Grafts only one CDR onto a framework. More...

#include <GraftOneCDRLoop.hh>

Inheritance diagram for protocols::antibody2::GraftOneCDRLoop:

Collaboration diagram for protocols::antibody2::GraftOneCDRLoop:

Public Member Functions
	GraftOneCDRLoop ()

	GraftOneCDRLoop (AntibodyCDRNameEnum const &cdr_name, AntibodyInfoOP antibody_info, Ab_TemplateInfoOP ab_t_info)

	~GraftOneCDRLoop ()

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

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

void	enable_benchmark_mode (bool setting)
	enable benchmark mode More...

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
	users can pass their own scorefunction for packing after grafting More...

void	h3_stem_off (bool setting)
	R2 just graft R2 by copying some stem residues, and remove H3 to do H3 loop modeling later. But the terminal has been changed by this grafting. Therefore, in R3, an option for not copying h3 stem is provided. More...

void	set_flank_size (double setting)

	GraftOneCDRLoop (GraftOneCDRLoop const &rhs)
	copy ctor More...

GraftOneCDRLoop &	operator= (GraftOneCDRLoop const &rhs)
	assignment operator 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 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 Member Functions
void	set_default ()

void	init ()

void	finalize_setup ()

void	initForEqualOperatorAndCopyConstructor (GraftOneCDRLoop &lhs, GraftOneCDRLoop const &rhs)

Private Attributes
core::Size	flank_size_

core::Size	stem_copy_size_

AntibodyCDRNameEnum	cdr_name_

AntibodyInfoOP	ab_info_

Ab_TemplateInfoOP	ab_t_info_

bool	benchmark_

bool	h3_stem_not_graft_

core::scoring::ScoreFunctionCOP	scorefxn_

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

Grafts only one CDR onto a framework.

Definition at line 31 of file GraftOneCDRLoop.hh.

Constructor & Destructor Documentation

protocols::antibody2::GraftOneCDRLoop::GraftOneCDRLoop ( )

Definition at line 35 of file GraftOneCDRLoop.cc.

protocols::antibody2::GraftOneCDRLoop::GraftOneCDRLoop	(	AntibodyCDRNameEnum const &	cdr_name,
		AntibodyInfoOP	antibody_info,
		Ab_TemplateInfoOP	ab_t_info
	)

Definition at line 39 of file GraftOneCDRLoop.cc.

References ab_info_, ab_t_info_, cdr_name_, init(), and set_default().

protocols::antibody2::GraftOneCDRLoop::~GraftOneCDRLoop ( )

Definition at line 55 of file GraftOneCDRLoop.cc.

protocols::antibody2::GraftOneCDRLoop::GraftOneCDRLoop ( GraftOneCDRLoop const & rhs)

copy ctor

Definition at line 231 of file GraftOneCDRLoop.cc.

References initForEqualOperatorAndCopyConstructor().

Member Function Documentation

void protocols::antibody2::GraftOneCDRLoop::apply ( core::pose::Pose & pose_in)

virtual

void protocols::antibody2::GraftOneCDRLoop::enable_benchmark_mode ( bool setting)

inline

enable benchmark mode

Definition at line 50 of file GraftOneCDRLoop.hh.

References benchmark_.

void protocols::antibody2::GraftOneCDRLoop::finalize_setup ( )

private

Definition at line 85 of file GraftOneCDRLoop.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), h3_stem_not_graft_, scorefxn_, and stem_copy_size_.

Referenced by apply().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 228 of file GraftOneCDRLoop.cc.

void protocols::antibody2::GraftOneCDRLoop::h3_stem_off ( bool setting)

inline

R2 just graft R2 by copying some stem residues, and remove H3 to do H3 loop modeling later. But the terminal has been changed by this grafting. Therefore, in R3, an option for not copying h3 stem is provided.

Definition at line 63 of file GraftOneCDRLoop.hh.

References h3_stem_not_graft_.

void protocols::antibody2::GraftOneCDRLoop::init ( void )

private

Definition at line 74 of file GraftOneCDRLoop.cc.

References protocols::idealize::IdealizeMover::fast().

Referenced by GraftOneCDRLoop().