jacobi

Bindings for protocols::loops::loop_closure::jacobi namespace

class pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Iterative loop closure mover, based on a linearization of the kinematics, which adjusts all free backbone torsion angles simultaneously in each iteration.

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Execute the loop closure

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, : pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::operator=(const class protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover &) –> class protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover &

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.loops.loop_closure.jacobi.JacobiLoopClosureMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::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>

current_closed_as_target(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Set current loop connection with subsequent residue as target connection.

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::current_closed_as_target(const class core::pose::Pose &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::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_allowed_norm_lin(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) float

Get value for norm of allowed linear error vector [Ang] that defines successful closure

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_allowed_norm_lin() –> double

get_allowed_norm_rot(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) float

Get value for norm of allowed rotational error vector [deg] that defines successful closure

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_allowed_norm_rot() –> double

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_jacobian_chain(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians

Get pointer to SeriesJacobian object

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_jacobian_chain() –> class std::shared_ptr<class core::kinematics::jacobian::SeriesJacobians>

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.loops.loop_closure.jacobi.JacobiLoopClosureMover) pyrosetta.rosetta.protocols.loops.Loop

Get the loop to be closed

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_loop() –> class std::shared_ptr<const class protocols::loops::Loop>

get_max_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) int

Get value for maximum number of iterations to find a loop closure solution

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_max_cycles() –> unsigned long

get_movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) pyrosetta.rosetta.core.kinematics.MoveMap

Get the MoveMap

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::get_movemap() –> class std::shared_ptr<const class core::kinematics::MoveMap>

get_name(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) str

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::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 > > &

init_apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Initializes private parameters of the Jacobi mover that depend on the pose

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::init_apply(class core::pose::Pose &) –> void

last_closure_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) int

Returns the number of cycles that were needed for the last closure

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::last_closure_cycles() –> unsigned long

last_closure_success(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) bool

Get boolean indicating whether last closure was successfully completed

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::last_closure_success() –> bool

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::loops::loop_closure::jacobi::JacobiLoopClosureMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::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::loops::loop_closure::jacobi::JacobiLoopClosureMover::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

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_error_norms(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, error_norm_rot: float, error_norm_lin: float) None

Set norm-values of allowed rotational [deg] and linear error vectors [Ang] that define successful closure

error_norm_rot should be supplied in degrees.

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_error_norms(double, double) –> 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.loops.loop_closure.jacobi.JacobiLoopClosureMover, new_loop: pyrosetta.rosetta.protocols.loops.Loop) None

Set the loop to be closed

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_loop(const class protocols::loops::Loop &) –> void

set_max_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, max_cycles: int) None

Set maximum number of iterations to find a loop closure solution

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_max_cycles(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, new_mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

Set the MoveMap

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_movemap(const class std::shared_ptr<class core::kinematics::MoveMap> &) –> 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

Set the ‘type’ string

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

set_verbose(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, setting: bool) None

Set whether or not to output non-critical information.

Default is false

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::set_verbose(bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

  1. 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.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator, : pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator) pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator::operator=(const class protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator &) –> class protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator) str

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void