ccd¶

Bindings for protocols::loops::loop_closure::ccd namespace

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover¶

Bases: Mover

Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent

This class was initially a wrapper for fast_ccd_loop_closure(), an exposed method in ccd_closure.cc. Before using this mover:

Set a proper foldtree - usually a regular loop foldtree is used. (see protocols::loops::foldtree_from_loops)

Add cutpoint variants to the loop cutpoint

The original description of the CCD algorithm in relation to protein loop closure can be found here:: Canutescu AA, Dunbrack RL Jr: Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003, 12:963-972.

actual_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → int¶

Get the number of cycles used to close the loop.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::actual_cycles() const –> unsigned long

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the corresponding move to <pose>.

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

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, object_to_copy: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover¶: C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::operator=(const class protocols::loops::loop_closure::ccd::CCDLoopClosureMover &) –> class protocols::loops::loop_closure::ccd::CCDLoopClosureMover &

check_rama_scores(*args, **kwargs)¶

Overloaded function.

check_rama_scores(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> bool

Are closure moves checked using the rama scores and the Metropolis criterion?

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores() const –> bool

check_rama_scores(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, setting: bool) -> None

Set whether or not closure moves are checked using the rama scores and the Metropolis criterion.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores(bool) –> 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.loops.loop_closure.ccd.CCDLoopClosureMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return the name of the Mover.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::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>

deviation(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → float¶

Get the RMS deviation of the target atoms after completion of loop closure.

sqrt( dev / number_of_atoms )

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::deviation() const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::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.loops.loop_closure.ccd.CCDLoopClosureMover) → str¶: C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::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 > > &

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

loop(*args, **kwargs)¶

Overloaded function.

loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> pyrosetta.rosetta.protocols.loops.Loop

Get the Loop to be closed.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop() const –> class protocols::loops::Loop

loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, new_loop: pyrosetta.rosetta.protocols.loops.Loop) -> None

Set the Loop to be closed.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop(class protocols::loops::Loop) –> void

max_cycles(*args, **kwargs)¶

Overloaded function.

max_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> int

Get the maximum number of cycles to attempt if the tolerance is not satisfied.

Each cycle includes both forward and backward directions.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_cycles() const –> unsigned long

max_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_ccd_cycles: int) -> None

Set the maximum number of cycles to attempt if the tolerance is not satisfied.

Each cycle includes both forward and backward directions.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_cycles(unsigned long) –> void

max_per_move_torsion_delta_per_residue(*args, **kwargs)¶

Overloaded function.

max_per_move_torsion_delta_per_residue(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_max_delta_helix: float, input_max_delta_strand: float, input_max_delta_coil: float) -> None

Set the maximum change in torsion angle a residue is allowed per closure move for each of the three

secondary structure types.

of parameters is helix, strand, coil. Angles are in degrees.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_per_move_torsion_delta_per_residue(double, double, double) –> void

max_per_move_torsion_delta_per_residue(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> float

Get the maximum change in torsion angle a residue is allowed for a single move for one of the: three secondary structure types.

angle in degrees

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_per_move_torsion_delta_per_residue(enum protocols::loops::loop_closure::ccd::SecondaryStructureType) const –> double

max_per_move_torsion_delta_per_residue(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct: str) -> float

Get the maximum allowed torsion angle deviation for the entire closure run for one of the three: secondary structure types ( H, E, L).

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_per_move_torsion_delta_per_residue(char) const –> double

max_total_torsion_delta_per_residue(*args, **kwargs)¶

Overloaded function.

max_total_torsion_delta_per_residue(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> float

Get the maximum change in torsion angle a residue is allowed for the entire closure run for one of the: three secondary structure types.

angle in degrees

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_per_residue(enum protocols::loops::loop_closure::ccd::SecondaryStructureType) const –> double

max_total_torsion_delta_per_residue(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct: str) -> float

Get the maximum allowed torsion angle deviation for the entire closure run for one of the three: secondary structure types ( H, E, L).

