#include <H3RefineCCD.hh>

Public Member Functions
	H3RefineCCD ()
	default constructor More...

	H3RefineCCD (AntibodyInfoOP antibody_info, CDRNameEnum loop_name)
	constructor with arguments More...

	H3RefineCCD (AntibodyInfoOP antibody_info, CDRNameEnum loop_name, core::scoring::ScoreFunctionCOP highres_scorefxn)
	constructor with arguments More...

	H3RefineCCD (AntibodyInfoOP antibody_info)
	constructor with arguments More...

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

virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

	~H3RefineCCD ()
	default destructor More...

void	pass_start_pose (core::pose::Pose &start_pose)

void	turn_on_benchmark ()

void	turn_off_flank_relax ()

void	turn_off_h3_filter ()

virtual void	apply (core::pose::Pose &pose)

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

void	set_highres_score_func (core::scoring::ScoreFunctionCOP highres_scorefxn)

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

void	set_type (std::string const &setting)

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 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

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
void	set_default ()

void	init ()

void	finalize_setup (core::pose::Pose &pose)

Private Attributes
AntibodyInfoOP	ab_info_

CDRNameEnum	loop_name_

loops::Loop	the_loop_

core::Real	high_cst_

core::Size	loop_begin_

core::Size	loop_end_

core::Size	loop_size_

core::Size	cutpoint_

core::Size	n_small_moves_

core::Size	inner_cycles_

core::Size	outer_cycles_

bool	include_neighbors_

core::kinematics::MoveMapOP	cdrh3_map_

core::kinematics::MoveMapOP	flank_cdrh3_map_

std::string	minimization_type_

bool	user_defined_

bool	benchmark_

bool	is_camelid_

moves::ChangeFoldTreeMoverOP	change_FT_to_simpleloop_

moves::ChangeFoldTreeMoverOP	change_FT_to_flankloop_

simple_moves::MinMoverOP	loop_min_mover_

moves::SequenceMoverOP	wiggle_cdr_h3_

simple_moves::PackRotamersMoverOP	loop_repack_

moves::MonteCarloOP	mc_

utility::vector1< bool >	allow_repack_

core::Real	init_temp_

core::Real	last_temp_

core::Real	gamma_

core::Real	min_tolerance_

core::Real	high_move_temp_

core::Real	neighbor_dist_

core::scoring::ScoreFunctionOP	highres_scorefxn_

bool	H3_filter_
	actually enables H3 filter for H3 operations More...

core::Size	flank_size_
	number of flanking residues:default 5 More...

bool	flank_relax_
	relax flanking regions of h3 More...

core::pose::Pose	start_pose_

core::pack::task::TaskFactoryOP	tf_

bool	refine_input_loop_
	just refine input loop More...

core::Size	max_cycle_close_trial_

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::antibody::H3RefineCCD::H3RefineCCD ( )

default constructor

Referenced by clone().

protocols::antibody::H3RefineCCD::H3RefineCCD	(	AntibodyInfoOP	antibody_info,
		CDRNameEnum	loop_name
	)

constructor with arguments

References ab_info_, init(), loop_name_, and user_defined_.

protocols::antibody::H3RefineCCD::H3RefineCCD	(	AntibodyInfoOP	antibody_info,
		CDRNameEnum	loop_name,
		core::scoring::ScoreFunctionCOP	highres_scorefxn
	)

constructor with arguments

References ab_info_, highres_scorefxn_, init(), loop_name_, and user_defined_.

protocols::antibody::H3RefineCCD::H3RefineCCD ( AntibodyInfoOP antibody_info )

constructor with arguments

References ab_info_, and init().

protocols::antibody::H3RefineCCD::~H3RefineCCD ( )

default destructor

Member Function Documentation

void protocols::antibody::H3RefineCCD::apply ( core::pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References ab_info_, allow_repack_, protocols::moves::ChangeFoldTreeMover::apply(), protocols::simple_moves::RotamerTrialsMover::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::simple_moves::MinMover::apply(), protocols::moves::SequenceMover::apply(), protocols::moves::MonteCarlo::boltzmann(), protocols::antibody::CDR_H3_cter_filter(), change_FT_to_flankloop_, protocols::antibody::cutpoints_separation(), finalize_setup(), gamma_, H3_filter_, highres_scorefxn_, include_neighbors_, init_temp_, inner_cycles_, core::pose::Pose::is_fullatom(), loop_min_mover_, loop_repack_, max_cycle_close_trial_, mc_, numeric::mod(), neighbor_dist_, outer_cycles_, core::pack::task::TaskFactory::push_back(), protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), protocols::loops::select_loop_residues(), protocols::moves::MonteCarlo::set_temperature(), protocols::antibody::setup_packer_task(), start_pose_, protocols::simple_moves::RotamerTrialsMover::task_factory(), protocols::simple_moves::PackRotamersMover::task_factory(), temperature, tf_, the_loop_, protocols::antibody::TR, utility_exit_with_message, and wiggle_cdr_h3_.

protocols::moves::MoverOP protocols::antibody::H3RefineCCD::clone ( ) const

virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References H3RefineCCD().

void protocols::antibody::H3RefineCCD::finalize_setup ( core::pose::Pose & pose )

private

References protocols::loops::add_cutpoint_variants(), protocols::moves::MoverContainer::add_mover(), allow_repack_, cdrh3_map_, change_FT_to_flankloop_, change_FT_to_simpleloop_, cutpoint_, flank_cdrh3_map_, flank_relax_, flank_size_, core::pose::Pose::fold_tree(), high_move_temp_, highres_scorefxn_, include_neighbors_, init_temp_, loop_begin_, loop_end_, loop_min_mover_, loop_repack_, mc_, min_tolerance_, minimization_type_, n_small_moves_, neighbor_dist_, core::pack::task::TaskFactory::push_back(), protocols::loops::remove_cutpoint_variants(), protocols::loops::select_loop_residues(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), protocols::antibody::setup_packer_task(), protocols::antibody::simple_fold_tree(), start_pose_, protocols::simple_moves::PackRotamersMover::task_factory(), tf_, the_loop_, core::pose::Pose::total_residue(), and wiggle_cdr_h3_.