protocols::loops::loop_closure::ccd::CcdLoopClosureMover Class Reference

#include <CcdLoopClosureMover.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::CcdLoopClosureMover:

Collaboration diagram for protocols::loops::loop_closure::ccd::CcdLoopClosureMover:

Public Member Functions
	CcdLoopClosureMover (Loop const &loop_def, core::kinematics::MoveMapCOP mm)
	~CcdLoopClosureMover ()
void	set_max_rama_score_increase (core::Real input_max_rama_score_increase)
void	set_max_total_delta (core::Real input_max_delta_helix, core::Real input_max_delta_strand, core::Real input_max_delta_loop)
void	set_tolerance (core::Real input_tolerance)
void	set_ccd_cycles (core::Size input_ccd_cycles)
void	set_bRama_check (bool input_bRama_check)
virtual void	apply (core::pose::Pose &pose)
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
core::Real	forward_deviation () const
core::Real	backward_deviation () const
bool	success () const
Loop	get_loop () const
core::Size	get_loop_start () const
core::Size	get_loop_stop () const
core::Size	get_loop_cut () const
core::Size	get_loop_size () const
core::Real	get_loop_skip_rate () const
std::string	get_loop_extended () const
core::Real	get_max_rama_score_increase () const
core::Real	get_tolerance () const
core::Real	get_max_total_delta (std::string secstr) const
core::Size	get_ccd_cycles () const
std::string	bRama_check () const
core::kinematics::MoveMap	movemap () const
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual	~Mover ()
virtual MoverSP	create ()
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	parse_state (SerializableState const &state)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void	save_state (SerializableState &state)
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
	Mover (Mover const &other)
Mover &	operator= (Mover const &other)
	assignment operator More...
virtual core::Real	last_proposal_density_ratio ()
std::string const &	type () const
std::string	get_current_tag () const
	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. More...
void	set_current_tag (std::string const &new_tag)
virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...
virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP	get_input_pose () const
PoseCOP	get_native_pose () const
virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
void	type (const std::string &type_in)
virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...
virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string	get_type () const
MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...
void	reset_status ()
	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. More...
virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...
virtual void	clear_info ()
	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. More...
virtual Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool	reinitialize_for_new_input () const
	this function informs 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). More...
virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const

Private Attributes
Loop	loop_
core::kinematics::MoveMapCOP	movemap_
core::Real	max_rama_score_increase_
core::Real	max_total_delta_helix_
core::Real	max_total_delta_strand_
core::Real	max_total_delta_loop_
core::Real	tolerance_
Size	ccd_cycles_
bool	bRama_check_
core::Real	forward_deviation_
core::Real	backward_deviation_
core::Real	torsion_delta_
core::Real	rama_delta_
Size	actual_cycles_

Friends
std::ostream &	operator<< (std::ostream &os, CcdLoopClosureMover const &mover)

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef protocols::filters::Filters_map	Filters_map
typedef std::list< std::string >	Strings
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	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. More...
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Definition at line 59 of file CcdLoopClosureMover.hh.

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::CcdLoopClosureMover::CcdLoopClosureMover	(	Loop const &	loop_def,
		core::kinematics::MoveMapCOP	mm
	)

Definition at line 46 of file CcdLoopClosureMover.cc.

protocols::loops::loop_closure::ccd::CcdLoopClosureMover::~CcdLoopClosureMover

(

)

Definition at line 99 of file CcdLoopClosureMover.cc.

Member Function Documentation

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::apply ( core::pose::Pose &  pose)

virtual

Implements protocols::moves::Mover.

Definition at line 102 of file CcdLoopClosureMover.cc.

References actual_cycles_, backward_deviation_, bRama_check_, ccd_cycles_, protocols::loops::Loop::cut(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), forward_deviation_, loop_, max_rama_score_increase_, max_total_delta_helix_, max_total_delta_loop_, max_total_delta_strand_, movemap_, rama_delta_, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), tolerance_, torsion_delta_, and TR_loop().

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::backward_deviation ( ) const

inline

Definition at line 88 of file CcdLoopClosureMover.hh.

References backward_deviation_.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::apply(), and success().

std::string protocols::loops::loop_closure::ccd::CcdLoopClosureMover::bRama_check ( ) const

inline

Definition at line 107 of file CcdLoopClosureMover.hh.

References bRama_check_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::forward_deviation ( ) const

inline

Definition at line 84 of file CcdLoopClosureMover.hh.

References forward_deviation_.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::apply(), and success().

core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_ccd_cycles ( ) const

inline

Definition at line 106 of file CcdLoopClosureMover.hh.

References ccd_cycles_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

Loop protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop ( ) const

inline

Definition at line 96 of file CcdLoopClosureMover.hh.

References loop_.

core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_cut ( ) const

inline

Definition at line 99 of file CcdLoopClosureMover.hh.

References protocols::loops::Loop::cut(), and loop_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

std::string protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_extended ( ) const

inline

Definition at line 102 of file CcdLoopClosureMover.hh.

References protocols::loops::Loop::is_extended(), and loop_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_size ( ) const

inline

Definition at line 100 of file CcdLoopClosureMover.hh.