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_per_residue(char) const –> double

max_total_torsion_delta_per_residue(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_max_delta_helix: float, input_max_delta_strand: float, input_max_delta_coil: float) -> None

Set the maximum change in torsion angle a residue is allowed for the entire closure run for each of

the three secondary structure types.

of parameters is helix, strand, coil. Angles are in degrees.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_per_residue(double, double, double) –> void

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the current MoveMap.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap() const –> class core::kinematics::MoveMap

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

Set the MoveMap.: Positions outside of the defined loop will be ignored.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

static mover_name() → str¶: C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::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::ccd::CCDLoopClosureMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

rama(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → protocols::loops::loop_closure::ccd::RamaCheckBase¶

Get a pointer to the RamaCheck instance being used.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::rama() const –> class std::shared_ptr<class protocols::loops::loop_closure::ccd::RamaCheckBase>

rama_delta(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → float¶

Get the average change in rama score for the residues in the loop after completion of loop closure.

This value will only be meaningful if the option for checking the rama score is turned on.

Change this name to match the datum. ~Labonte

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::rama_delta() const –> double

static register_options() → None¶

Register options with the option system.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::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_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¶

Set the ‘type’ string

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

set_verbose(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, setting: bool) → None¶

Set whether or not to output loop start/end points at beginning of Mover apply().

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::set_verbose(bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> None
show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate a string representation of CCDLoopClosureMover for debugging purposes.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::show(std::ostream &) const –> void

success(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → bool¶

Return true if the forward and backward RMS deviations are each lower than the tolerance value.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::success() const –> bool

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

tolerance(*args, **kwargs)¶

Overloaded function.

tolerance(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> float

Get the tolerance for loop closure in Angstroms.

A forward and backward splice of RMS over N, CA, and C (or target atoms) must be less than the tolerance for an early return; otherwise, the algorithm will go through the loop the requested number of cycles. RMS Deviation is calculation as sqrt( dev / number_of_atoms )

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::tolerance() const –> double

tolerance(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_tolerance: float) -> None

Set the tolerance for loop closure in Angstroms.

A forward and backward splice of RMS deviation over N, CA, and C (or target atoms)must be less than the tolerance for an early return; otherwise, the algorithm will go through the loop the requested number of cycles. RMS Deviation is calculation as sqrt( dev / number_of_atoms )

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::tolerance(double) –> void

torsion_delta(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → float¶

Get the average change in the main-chain torsion angles of the loop after completion of loop closure.

Change this name to match the datum. ~Labonte

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::torsion_delta() const –> double

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 &

use_rama_2B(*args, **kwargs)¶

Overloaded function.

use_rama_2B(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> bool

Are two-body (neighbor-dependent) Ramachandran maps being used?

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::use_rama_2B() const –> bool

use_rama_2B(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, setting: bool) -> None

Set whether or not two-body (neighbor-dependent) Ramachandran maps should be used.

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::use_rama_2B(bool) –> void

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator¶

Bases: MoverCreator

%CCDLoopClosureMoverCreator allows the MoverFactory to create a CCDLoopClosureMover instance.

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator, : pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator¶: C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator::operator=(const class protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator &) –> class protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶

Static method that returns the keyname for performance reasons.

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

keyname(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator) → str¶: C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator::keyname() const –> std::string

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

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ChainDirection¶

Bases: pybind11_object

Members:

forward

backward

n_chain_directions

backward = <ChainDirection.backward: 2>¶

forward = <ChainDirection.forward: 1>¶

n_chain_directions = <ChainDirection.backward: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure¶

Bases: WidthFirstSlidingWindowLoopClosure

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(class core::pose::Pose &, class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose) -> None

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

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure, : pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure¶: C++: protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::operator=(const class protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure &) –> class protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure &

bIdealLoopClosing(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) → bool¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bIdealLoopClosing() 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>

closure_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) → pyrosetta.rosetta.core.fragment.FragSet¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

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>

determine_loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.loops.Loop¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(const class core::pose::Pose &, class core::pose::Pose &) –> class protocols::loops::Loop

fascore(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure, fa_pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(class core::pose::Pose &) const –> double

fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, frags: pyrosetta.rosetta.core.fragment.FragSet) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_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.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure) → str¶: C++: protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::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 > > &

keep_fragments(*args, **kwargs)¶

Overloaded function.

keep_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> None
keep_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: bool) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::keep_fragments(bool) –> void

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

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap() const –> const class core::kinematics::MoveMap &

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

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

output_debug_structure(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::output_debug_structure(class core::pose::Pose &, std::string) –> void

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

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::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 register_options() → None¶: C++: protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::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

sample_loops(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(class core::pose::Pose &, class core::pose::Pose &) –> void

scored_frag_cycle_ratio(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio(double) –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn() const –> const class core::scoring::ScoreFunction &

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

select_final_loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(class core::pose::Pose &, class core::pose::Pose &) –> void

static setPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setPoseExtraScore(class core::pose::Pose &) –> void

set_bIdealLoopClosing(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: bool) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_bIdealLoopClosing(bool) –> void

set_chainbreak_max(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_chainbreak_max(double) –> 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_defaults(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure) → None¶: C++: protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::set_defaults() –> void

set_evaluation(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, ev: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_evaluation(class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>) –> void

set_fullatom_pose(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure, fa_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::set_fullatom_pose(class core::pose::Pose &) –> 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.ccd.SlidingWindowLoopClosure, loop_in: pyrosetta.rosetta.protocols.loops.Loop) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_loop(const class protocols::loops::Loop &) –> 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

short_frag_cycle_ratio(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio(double) –> 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

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.loops.loop_closure.ccd.LoopClosure¶

Bases: pybind11_object

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::apply(const class core::pose::Pose &) –> bool

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, : pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::operator=(const class protocols::loops::loop_closure::ccd::LoopClosure &) –> class protocols::loops::loop_closure::ccd::LoopClosure &

closure_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.core.fragment.Frame¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::closure_fragments() const –> class std::shared_ptr<class core::fragment::Frame>

mc(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::mc() –> class protocols::moves::MonteCarlo &

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.core.kinematics.MoveMap¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

nr_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → int¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::nr_fragments() const –> unsigned long

ramp_chainbreak(*args, **kwargs)¶

Overloaded function.

ramp_chainbreak(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> None
ramp_chainbreak(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, setting: bool) -> None

C++: protocols::loops::loop_closure::ccd::LoopClosure::ramp_chainbreak(bool) –> void

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::scorefxn() –> const class core::scoring::ScoreFunction &

set_cycles(*args, **kwargs)¶

Overloaded function.

set_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> None
set_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, cycle_ratio: float) -> None

C++: protocols::loops::loop_closure::ccd::LoopClosure::set_cycles(double) –> void

set_nr_fragments(*args, **kwargs)¶

Overloaded function.

set_nr_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> None
set_nr_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, nr_fragments: int) -> None

C++: protocols::loops::loop_closure::ccd::LoopClosure::set_nr_fragments(unsigned long) –> void

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B¶

Bases: RamaCheckBase

accept_new_conformation(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID, alpha: float) → bool¶

Determine whether or not a candidate conformation should be accepted based on the Ramachandran score.

true if the move should be accepted, false if it should be rejected.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(const class core::pose::Pose &, const class core::id::TorsionID &, const double) const –> bool

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B, object_to_copy: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B¶: C++: protocols::loops::loop_closure::ccd::RamaCheck1B::operator=(const class protocols::loops::loop_closure::ccd::RamaCheck1B &) –> class protocols::loops::loop_closure::ccd::RamaCheck1B &

average_change_in_rama_score_over_range(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, first_res: int, last_res: int) → float¶

Compute the average change in Ramachandran score between the initial pose and the current pose from

<first_res> to <last_res>.

The average change in Ramachandran score.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::average_change_in_rama_score_over_range(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> double

clone(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase¶

Return a pointer to a new, fully configured copy of RamaCheck1B

C++: protocols::loops::loop_closure::ccd::RamaCheck1B::clone() const –> class std::shared_ptr<class protocols::loops::loop_closure::ccd::RamaCheckBase>

compute_rama_score(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, phi: float, psi: float) → float¶

Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>.: The score is independent of the identity of the neighboring residues.

