#include <RefineOneCDRLoop.hh>

Inheritance diagram for protocols::antibody2::RefineOneCDRLoop:

Collaboration diagram for protocols::antibody2::RefineOneCDRLoop:

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

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

	RefineOneCDRLoop (AntibodyInfoOP antibody_info, std::string refine_mode)
	constructor with arguments More...

	RefineOneCDRLoop (AntibodyInfoOP antibody_info, std::string refine_mode, core::scoring::ScoreFunctionCOP scorefxn)
	constructor with arguments More...

	RefineOneCDRLoop (AntibodyInfoOP antibody_info, AntibodyCDRNameEnum const &cdr_loop_name, std::string refine_mode, core::scoring::ScoreFunctionCOP scorefxn)
	constructor with arguments More...

	~RefineOneCDRLoop ()
	default destructor More...

void	turn_on_benchmark ()

void	set_h3_filter (bool setting)

void	set_num_filter_tries (core::Size setting)

void	set_flank_relax (bool setting)

void	set_flank_size (core::Size setting)

void	set_refine_mode (std::string refine_mode)

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

void	set_score_function (core::scoring::ScoreFunctionCOP scorefxn)

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

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

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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 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 Member Functions
void	set_default ()

void	init ()

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

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 38 of file RefineOneCDRLoop.hh.

Constructor & Destructor Documentation

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop ( )

default constructor

Definition at line 64 of file RefineOneCDRLoop.cc.

Referenced by clone().

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop ( AntibodyInfoOP antibody_info)

constructor with arguments

Definition at line 66 of file RefineOneCDRLoop.cc.

References ab_info_, init(), and user_defined_.

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop	(	AntibodyInfoOP	antibody_info,
		std::string	refine_mode
	)

constructor with arguments

Definition at line 73 of file RefineOneCDRLoop.cc.

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

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop	(	AntibodyInfoOP	antibody_info,
		std::string	refine_mode,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

constructor with arguments

Definition at line 81 of file RefineOneCDRLoop.cc.

References ab_info_, cdr_loop_name_, protocols::antibody2::h3, init(), refine_mode_, scorefxn_, and user_defined_.

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop	(	AntibodyInfoOP	antibody_info,
		AntibodyCDRNameEnum const &	cdr_loop_name,
		std::string	refine_mode,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

constructor with arguments

Definition at line 95 of file RefineOneCDRLoop.cc.

References ab_info_, cdr_loop_name_, init(), refine_mode_, scorefxn_, and user_defined_.

protocols::antibody2::RefineOneCDRLoop::~RefineOneCDRLoop ( )

default destructor

Definition at line 141 of file RefineOneCDRLoop.cc.

Member Function Documentation

void protocols::antibody2::RefineOneCDRLoop::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 167 of file RefineOneCDRLoop.cc.

References ab_info_, protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::antibody2::CDR_H3_cter_filter(), cdr_loop_name_, protocols::loops::Loop::cut(), core::pose::Pose::energies(), core::scoring::fa_rep, flank_relax_, flank_size_, protocols::moves::Mover::get_native_pose(), H3_filter_, core::pose::Pose::is_fullatom(), num_filter_tries_, pass_start_pose(), refine_mode_, scorefxn_, protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_flank_residue_min(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_flank_residue_min(), protocols::moves::Mover::set_native_pose(), protocols::antibody2::simple_fold_tree(), protocols::loops::Loop::start(), start_pose_, protocols::loops::Loop::stop(), core::scoring::Energies::total_energy(), and protocols::TR().

protocols::moves::MoverOP protocols::antibody2::RefineOneCDRLoop::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 144 of file RefineOneCDRLoop.cc.

References RefineOneCDRLoop().

void protocols::antibody2::RefineOneCDRLoop::finalize_setup ( core::pose::Pose & pose)

private

std::string protocols::antibody2::RefineOneCDRLoop::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 150 of file RefineOneCDRLoop.cc.

void protocols::antibody2::RefineOneCDRLoop::init ( void )

private

Definition at line 111 of file RefineOneCDRLoop.cc.

References set_default().

Referenced by RefineOneCDRLoop().

void protocols::antibody2::RefineOneCDRLoop::pass_start_pose ( core::pose::Pose & start_pose)

Definition at line 159 of file RefineOneCDRLoop.cc.

References start_pose_.

Referenced by apply().

void protocols::antibody2::RefineOneCDRLoop::set_default ( )

private

Definition at line 119 of file RefineOneCDRLoop.cc.

References core::scoring::atom_pair_constraint, cdr_loop_name_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), flank_relax_, flank_size_, protocols::antibody2::h3, H3_filter_, high_cst_, num_filter_tries_, core::scoring::overlap_chainbreak, refine_mode_, scorefxn_, and user_defined_.

