distance(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → float¶

@ brief Return a distance metric indicating how similar this solution: is to the given problem.

C++: protocols::kinematic_closure::ClosureSolution::get_distance(const class protocols::kinematic_closure::ClosureProblem *) const –> double

get_index(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution) → int¶

Return a unique number identifying this solution.

C++: protocols::kinematic_closure::ClosureSolution::get_index() const –> unsigned long

get_jacobian(self: pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution) → float¶

Return the Jacobian for this solution.

C++: protocols::kinematic_closure::ClosureSolution::get_jacobian() const –> double

class pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters¶

Bases: pybind11_object

Catalog ideal geometries for a number of different lengths, angles, and torsions.

This class should definitely not exist. It is basically just a bunch of magic numbers that must exist somewhere in the database already. Unfortunately, I can’t find them and so we’re stuck with this nonsense.

class pyrosetta.rosetta.protocols.kinematic_closure.KicMover¶

Bases: LoopMover

Find a new backbone conformation for some region of a protein.

The first step in the kinematic closure algorithm is to pick a loop and three pivot residues. Any residues in the loop that are not pivots are called non-pivots. The non-pivot backbone torsions are used to make new conformations, while the pivot torsions are used to ensure that the backbone stays closed. Use set_loops() to specify loops to sample. Use set_pivot_picker() to specify how the pivots should be chosen. Use add_perturber() to specify how the non-pivots should be sampled. By default, the algorithm will pick pivots randomly within the region being sampled and will sample the non-pivot torsions from a rama distribution.

Given a set of pivot residues and nonpivot torsion angles, the algorithm will find up to 16 possible solutions. The set_solution_picker() method allows you to control which solution, if any, is picked. By default, the first solution found which passes both a rama and a bump check is used.

The default kinematic closure algorithm samples both pivot and nonpivot torsions from a rama distribution. Because this algorithm is often used in situations where the score function also contains a rama term, the rama bias is usually double-counted. This is bad, because it means that backbone torsions are normally sampled too narrowly. There are two proper ways to deal with this, but they both have drawbacks. The first would be to sample from a uniform distribution and to let the score function take care of preferring angles that fit the rama distribution. Unfortunately, this would be much less efficient than the current approach, primarily because the rama check is fast and filters out a lot of bad solutions. The second approach would be to sample from a rama distribution and to remove the rama term from the score function. This would be even more efficient than the current approach, but it would be prone to bugs because other parts of the code wouldn’t expect the score function to be changing on every invocation of KIC.

Once the algorithm has been setup using the helper methods described above, apply() can be called to actually sample a new backbone conformation.

add_perturber(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover, perturber: protocols::kinematic_closure::perturbers::Perturber) → None¶

Specify how the non-pivot torsions should be sampled.

C++: protocols::kinematic_closure::KicMover::add_perturber(class std::shared_ptr<class protocols::kinematic_closure::perturbers::Perturber>) –> void

apply(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sample the pose in the regions specified by get_loops().

The parent class apply() method automatically sets up a fold tree (if necessary) and keeps track of whether or not the move succeeded. Child classes should reimplement do_apply() instead of this method.

C++: protocols::loop_modeling::LoopMover::apply(class core::pose::Pose &) –> void

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

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

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

clear_info is called by jd2 before calling apply

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

clear_perturbers(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover) → None¶

Forget any perturbers that had been previously added.

C++: protocols::kinematic_closure::KicMover::clear_perturbers() –> void

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

Return a clone of the Mover object.