C++: protocols::loops::loop_closure::ccd::RamaCheck1B::compute_rama_score(const class core::pose::Pose &, const unsigned long, const double, const double) const –> double

initialize_starting_rama_scores(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Store the Ramachandran scores of each residue in the supplied pose.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores(const class core::pose::Pose &) const –> void

max_rama_score_increase(*args, **kwargs)¶

Overloaded function.

max_rama_score_increase(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float

Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase() const –> double

max_rama_score_increase(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_max_rama_score_increase: float) -> None

Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase(double) –> void

name(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B) → str¶

Return “RamaCheck1B”

C++: protocols::loops::loop_closure::ccd::RamaCheck1B::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::loops::loop_closure::ccd::RamaCheckBase::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static register_options() → None¶

Register options with the option system.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::register_options() –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> None
show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, output: pyrosetta.rosetta.std.ostream) -> None

Generate a string representation of RamaCheck for debugging purposes.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float

Get the “temperature” used for rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_temperature: float) -> None

Set the “temperature” used for rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::temperature(double) –> void

total_net_change_in_rama_score_over_range(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, first_res: int, last_res: int) → float¶

Compute the total net change in Ramachandran score between the initial pose and the current pose from

<first_res> to <last_res>.

The total net change in Ramachandran score.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::total_net_change_in_rama_score_over_range(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> double

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B¶

Bases: RamaCheckBase

accept_new_conformation(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID, alpha: float) → bool¶

Determine whether or not a candidate conformation should be accepted based on the Ramachandran score.

true if the move should be accepted, false if it should be rejected.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(const class core::pose::Pose &, const class core::id::TorsionID &, const double) const –> bool

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B, object_to_copy: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B¶: C++: protocols::loops::loop_closure::ccd::RamaCheck2B::operator=(const class protocols::loops::loop_closure::ccd::RamaCheck2B &) –> class protocols::loops::loop_closure::ccd::RamaCheck2B &

average_change_in_rama_score_over_range(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, first_res: int, last_res: int) → float¶

Compute the average change in Ramachandran score between the initial pose and the current pose from

<first_res> to <last_res>.

The average change in Ramachandran score.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::average_change_in_rama_score_over_range(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> double

clone(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase¶

Return a pointer to a new, fully configured copy of RamaCheck2B

C++: protocols::loops::loop_closure::ccd::RamaCheck2B::clone() const –> class std::shared_ptr<class protocols::loops::loop_closure::ccd::RamaCheckBase>

compute_rama_score(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, phi: float, psi: float) → float¶

Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>.: The score depends on the identity of the neighboring residues.

C++: protocols::loops::loop_closure::ccd::RamaCheck2B::compute_rama_score(const class core::pose::Pose &, const unsigned long, const double, const double) const –> double

initialize_starting_rama_scores(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Store the Ramachandran scores of each residue in the supplied pose.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores(const class core::pose::Pose &) const –> void

max_rama_score_increase(*args, **kwargs)¶

Overloaded function.

max_rama_score_increase(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float

Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase() const –> double

max_rama_score_increase(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_max_rama_score_increase: float) -> None

Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase(double) –> void

name(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B) → str¶

Return “RamaCheck2B”

C++: protocols::loops::loop_closure::ccd::RamaCheck2B::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::loops::loop_closure::ccd::RamaCheckBase::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static register_options() → None¶

Register options with the option system.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::register_options() –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> None
show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, output: pyrosetta.rosetta.std.ostream) -> None

Generate a string representation of RamaCheck for debugging purposes.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float

Get the “temperature” used for rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_temperature: float) -> None

Set the “temperature” used for rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::temperature(double) –> void

total_net_change_in_rama_score_over_range(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, first_res: int, last_res: int) → float¶

Compute the total net change in Ramachandran score between the initial pose and the current pose from

<first_res> to <last_res>.

The total net change in Ramachandran score.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::total_net_change_in_rama_score_over_range(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> double

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase¶

Bases: pybind11_object

accept_new_conformation(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, torsion_id: pyrosetta.rosetta.core.id.TorsionID, alpha: float) → bool¶

Determine whether or not a candidate conformation should be accepted based on the Ramachandran score.

true if the move should be accepted, false if it should be rejected.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(const class core::pose::Pose &, const class core::id::TorsionID &, const double) const –> bool

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, object_to_copy: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase¶: C++: protocols::loops::loop_closure::ccd::RamaCheckBase::operator=(const class protocols::loops::loop_closure::ccd::RamaCheckBase &) –> class protocols::loops::loop_closure::ccd::RamaCheckBase &

average_change_in_rama_score_over_range(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, first_res: int, last_res: int) → float¶

Compute the average change in Ramachandran score between the initial pose and the current pose from

<first_res> to <last_res>.