Referenced by init().

void protocols::antibody2::RefineOneCDRLoop::set_flank_relax ( bool setting)

inline

Definition at line 75 of file RefineOneCDRLoop.hh.

void protocols::antibody2::RefineOneCDRLoop::set_flank_size ( core::Size setting)

inline

Definition at line 78 of file RefineOneCDRLoop.hh.

void protocols::antibody2::RefineOneCDRLoop::set_h3_filter ( bool setting)

inline

Definition at line 69 of file RefineOneCDRLoop.hh.

void protocols::antibody2::RefineOneCDRLoop::set_num_filter_tries ( core::Size setting)

inline

Definition at line 72 of file RefineOneCDRLoop.hh.

void protocols::antibody2::RefineOneCDRLoop::set_refine_mode ( std::string refine_mode)

inline

Definition at line 81 of file RefineOneCDRLoop.hh.

void protocols::antibody2::RefineOneCDRLoop::set_score_function ( core::scoring::ScoreFunctionCOP scorefxn)

Definition at line 154 of file RefineOneCDRLoop.cc.

References scorefxn_.

void protocols::antibody2::RefineOneCDRLoop::turn_on_benchmark ( )

inline

Definition at line 66 of file RefineOneCDRLoop.hh.

Member Data Documentation

AntibodyInfoOP protocols::antibody2::RefineOneCDRLoop::ab_info_

private

Definition at line 96 of file RefineOneCDRLoop.hh.

Referenced by apply(), and RefineOneCDRLoop().

bool protocols::antibody2::RefineOneCDRLoop::benchmark_

private

Definition at line 98 of file RefineOneCDRLoop.hh.

AntibodyCDRNameEnum protocols::antibody2::RefineOneCDRLoop::cdr_loop_name_

private

Definition at line 107 of file RefineOneCDRLoop.hh.

Referenced by apply(), RefineOneCDRLoop(), and set_default().

bool protocols::antibody2::RefineOneCDRLoop::flank_relax_

private

Definition at line 101 of file RefineOneCDRLoop.hh.

Referenced by apply(), and set_default().

core::Size protocols::antibody2::RefineOneCDRLoop::flank_size_

private

Definition at line 100 of file RefineOneCDRLoop.hh.

Referenced by apply(), and set_default().

bool protocols::antibody2::RefineOneCDRLoop::H3_filter_

private

Definition at line 104 of file RefineOneCDRLoop.hh.

Referenced by apply(), and set_default().

core::Real protocols::antibody2::RefineOneCDRLoop::high_cst_

private

Definition at line 108 of file RefineOneCDRLoop.hh.

Referenced by set_default().

core::Size protocols::antibody2::RefineOneCDRLoop::num_filter_tries_

private

Definition at line 105 of file RefineOneCDRLoop.hh.

Referenced by apply(), and set_default().

std::string protocols::antibody2::RefineOneCDRLoop::refine_mode_

private

Definition at line 106 of file RefineOneCDRLoop.hh.

Referenced by apply(), RefineOneCDRLoop(), and set_default().

core::scoring::ScoreFunctionOP protocols::antibody2::RefineOneCDRLoop::scorefxn_

private

Definition at line 99 of file RefineOneCDRLoop.hh.

Referenced by apply(), RefineOneCDRLoop(), set_default(), and set_score_function().

core::pose::Pose protocols::antibody2::RefineOneCDRLoop::start_pose_

private

Definition at line 102 of file RefineOneCDRLoop.hh.

Referenced by apply(), and pass_start_pose().

core::pack::task::TaskFactoryOP protocols::antibody2::RefineOneCDRLoop::tf_

private

Definition at line 103 of file RefineOneCDRLoop.hh.

bool protocols::antibody2::RefineOneCDRLoop::user_defined_

private

Definition at line 97 of file RefineOneCDRLoop.hh.

Referenced by RefineOneCDRLoop(), and set_default().

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

src/protocols/antibody2/RefineOneCDRLoop.hh
src/protocols/antibody2/RefineOneCDRLoop.cc

Private Attributes
AntibodyInfoOP	ab_info_

bool	user_defined_

bool	benchmark_

core::scoring::ScoreFunctionOP	scorefxn_

core::Size	flank_size_

bool	flank_relax_

core::pose::Pose	start_pose_

core::pack::task::TaskFactoryOP	tf_

bool	H3_filter_

core::Size	num_filter_tries_

std::string	refine_mode_

AntibodyCDRNameEnum	cdr_loop_name_

core::Real	high_cst_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation