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

#include <GraftedStemOptimizer.hh>

Inheritance diagram for protocols::antibody::GraftedStemOptimizer:

[legend]

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

	~GraftedStemOptimizer () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	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...

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

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

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

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

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

void	set_stem_size (core::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 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 const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

virtual MoverOP	clone () const
	Return a clone of the Mover object. 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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	init ()

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

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

Private Attributes
core::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 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

◆ GraftedStemOptimizer() [1/2]

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

References ab_info_, cdr_name_, and init().

◆ ~GraftedStemOptimizer()

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

overridedefault

◆ GraftedStemOptimizer() [2/2]

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

copy ctor

References initForEqualOperatorAndCopyConstructor().

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ab_info_, protocols::loops::add_cutpoint_variants(), benchmark_, cdr_name_, core::pose::Pose::fold_tree(), get_N_C_stems_foldtree(), mc_, optimize_stems_, protocols::loops::remove_cutpoint_variants(), scorefxn_, setup_protocol(), stem_size_, and TRG().

◆ enable_benchmark_mode()

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

inline

enable benchmark mode

References benchmark_.

◆ get_Cstem_foldtree()

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

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

◆ get_N_C_stems_foldtree()

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

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

Referenced by apply().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_Nstem_foldtree()

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

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

◆ get_stem_movemap()

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

References cdr_loop_, core::select::get_tenA_neighbor_residues(), core::pose::Pose::size(), protocols::loops::start, stem_size_, protocols::loops::stop, and protocols::moves::Mover::type().

Referenced by setup_protocol().

◆ get_stem_taskfactory()

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

References cdr_loop_, core::select::get_tenA_neighbor_residues(), protocols::antibody::setup_packer_task(), core::pose::Pose::size(), protocols::loops::start, stem_size_, protocols::loops::stop, and protocols::moves::Mover::type().

Referenced by setup_protocol().

◆ init()

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

private

References ab_info_, benchmark_, cdr_loop_, cdr_name_, deep_optimization_, mc_, optimize_stems_, scorefxn_, and stem_size_.

Referenced by GraftedStemOptimizer().

◆ initForEqualOperatorAndCopyConstructor()

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=().

◆ operator=()

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

assignment operator

References initForEqualOperatorAndCopyConstructor().

◆ set_deep_optimization()

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

inline

deep optimization will do small_share_ccd

References deep_optimization_.

◆ set_scorefxn()

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_.

◆ set_stem_size()

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

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

References stem_size_, and TRG().

◆ setup_protocol()

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

private

References cdr_loop_, core::scoring::chainbreak, deep_optimization_, core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::scoring::get_score_function(), get_stem_movemap(), get_stem_taskfactory(), optimize_stems_, protocols::antibody::design::repack, scorefxn_, stem_size_, and TRG().

Referenced by apply().

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::GraftedStemOptimizer::ab_info_

private

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

◆ benchmark_

bool protocols::antibody::GraftedStemOptimizer::benchmark_

private

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

◆ cdr_loop_

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().

◆ cdr_name_

CDRNameEnum protocols::antibody::GraftedStemOptimizer::cdr_name_

private

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

◆ deep_optimization_

bool protocols::antibody::GraftedStemOptimizer::deep_optimization_

private

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

◆ mc_

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

private

Referenced by apply(), and init().

◆ optimize_stems_

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

private

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

◆ scorefxn_

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

private

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

◆ stem_size_

core::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

◆ GraftedStemOptimizer() [1/2]

◆ ~GraftedStemOptimizer()

◆ GraftedStemOptimizer() [2/2]

Member Function Documentation

◆ apply()

◆ enable_benchmark_mode()

◆ get_Cstem_foldtree()

◆ get_N_C_stems_foldtree()

◆ get_name()

◆ get_Nstem_foldtree()

◆ get_stem_movemap()

◆ get_stem_taskfactory()

◆ init()

◆ initForEqualOperatorAndCopyConstructor()

◆ operator=()

◆ set_deep_optimization()

◆ set_scorefxn()

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

◆ set_stem_size()

◆ setup_protocol()

Member Data Documentation

◆ ab_info_

◆ benchmark_

◆ cdr_loop_

◆ cdr_name_

◆ deep_optimization_

◆ mc_

◆ optimize_stems_

◆ scorefxn_

◆ stem_size_