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

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

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition, ct_gen: utility::tag::XMLSchemaComplexTypeGenerator, subelements: utility::tag::XMLSchemaSimpleSubelementList) → None¶: C++: protocols::loop_modeling::LoopMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &, class utility::tag::XMLSchemaComplexTypeGenerator &, class utility::tag::XMLSchemaSimpleSubelementList &) –> 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.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_children_names(*args, **kwargs)¶

Overloaded function.

get_children_names(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover, names: pyrosetta.rosetta.utility.vector1_std_string) -> None
get_children_names(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover, names: pyrosetta.rosetta.utility.vector1_std_string, indent: str) -> None

LoopMover::get_children_names

C++: protocols::kinematic_closure::KicMover::get_children_names(class utility::vector1<std::string, class std::allocator<std::string > > &, std::string) const –> void

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_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, index: int) → pyrosetta.rosetta.protocols.loops.Loop¶

Return the specified loop.

C++: protocols::loop_modeling::LoopMover::get_loop(unsigned long) const –> const class protocols::loops::Loop &

get_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loops.Loops¶

Return the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::get_loops() –> class std::shared_ptr<class protocols::loops::Loops>

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover) → str¶: C++: protocols::kinematic_closure::KicMover::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_pivot_picker(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover) → protocols::kinematic_closure::pivot_pickers::PivotPicker¶

Return the PivotPicker being used by this mover.

C++: protocols::kinematic_closure::KicMover::get_pivot_picker() –> class std::shared_ptr<class protocols::kinematic_closure::pivot_pickers::PivotPicker>

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_solution_picker(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover) → protocols::kinematic_closure::solution_pickers::SolutionPicker¶

Return the SolutionPicker being used by this mover.

C++: protocols::kinematic_closure::KicMover::get_solution_picker() –> class std::shared_ptr<class protocols::kinematic_closure::solution_pickers::SolutionPicker>

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_t¶

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::kinematic_closure::KicMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Configure from a RosettaScripts tag.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::kinematic_closure::KicMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

request_fold_tree(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover) → pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest¶

LoopMover::request_fold_tree

C++: protocols::kinematic_closure::KicMover::request_fold_tree() const –> enum protocols::loop_modeling::FoldTreeRequest

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

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

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

setter for poses contained for rms

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

set_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loop: pyrosetta.rosetta.protocols.loops.Loop) → None¶

Set the loop to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loop(const class protocols::loops::Loop &) –> void

set_loops(*args, **kwargs)¶

Overloaded function.

set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(const class protocols::loops::Loops &) –> 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_pivot_picker(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover, picker: protocols::kinematic_closure::pivot_pickers::PivotPicker) → None¶

Specify how the pivot residues should be chosen.

C++: protocols::kinematic_closure::KicMover::set_pivot_picker(class std::shared_ptr<class protocols::kinematic_closure::pivot_pickers::PivotPicker>) –> void

set_solution_picker(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMover, picker: protocols::kinematic_closure::solution_pickers::SolutionPicker) → None¶

Specify how a solution should be chosen.

C++: protocols::kinematic_closure::KicMover::set_solution_picker(class std::shared_ptr<class protocols::kinematic_closure::solution_pickers::SolutionPicker>) –> void

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

Set the ‘type’ string

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

static setup_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops, request: pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest) → None¶

Setup the given pose with a fold tree that is compatible with the: given loops and requests.

C++: protocols::loop_modeling::LoopMover::setup_fold_tree(class core::pose::Pose &, class std::shared_ptr<const class protocols::loops::Loops>, enum protocols::loop_modeling::FoldTreeRequest) –> void

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

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

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

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

trust_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → None¶

Promise that the calling code will setup a fold tree compatible: with request_fold_tree(). If this method is not called, this mover will setup a fold tree on its own every time apply() is called.

C++: protocols::loop_modeling::LoopMover::trust_fold_tree() –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

was_successful(*args, **kwargs)¶

Overloaded function.

was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) -> bool

Return true if the previous move was successful.

C++: protocols::loop_modeling::LoopMover::was_successful() const –> bool

was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, value: bool) -> None

Set the success status of a loop mover

C++: protocols::loop_modeling::LoopMover::was_successful(bool) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator¶

Bases: MoverCreator

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

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

keyname(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator) → str¶: C++: protocols::kinematic_closure::KicMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::kinematic_closure::KicMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void