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

#include <GraftedStemOptimizer.hh>

Public Member Functions
	GraftedStemOptimizer (CDRNameEnum const &cdr_name, AntibodyInfoOP antibody_info)

	~GraftedStemOptimizer ()

virtual void	apply (pose::Pose &pose)

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

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

void	set_scorefxn (core::scoring::ScoreFunctionOP setting)
	users can pass their own scorefunction, foldtree, movemap, and taskfactory More...

void	set_deep_optimization (bool const &setting)
	deep optimization will do small_share_ccd More...

kinematics::FoldTreeOP	get_N_C_stems_foldtree (pose::Pose const &pose) const

kinematics::FoldTreeOP	get_Nstem_foldtree (pose::Pose const &pose) const

kinematics::FoldTreeOP	get_Cstem_foldtree (pose::Pose const &pose) const

kinematics::MoveMapOP	get_stem_movemap (pose::Pose const &pose, std::string const &type, bool const &include_nb_sc=false) const

pack::task::TaskFactoryOP	get_stem_taskfactory (pose::Pose &pose, std::string const &type, bool const &include_nb_sc=false) const

void	set_stem_size (Size const &setting)
	stem that was replaced by the extra reesidues at the end of the loop terminus. Default is "2" More...

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

GraftedStemOptimizer &	operator= (GraftedStemOptimizer 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

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 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	init ()

void	setup_protocol (pose::Pose &pose)

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

Private Attributes
Size	stem_size_

CDRNameEnum	cdr_name_

AntibodyInfoOP	ab_info_

bool	benchmark_

loops::LoopOP	cdr_loop_

core::scoring::ScoreFunctionOP	scorefxn_

moves::MonteCarloOP	mc_

moves::SequenceMoverOP	optimize_stems_

bool	deep_optimization_

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::GraftedStemOptimizer::GraftedStemOptimizer	(	CDRNameEnum const &	cdr_name,
		AntibodyInfoOP	antibody_info
	)

References ab_info_, cdr_name_, and init().

protocols::antibody::GraftedStemOptimizer::~GraftedStemOptimizer ( )

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

copy ctor

References initForEqualOperatorAndCopyConstructor().

Member Function Documentation

void protocols::antibody::GraftedStemOptimizer::apply ( pose::Pose & pose )

virtual

void protocols::antibody::GraftedStemOptimizer::enable_benchmark_mode ( bool const & setting )

inline

enable benchmark mode

kinematics::FoldTreeOP protocols::antibody::GraftedStemOptimizer::get_Cstem_foldtree ( pose::Pose const & pose ) const

References cdr_loop_, core::kinematics::Edge::PEPTIDE, stem_size_, and core::pose::Pose::total_residue().

kinematics::FoldTreeOP protocols::antibody::GraftedStemOptimizer::get_N_C_stems_foldtree ( pose::Pose const & pose ) const

References cdr_loop_, core::kinematics::Edge::PEPTIDE, stem_size_, and core::pose::Pose::total_residue().

Referenced by apply().

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

virtual

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

Implements protocols::moves::Mover.

kinematics::FoldTreeOP protocols::antibody::GraftedStemOptimizer::get_Nstem_foldtree ( pose::Pose const & pose ) const

References cdr_loop_, core::kinematics::Edge::PEPTIDE, stem_size_, and core::pose::Pose::total_residue().

kinematics::MoveMapOP protocols::antibody::GraftedStemOptimizer::get_stem_movemap	(	pose::Pose const &	pose,
		std::string const &	type,
		bool const &	include_nb_sc = `false`
	)		const

References cdr_loop_, protocols::loops::get_tenA_neighbor_residues(), stem_size_, and core::pose::Pose::total_residue().

Referenced by setup_protocol().

pack::task::TaskFactoryOP protocols::antibody::GraftedStemOptimizer::get_stem_taskfactory	(	pose::Pose &	pose,
		std::string const &	type,
		bool const &	include_nb_sc = `false`
	)		const

References cdr_loop_, core::pack::task::TaskFactory::clear(), protocols::loops::get_tenA_neighbor_residues(), core::pack::task::TaskFactory::push_back(), protocols::antibody::setup_packer_task(), stem_size_, and core::pose::Pose::total_residue().

Referenced by setup_protocol().

void protocols::antibody::GraftedStemOptimizer::init ( void )

private

References ab_info_, benchmark_, cdr_loop_, cdr_name_, deep_optimization_, protocols::antibody::AntibodyInfo::get_CDR_loop(), mc_, optimize_stems_, scorefxn_, and stem_size_.

Referenced by GraftedStemOptimizer().

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

private

References ab_info_, benchmark_, cdr_loop_, cdr_name_, scorefxn_, and stem_size_.

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

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

assignment operator

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

void protocols::antibody::GraftedStemOptimizer::set_deep_optimization ( bool const & setting )

inline

deep optimization will do small_share_ccd

void protocols::antibody::GraftedStemOptimizer::set_scorefxn ( core::scoring::ScoreFunctionOP setting )

users can pass their own scorefunction, foldtree, movemap, and taskfactory

LLLLLLLLLLLLLLLLLLL#### L1-3.pdb, H1-3.pdb

..ffffffff@@ @@ffffffffff.. framework.pdb || || grafting \/ ffffffff@##LLLLLLLLLLLLLLLLLLL##@ffffffffff

      _____ set up fold tree  _____
     |     |                 |     |
     |  |  |                 |  |  |

ffffffff@|##LLLLLLLLLLLLLLLLLLL##|@ffffffffff

References scorefxn_.

void protocols::antibody::GraftedStemOptimizer::set_stem_size ( Size const & setting )

stem that was replaced by the extra reesidues at the end of the loop terminus. Default is "2"

References exit, stem_size_, and TRG.

void protocols::antibody::GraftedStemOptimizer::setup_protocol ( pose::Pose & pose )

private

References cdr_loop_, deep_optimization_, get_stem_movemap(), get_stem_taskfactory(), optimize_stems_, protocols::forge::methods::overlap_chainbreak(), protocols::antibody::design::repack, scorefxn_, stem_size_, and TRG.

Referenced by apply().

Member Data Documentation

AntibodyInfoOP protocols::antibody::GraftedStemOptimizer::ab_info_

private

Referenced by apply(), GraftedStemOptimizer(), init(), and initForEqualOperatorAndCopyConstructor().

bool protocols::antibody::GraftedStemOptimizer::benchmark_

private

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

loops::LoopOP protocols::antibody::GraftedStemOptimizer::cdr_loop_

private

Referenced by get_Cstem_foldtree(), get_N_C_stems_foldtree(), get_Nstem_foldtree(), get_stem_movemap(), get_stem_taskfactory(), init(), initForEqualOperatorAndCopyConstructor(), and setup_protocol().

CDRNameEnum protocols::antibody::GraftedStemOptimizer::cdr_name_

private

Referenced by apply(), GraftedStemOptimizer(), init(), and initForEqualOperatorAndCopyConstructor().

bool protocols::antibody::GraftedStemOptimizer::deep_optimization_

private

Referenced by init(), and setup_protocol().

moves::MonteCarloOP protocols::antibody::GraftedStemOptimizer::mc_

private

Referenced by apply(), and init().

moves::SequenceMoverOP protocols::antibody::GraftedStemOptimizer::optimize_stems_

private

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

core::scoring::ScoreFunctionOP protocols::antibody::GraftedStemOptimizer::scorefxn_

private

Referenced by apply(), init(), initForEqualOperatorAndCopyConstructor(), set_scorefxn(), and setup_protocol().

Size protocols::antibody::GraftedStemOptimizer::stem_size_

mutableprivate

Referenced by apply(), get_Cstem_foldtree(), get_N_C_stems_foldtree(), get_Nstem_foldtree(), get_stem_movemap(), get_stem_taskfactory(), init(), initForEqualOperatorAndCopyConstructor(), set_stem_size(), and setup_protocol().

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

src/protocols/antibody/GraftedStemOptimizer.hh
src/protocols/antibody/GraftedStemOptimizer.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

LLLLLLLLLLLLLLLLLLL#### L1-3.pdb, H1-3.pdb

Member Data Documentation