The average change in Ramachandran score.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::average_change_in_rama_score_over_range(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> double

clone(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase¶

Return a pointer to a new, fully configured copy of RamaCheckBase

The clone method should be used to copy an instance of RamaCheck if the derived class type is unknown.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::clone() const –> class std::shared_ptr<class protocols::loops::loop_closure::ccd::RamaCheckBase>

compute_rama_score(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, phi: float, psi: float) → float¶

Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::compute_rama_score(const class core::pose::Pose &, const unsigned long, const double, const double) const –> double

initialize_starting_rama_scores(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Store the Ramachandran scores of each residue in the supplied pose.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores(const class core::pose::Pose &) const –> void

max_rama_score_increase(*args, **kwargs)¶

Overloaded function.

max_rama_score_increase(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float

Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase() const –> double

max_rama_score_increase(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_max_rama_score_increase: float) -> None

Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase(double) –> void

name(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) → str¶

Return the name of the RamaCheck class being used

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::loops::loop_closure::ccd::RamaCheckBase::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static register_options() → None¶

Register options with the option system.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::register_options() –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> None
show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, output: pyrosetta.rosetta.std.ostream) -> None

Generate a string representation of RamaCheck for debugging purposes.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::show(std::ostream &) const –> void

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float

Get the “temperature” used for rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_temperature: float) -> None

Set the “temperature” used for rama score-checking with the Metropolis criterion.

This value will only be used if the option for checking the rama score is turned on.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::temperature(double) –> void

total_net_change_in_rama_score_over_range(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose: pyrosetta.rosetta.core.pose.Pose, first_res: int, last_res: int) → float¶

Compute the total net change in Ramachandran score between the initial pose and the current pose from

<first_res> to <last_res>.

The total net change in Ramachandran score.

C++: protocols::loops::loop_closure::ccd::RamaCheckBase::total_net_change_in_rama_score_over_range(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> double

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType¶

Bases: pybind11_object

Members:

helix

strand

coil

n_secondary_structure_types

coil = <SecondaryStructureType.coil: 3>¶

helix = <SecondaryStructureType.helix: 1>¶

n_secondary_structure_types = <SecondaryStructureType.coil: 3>¶

property name¶

strand = <SecondaryStructureType.strand: 2>¶

property value¶

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure¶

Bases: LoopClosure

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(const class core::pose::Pose &) –> bool

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure, : pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure¶: C++: protocols::loops::loop_closure::ccd::ShortLoopClosure::operator=(const class protocols::loops::loop_closure::ccd::ShortLoopClosure &) –> class protocols::loops::loop_closure::ccd::ShortLoopClosure &

catch_fragment(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure, short_pose: pyrosetta.rosetta.core.pose.Pose) → None¶

save the loop-fragment in closure_frames_

C++: protocols::loops::loop_closure::ccd::ShortLoopClosure::catch_fragment(const class core::pose::Pose &) –> void

closure_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.core.fragment.Frame¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::closure_fragments() const –> class std::shared_ptr<class core::fragment::Frame>

mc(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.protocols.moves.MonteCarlo¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::mc() –> class protocols::moves::MonteCarlo &

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.core.kinematics.MoveMap¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

nr_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → int¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::nr_fragments() const –> unsigned long

ramp_chainbreak(*args, **kwargs)¶

Overloaded function.

ramp_chainbreak(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> None
ramp_chainbreak(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, setting: bool) -> None

C++: protocols::loops::loop_closure::ccd::LoopClosure::ramp_chainbreak(bool) –> void

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::loops::loop_closure::ccd::LoopClosure::scorefxn() –> const class core::scoring::ScoreFunction &

set_cycles(*args, **kwargs)¶

Overloaded function.

set_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> None
set_cycles(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, cycle_ratio: float) -> None

C++: protocols::loops::loop_closure::ccd::LoopClosure::set_cycles(double) –> void

set_nr_fragments(*args, **kwargs)¶

Overloaded function.

set_nr_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> None
set_nr_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure, nr_fragments: int) -> None

C++: protocols::loops::loop_closure::ccd::LoopClosure::set_nr_fragments(unsigned long) –> void

class pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure¶

Bases: Mover

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(class core::pose::Pose &, class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose) -> None

