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

#include <GraftOneCDRLoop.hh>

Inheritance diagram for protocols::antibody::GraftOneCDRLoop:

Public Member Functions
	GraftOneCDRLoop ()

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

	~GraftOneCDRLoop () override

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

std::string	get_name () const override
	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	set_no_stem_copy (bool const &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 (Size 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 ()

	~Mover () override

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 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...

virtual 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

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 ()

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

Private Attributes
core::Size	flank_size_

core::Size	stem_copy_size_

CDRNameEnum	cdr_name_

AntibodyInfoOP	ab_info_

Ab_TemplateInfoOP	ab_t_info_

bool	benchmark_

bool	stem_not_graft_

core::scoring::ScoreFunctionCOP	scorefxn_

std::string	preprocessing_script_version_

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...

Detailed Description

Grafts only one CDR onto a framework.

Constructor & Destructor Documentation

protocols::antibody::GraftOneCDRLoop::GraftOneCDRLoop ( )

protocols::antibody::GraftOneCDRLoop::GraftOneCDRLoop	(	CDRNameEnum const &	cdr_name,
		AntibodyInfoOP	antibody_info,
		Ab_TemplateInfoOP	ab_t_info
	)

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

protocols::antibody::GraftOneCDRLoop::~GraftOneCDRLoop ( )

overridedefault

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

copy ctor

References initForEqualOperatorAndCopyConstructor().

Member Function Documentation

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

overridevirtual

Implements protocols::moves::Mover.

References ab_info_, ab_t_info_, core::chemical::ResidueType::atom_index(), core::id::BOGUS_ATOM_ID, cdr_name_, core::pose::Pose::conformation(), core::conformation::Conformation::fill_missing_atoms(), finalize_setup(), flank_size_, core::pose::initialize_atomid_map(), preprocessing_script_version_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_secstruct(), core::pose::Pose::set_xyz(), stem_copy_size_, core::scoring::superimpose_pose(), and TRG().

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

inline

enable benchmark mode

References benchmark_.

void protocols::antibody::GraftOneCDRLoop::finalize_setup ( )

private

References core::scoring::get_score_function(), scorefxn_, stem_copy_size_, and stem_not_graft_.

Referenced by apply().

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

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::antibody::GraftOneCDRLoop::init ( void )

private

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

Referenced by GraftOneCDRLoop().

void protocols::antibody::GraftOneCDRLoop::initForEqualOperatorAndCopyConstructor	(	GraftOneCDRLoop &	lhs,
		GraftOneCDRLoop const &	rhs
	)

private

References ab_info_, ab_t_info_, benchmark_, cdr_name_, flank_size_, stem_copy_size_, and stem_not_graft_.

Referenced by GraftOneCDRLoop(), and operator=().

GraftOneCDRLoop & protocols::antibody::GraftOneCDRLoop::operator= ( GraftOneCDRLoop const & rhs )

assignment operator

References initForEqualOperatorAndCopyConstructor(), and protocols::moves::Mover::operator=().

void protocols::antibody::GraftOneCDRLoop::set_default ( )

private

References ab_info_, ab_t_info_, benchmark_, flank_size_, preprocessing_script_version_, stem_copy_size_, and stem_not_graft_.

Referenced by GraftOneCDRLoop().

void protocols::antibody::GraftOneCDRLoop::set_flank_size ( Size setting )

inline

References flank_size_.

void protocols::antibody::GraftOneCDRLoop::set_no_stem_copy ( bool const & 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.

References stem_not_graft_.

void protocols::antibody::GraftOneCDRLoop::set_scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

inline

users can pass their own scorefunction for packing after grafting

References scorefxn_.