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

#include <CcdLoopClosureMover.hh>

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...
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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
	Return a clone of the Mover object. More...
virtual void	parse_my_tag (TagCOP tag, basic::datacache::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
	Inform 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
	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). More...
virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP
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. 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...

Constructor & Destructor Documentation

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

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

(

)

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

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

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

References bRama_check_.

Referenced by show().

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

inline

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

References ccd_cycles_.

Referenced by show().

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

inline

References loop_.

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

inline

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

Referenced by show().

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

inline

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

Referenced by show().

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

inline

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

Referenced by show().

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

inline

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

Referenced by show().

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

inline

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

Referenced by show().

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

inline

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

Referenced by show().

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

(

)

const

References max_rama_score_increase_.

Referenced by show().

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

(

std::string

secstr

)

const

References max_total_delta_helix_, max_total_delta_loop_, max_total_delta_strand_, and PyAssert.

Referenced by show().

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.

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

(

)

const

References tolerance_.

Referenced by show().

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

(

)

const

References movemap_.

Referenced by show().

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

(

bool

input_bRama_check

)

References bRama_check_.

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

(

core::Size

input_ccd_cycles

)

References ccd_cycles_.

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

(

core::Real

input_max_rama_score_increase

)

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
	)

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

)

References tolerance_.

void protocols::loops::loop_closure::ccd::CcdLoopClosureMover::show ( std::ostream &  output = std::cout ) const

virtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References bRama_check(), get_ccd_cycles(), get_loop_cut(), get_loop_extended(), get_loop_size(), get_loop_skip_rate(), get_loop_start(), get_loop_stop(), get_max_rama_score_increase(), get_max_total_delta(), get_tolerance(), movemap(), and core::kinematics::MoveMap::show().

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

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

inline

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().

Member Data Documentation

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

private

Referenced by apply().

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

private

Referenced by apply(), and backward_deviation().

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

private

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

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

private

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

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

private

Referenced by apply(), and forward_deviation().

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

private

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

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

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

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

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

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

private

Referenced by apply(), and movemap().

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

private

Referenced by apply().

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

private

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

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

private

Referenced by apply().

---

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

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