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

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, : pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::operator=(const class protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure &) –> class protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure &

bIdealLoopClosing(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) → bool¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bIdealLoopClosing() 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>

closure_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) → pyrosetta.rosetta.core.fragment.FragSet¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

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>

determine_loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.loops.Loop¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(const class core::pose::Pose &, class core::pose::Pose &) –> class protocols::loops::Loop

fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, frags: pyrosetta.rosetta.core.fragment.FragSet) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_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.loops.loop_closure.ccd.SlidingWindowLoopClosure) → str¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::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 > > &

keep_fragments(*args, **kwargs)¶

Overloaded function.

keep_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> None
keep_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: bool) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::keep_fragments(bool) –> void

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

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap() const –> const class core::kinematics::MoveMap &

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

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

output_debug_structure(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::output_debug_structure(class core::pose::Pose &, std::string) –> void

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

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::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 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

sample_loops(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(class core::pose::Pose &, class core::pose::Pose &) –> void

scored_frag_cycle_ratio(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio(double) –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn() const –> const class core::scoring::ScoreFunction &

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

select_final_loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop(class core::pose::Pose &, class core::pose::Pose &) –> void

static setPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setPoseExtraScore(class core::pose::Pose &) –> void

set_bIdealLoopClosing(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: bool) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_bIdealLoopClosing(bool) –> void

set_chainbreak_max(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_chainbreak_max(double) –> 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_evaluation(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, ev: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_evaluation(class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>) –> 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.ccd.SlidingWindowLoopClosure, loop_in: pyrosetta.rosetta.protocols.loops.Loop) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_loop(const class protocols::loops::Loop &) –> 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

short_frag_cycle_ratio(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio(double) –> 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

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.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure¶

Bases: SlidingWindowLoopClosure

it will switch between different windows. If nothing good is found after one sweep of window sizes we bail out… (assuming that it is fruitless) if things look promising more sampling time is spend to find a good loop

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(class core::pose::Pose &, class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose) -> None

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

assign(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure, : pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure) → pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure¶: C++: protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::operator=(const class protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure &) –> class protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure &

bIdealLoopClosing(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) → bool¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bIdealLoopClosing() 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>

closure_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) → pyrosetta.rosetta.core.fragment.FragSet¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

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>

determine_loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.loops.Loop¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(const class core::pose::Pose &, class core::pose::Pose &) –> class protocols::loops::Loop

fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, frags: pyrosetta.rosetta.core.fragment.FragSet) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_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.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure) → str¶: C++: protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::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 > > &

keep_fragments(*args, **kwargs)¶

Overloaded function.

keep_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> None
keep_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: bool) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::keep_fragments(bool) –> void

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

movemap(*args, **kwargs)¶

Overloaded function.

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap() const –> const class core::kinematics::MoveMap &

movemap(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

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

output_debug_structure(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::output_debug_structure(class core::pose::Pose &, std::string) –> void

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

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::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 register_options() → None¶: C++: protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::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

sample_loops(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(class core::pose::Pose &, class core::pose::Pose &) –> void

scored_frag_cycle_ratio(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio(double) –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn() const –> const class core::scoring::ScoreFunction &

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

select_final_loop(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut: pyrosetta.rosetta.core.pose.Pose, less_cut: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop(class core::pose::Pose &, class core::pose::Pose &) –> void

static setPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setPoseExtraScore(class core::pose::Pose &) –> void

set_bIdealLoopClosing(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: bool) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_bIdealLoopClosing(bool) –> void

set_chainbreak_max(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_chainbreak_max(double) –> 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_evaluation(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, ev: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_evaluation(class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>) –> 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.ccd.SlidingWindowLoopClosure, loop_in: pyrosetta.rosetta.protocols.loops.Loop) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_loop(const class protocols::loops::Loop &) –> 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

short_frag_cycle_ratio(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting: float) → None¶: C++: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio(double) –> 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

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 &

pyrosetta.rosetta.protocols.loops.loop_closure.ccd.get_deviation(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint: int) → Tuple[float, float]¶: C++: protocols::loops::loop_closure::ccd::get_deviation(const class core::pose::Pose &, const unsigned long) –> struct std::pair<double, double>