References loop_, and protocols::loops::Loop::size().

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_skip_rate ( ) const

inline

Definition at line 101 of file CcdLoopClosureMover.hh.

References loop_, and protocols::loops::Loop::skip_rate().

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_start ( ) const

inline

Definition at line 97 of file CcdLoopClosureMover.hh.

References loop_, and protocols::loops::Loop::start().

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_loop_stop ( ) const

inline

Definition at line 98 of file CcdLoopClosureMover.hh.

References loop_, and protocols::loops::Loop::stop().

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_max_rama_score_increase

(

)

const

Definition at line 130 of file CcdLoopClosureMover.cc.

References max_rama_score_increase_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_max_total_delta

(

std::string

secstr)

const

Definition at line 140 of file CcdLoopClosureMover.cc.

References max_total_delta_helix_, max_total_delta_loop_, and max_total_delta_strand_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

std::string protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Definition at line 125 of file CcdLoopClosureMover.cc.

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::get_tolerance

(

)

const

Definition at line 135 of file CcdLoopClosureMover.cc.

References tolerance_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::kinematics::MoveMap protocols::loops::loop_closure::ccd::CcdLoopClosureMover::movemap

(

)

const

Definition at line 153 of file CcdLoopClosureMover.cc.

References movemap_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_bRama_check

(

bool

input_bRama_check)

Definition at line 94 of file CcdLoopClosureMover.cc.

References bRama_check_.

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_ccd_cycles

(

core::Size

input_ccd_cycles)

Definition at line 88 of file CcdLoopClosureMover.cc.

References ccd_cycles_.

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_max_rama_score_increase

(

core::Real

input_max_rama_score_increase)

Definition at line 62 of file CcdLoopClosureMover.cc.

References max_rama_score_increase_.

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_max_total_delta	(	core::Real	input_max_delta_helix,
		core::Real	input_max_delta_strand,
		core::Real	input_max_delta_loop
	)

Definition at line 70 of file CcdLoopClosureMover.cc.

References max_total_delta_helix_, max_total_delta_loop_, and max_total_delta_strand_.

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::set_tolerance

(

core::Real

input_tolerance)

Definition at line 82 of file CcdLoopClosureMover.cc.

References tolerance_.

bool protocols::loops::loop_closure::ccd::CcdLoopClosureMover::success ( ) const

inline

Definition at line 92 of file CcdLoopClosureMover.hh.

References backward_deviation(), forward_deviation(), and tolerance_.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os, CcdLoopClosureMover const &  mover  )

friend

Definition at line 157 of file CcdLoopClosureMover.cc.

Member Data Documentation

Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::actual_cycles_

private

Definition at line 128 of file CcdLoopClosureMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::backward_deviation_

private

Definition at line 124 of file CcdLoopClosureMover.hh.

Referenced by apply(), and backward_deviation().

bool protocols::loops::loop_closure::ccd::CcdLoopClosureMover::bRama_check_

private

Definition at line 121 of file CcdLoopClosureMover.hh.

Referenced by apply(), bRama_check(), and set_bRama_check().

Size protocols::loops::loop_closure::ccd::CcdLoopClosureMover::ccd_cycles_

private

Definition at line 120 of file CcdLoopClosureMover.hh.

Referenced by apply(), get_ccd_cycles(), and set_ccd_cycles().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::forward_deviation_

private

Definition at line 123 of file CcdLoopClosureMover.hh.

Referenced by apply(), and forward_deviation().

Loop protocols::loops::loop_closure::ccd::CcdLoopClosureMover::loop_

private

Definition at line 112 of file CcdLoopClosureMover.hh.

Referenced by apply(), get_loop(), get_loop_cut(), get_loop_extended(), get_loop_size(), get_loop_skip_rate(), get_loop_start(), and get_loop_stop().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_rama_score_increase_

private

Definition at line 114 of file CcdLoopClosureMover.hh.

Referenced by apply(), get_max_rama_score_increase(), and set_max_rama_score_increase().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_total_delta_helix_

private

Definition at line 115 of file CcdLoopClosureMover.hh.

Referenced by apply(), get_max_total_delta(), and set_max_total_delta().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_total_delta_loop_

private

Definition at line 117 of file CcdLoopClosureMover.hh.

Referenced by apply(), get_max_total_delta(), and set_max_total_delta().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::max_total_delta_strand_

private

Definition at line 116 of file CcdLoopClosureMover.hh.

Referenced by apply(), get_max_total_delta(), and set_max_total_delta().

core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::CcdLoopClosureMover::movemap_

private

Definition at line 113 of file CcdLoopClosureMover.hh.

Referenced by apply(), and movemap().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::rama_delta_

private

Definition at line 126 of file CcdLoopClosureMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::tolerance_

private

Definition at line 118 of file CcdLoopClosureMover.hh.

Referenced by apply(), get_tolerance(), set_tolerance(), and success().

core::Real protocols::loops::loop_closure::ccd::CcdLoopClosureMover::torsion_delta_

private

Definition at line 125 of file CcdLoopClosureMover.hh.

Referenced by apply().

---

The documentation for this class was generated from the following files:

• src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.hh
• src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.cc