#include <CDRsMinPackMin.hh>

Inheritance diagram for protocols::antibody::CDRsMinPackMin:

Public Member Functions
	CDRsMinPackMin ()

	CDRsMinPackMin (AntibodyInfoOP antibody_info)

	CDRsMinPackMin (AntibodyInfoOP antibody_info, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf, core::kinematics::MoveMapOP movemap)

	~CDRsMinPackMin () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

void	set_move_map (core::kinematics::MoveMapCOP movemap)

void	set_sc_min (bool scmin)

void	set_rt_min (bool rtmin)

void	set_turnoff_minimization (bool setting)

void	set_alter_foldtree (bool setting)

void	show (std::ostream &out=std::cout) const override

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

virtual MoverOP	clone () const
	Return a clone of the Mover object. 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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	finalize_setup (core::pose::Pose &pose)

void	init ()

Friends
std::ostream &	operator<< (std::ostream &out, const CDRsMinPackMin &ab_m_2)

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 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::antibody::CDRsMinPackMin::CDRsMinPackMin ( )

References ab_info_, init(), and user_defined_.

protocols::antibody::CDRsMinPackMin::CDRsMinPackMin ( AntibodyInfoOP antibody_info )

References ab_info_, init(), and user_defined_.

protocols::antibody::CDRsMinPackMin::CDRsMinPackMin	(	AntibodyInfoOP	antibody_info,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::pack::task::TaskFactoryOP	tf,
		core::kinematics::MoveMapOP	movemap
	)

References ab_info_, allcdr_map_, init(), loop_scorefxn_highres_, tf_, and user_defined_.

protocols::antibody::CDRsMinPackMin::~CDRsMinPackMin ( )

overridedefault

Member Function Documentation

void protocols::antibody::CDRsMinPackMin::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References cdr_sequence_move_, finalize_setup(), and update_rounds_.

void protocols::antibody::CDRsMinPackMin::finalize_setup ( core::pose::Pose & pose )

private

References ab_info_, protocols::loops::add_cutpoint_variants(), allcdr_map_, alter_foldtree_, cdr_sequence_move_, core::pose::Pose::fold_tree(), loop_scorefxn_highres_, min_tolerance_, min_type_, protocols::loops::remove_cutpoint_variants(), protocols::antibody::design::repack, rt_min_, sc_min_, Temperature_, tf_, protocols::antibody::TR(), turnoff_minimization_, and update_rounds_.

Referenced by apply().

std::string protocols::antibody::CDRsMinPackMin::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::antibody::CDRsMinPackMin::init ( void )

private

References allcdr_map_, alter_foldtree_, benchmark_, core::scoring::chainbreak, core::scoring::get_score_function(), loop_scorefxn_highres_, min_tolerance_, min_type_, core::scoring::overlap_chainbreak, rt_min_, sc_min_, Temperature_, tf_, turnoff_minimization_, update_rounds_, and user_defined_.

Referenced by CDRsMinPackMin().

void protocols::antibody::CDRsMinPackMin::set_alter_foldtree ( bool setting )

inline

References alter_foldtree_.

void protocols::antibody::CDRsMinPackMin::set_move_map ( core::kinematics::MoveMapCOP movemap )

References allcdr_map_.

void protocols::antibody::CDRsMinPackMin::set_rt_min ( bool rtmin )

inline

References rt_min_.

void protocols::antibody::CDRsMinPackMin::set_sc_min ( bool scmin )

inline

References sc_min_.

void protocols::antibody::CDRsMinPackMin::set_task_factory ( core::pack::task::TaskFactoryCOP tf )

References tf_.

void protocols::antibody::CDRsMinPackMin::set_turnoff_minimization ( bool setting )

inline

References turnoff_minimization_.

void protocols::antibody::CDRsMinPackMin::show ( std::ostream & out = std::cout ) const

overridevirtual

Show the complete setup of the antibody modeler protocol

Reimplemented from protocols::moves::Mover.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const CDRsMinPackMin &	ab_m_2
	)

friend

Member Data Documentation

AntibodyInfoOP protocols::antibody::CDRsMinPackMin::ab_info_

private

Referenced by CDRsMinPackMin(), and finalize_setup().

core::kinematics::MoveMapOP protocols::antibody::CDRsMinPackMin::allcdr_map_

private

Referenced by CDRsMinPackMin(), finalize_setup(), init(), and set_move_map().

bool protocols::antibody::CDRsMinPackMin::alter_foldtree_

private

Referenced by finalize_setup(), init(), and set_alter_foldtree().

bool protocols::antibody::CDRsMinPackMin::benchmark_

private

Referenced by init().

protocols::moves::SequenceMoverOP protocols::antibody::CDRsMinPackMin::cdr_sequence_move_

private

Referenced by apply(), and finalize_setup().

core::scoring::ScoreFunctionOP protocols::antibody::CDRsMinPackMin::loop_scorefxn_highres_

private

Referenced by CDRsMinPackMin(), finalize_setup(), and init().

core::Real protocols::antibody::CDRsMinPackMin::min_tolerance_

private

Referenced by finalize_setup(), and init().

std::string protocols::antibody::CDRsMinPackMin::min_type_

private

Referenced by finalize_setup(), and init().

bool protocols::antibody::CDRsMinPackMin::rt_min_

private

Referenced by finalize_setup(), init(), protocols::antibody::operator<<(), and set_rt_min().

bool protocols::antibody::CDRsMinPackMin::sc_min_

private

Referenced by finalize_setup(), init(), protocols::antibody::operator<<(), and set_sc_min().

core::Real protocols::antibody::CDRsMinPackMin::Temperature_

private

Referenced by finalize_setup(), and init().

core::pack::task::TaskFactoryOP protocols::antibody::CDRsMinPackMin::tf_

private

Referenced by CDRsMinPackMin(), finalize_setup(), init(), and set_task_factory().

bool protocols::antibody::CDRsMinPackMin::turnoff_minimization_

private

Referenced by finalize_setup(), init(), and set_turnoff_minimization().

core::Size protocols::antibody::CDRsMinPackMin::update_rounds_

private

Referenced by apply(), finalize_setup(), and init().

bool protocols::antibody::CDRsMinPackMin::user_defined_

private

Referenced by CDRsMinPackMin(), and init().

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

src/protocols/antibody/CDRsMinPackMin.hh
src/protocols/antibody/CDRsMinPackMin.cc

Private Attributes
bool	sc_min_

bool	rt_min_

bool	turnoff_minimization_

bool	alter_foldtree_

bool	benchmark_

core::Size	update_rounds_

bool	user_defined_

AntibodyInfoOP	ab_info_

core::scoring::ScoreFunctionOP	loop_scorefxn_highres_

protocols::moves::SequenceMoverOP	cdr_sequence_move_

core::kinematics::MoveMapOP	allcdr_map_

core::pack::task::TaskFactoryOP	tf_

std::string	min_type_

core::Real	Temperature_

core::Real	min_tolerance_

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation