single loop definition More...

#include <Loop.hh>

Public Member Functions
virtual	~Loop ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	Loop ()
	default constructor More...

	Loop (SerializedLoop loop)

	Loop (core::Size const start_in, core::Size const stop_in, core::Size const cut_in=0, core::Real skip_rate=0.0, bool const extended_in=false)
	input constructor More...

bool	is_extended () const

core::Size	start () const

core::Size	stop () const

core::Size	cut () const

core::Size	size () const

core::Real	skip_rate () const

void	set_extended (bool input)

void	set_start (core::Size input)

void	set_stop (core::Size input)

void	set_cut (core::Size input)

core::Size	length () const
	Assuming that the loop represents a contiguous stretch of residues, returns the length. Makes no assumptions about directionality. That is, Loop(3,8).length() == Loop(8,3).length(). Constant time procedure. More...

bool	increasing () const
	Returns true if the loop's elements are increasing. More...

bool	decreasing () const
	Returns true if the loop's elements are decreasing. More...

core::Size	midpoint () const
	Returns the midpoint of the loop. More...

bool	operator< (Loop const &larger) const

bool	operator== (Loop const &other) const

bool	operator!= (Loop const &other) const

void	get_residues (utility::vector1< Size > &selection) const
	add all residues within this loop definition into selection More...

void	switch_movemap (core::kinematics::MoveMap &movemap, core::id::TorsionType, bool allow_moves=true) const
	switch DOF_Type for residues in loop. id::CHI, id::BB — don't use with id::JUMP More...

void	choose_cutpoint (core::pose::Pose const &pose)

void	auto_choose_cutpoint (core::pose::Pose const &pose)
	Autochoose a cutpoint using the secondary structure of the pose unless cutpoint is already set. More...

bool	is_terminal (core::pose::Pose const &pose) const

Private Attributes
core::Size	start_

core::Size	stop_

core::Size	cut_

core::Real	skip_rate_

bool	extended_

Friends
std::ostream &	operator<< (std::ostream &os, const Loop &loop)

Detailed Description

single loop definition

Constructor & Destructor Documentation

protocols::loops::Loop::~Loop ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::loops::Loop::Loop ( )

inline

default constructor

protocols::loops::Loop::Loop ( SerializedLoop loop )

inline

References extended.

protocols::loops::Loop::Loop	(	core::Size const	start_in,
		core::Size const	stop_in,
		core::Size const	cut_in = `0`,
		core::Real	skip_rate = `0.0`,
		bool const	extended_in = `false`
	)

inline

input constructor

Member Function Documentation

void protocols::loops::Loop::auto_choose_cutpoint ( core::pose::Pose const & pose )

inline

Autochoose a cutpoint using the secondary structure of the pose unless cutpoint is already set.

References choose_cutpoint(), and cut_.

Referenced by protocols::loops::loop_mover::IndependentLoopMover::apply().

void protocols::loops::Loop::choose_cutpoint ( core::pose::Pose const & pose )

Choose a cutpoint for the loop if one is not specified. Allow any residue to serve as the cutpoint, but prefer those to the center.

References core::conformation::Residue::aa(), core::chemical::aa_pro, cut_, nres, core::pose::Pose::residue(), runtime_assert, core::pose::Pose::secstruct(), ss, start_, stop_, core::pose::Pose::total_residue(), protocols::loops::tr, numeric::random::uniform(), utility_exit_with_message, and weight.

Referenced by protocols::LoopRefine::apply(), auto_choose_cutpoint(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::abinitio::AbrelaxApplication::fold(), and protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub().

core::Size protocols::loops::Loop::cut ( ) const

inline

References cut_.

bool protocols::loops::Loop::decreasing ( ) const

inline

Returns true if the loop's elements are decreasing.

References increasing().

void protocols::loops::Loop::get_residues ( utility::vector1< Size > & selection ) const

add all residues within this loop definition into selection

References start_, and stop_.

bool protocols::loops::Loop::increasing ( ) const

inline

Returns true if the loop's elements are increasing.

References start(), and stop().

Referenced by decreasing(), and midpoint().

bool protocols::loops::Loop::is_extended ( ) const

inline

References extended_.

Referenced by protocols::loops::Loops::add_overlap_loop(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loop_modeling::LoopBuilder::do_apply(), protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_extended(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop().

bool protocols::loops::Loop::is_terminal ( core::pose::Pose const & pose ) const

Detect a terminal loop, logic is more complicated for multi-chain poses. Returns TRUE for terminal loops.

References core::pose::Pose::chain(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), start(), stop(), and core::pose::Pose::total_residue().

Referenced by protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

core::Size protocols::loops::Loop::length ( ) const

inline

Assuming that the loop represents a contiguous stretch of residues, returns the length. Makes no assumptions about directionality. That is, Loop(3,8).length() == Loop(8,3).length(). Constant time procedure.

References start(), and stop().

Referenced by protocols::nonlocal::avg_ca_position(), protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchor_position(), protocols::nonlocal::StarTreeBuilder::choose_anchor_position(), protocols::medal::chunk_probabilities(), protocols::nonlocal::decompose(), protocols::nonlocal::HelixRotate::get_rotation_parameters(), midpoint(), protocols::kinematic_closure::ClosureProblem::num_residues(), and protocols::antibody::operator<<().