ccd

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

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

Bases: pyrosetta.rosetta.protocols.moves.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:

1. Set a proper foldtree - usually a regular loop foldtree is used. (see protocols::loops::foldtree_from_loops)
2. 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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, arg0: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> None
3. __init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, loop: pyrosetta.rosetta.protocols.loops.Loop) -> None
4. __init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, loop: pyrosetta.rosetta.protocols.loops.Loop, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

1. 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

2. 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.

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_std_allocator_std_string_t

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

loop(*args, **kwargs)

Overloaded function.

1. 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

2. 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.

1. 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

2. 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.

1. 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

2. 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

3. 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.

1. 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

2. 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

3. 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.

1. 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

2. 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

mover_name() → str

C++: protocols::loops::loop_closure::ccd::CCDLoopClosureMover::mover_name() –> std::string

name() → str

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

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

C++: protocols::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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

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

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.

1. show(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> None
2. 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(class std::basic_ostream<char> &) 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.

1. 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

2. 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.

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

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

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

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

use_rama_2B(*args, **kwargs)

Overloaded function.

1. 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

2. 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: pyrosetta.rosetta.protocols.moves.MoverCreator

%CCDLoopClosureMoverCreator allows the MoverFactory to create a CCDLoopClosureMover instance.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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: pyrosetta.rosetta.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.WidthFirstSlidingWindowLoopClosure

Bases: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure, fragset: pyrosetta.rosetta.core.fragment.FragSet, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
2. __init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure) -> None
3. __init__(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure, arg0: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(*args, **kwargs)

Overloaded function.

1. 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

2. 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.

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_std_allocator_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.

1. keep_fragments(self: pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> None
2. 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.

1. 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 &

2. 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

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 &, class std::basic_string<char>) –> void

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.

1. 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 &

2. 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

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

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

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

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

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

set_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

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

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

Outputs details about the Mover, including current settings.

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

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

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>