#include <GraftCDRLoopsProtocol.hh>

Inheritance diagram for protocols::antibody::GraftCDRLoopsProtocol:

[legend]

Public Types
typedef std::map< std::string, bool >	GraftMap

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

Public Member Functions
	GraftCDRLoopsProtocol ()

	~GraftCDRLoopsProtocol () override

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	set_default ()
	Assigns default values to primitive members. More...

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

void	set_graft_l1 (bool graft_l1)

void	set_graft_l2 (bool graft_l2)

void	set_graft_l3 (bool graft_l3)

void	set_graft_h1 (bool graft_h1)

void	set_graft_h2 (bool graft_h2)

void	set_graft_h3 (bool graft_h3)

void	set_h3_stem_graft (bool h3_stem_graft)

void	set_packonly_after_graft (bool setting)

void	set_stem_optimize (bool setting)

void	set_camelid (bool camelid)

void	set_camelid_constraints (bool camelid_constraints)

void	set_benchmark (bool benchmark)

void	set_cst_weight (core::Real cst_weight)

void	set_sc_min (bool scmin)

void	set_rt_min (bool rtmin)

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

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

void	show (std::ostream &out=std::cout) const override

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 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 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...

Static Public Member Functions
static void	register_options ()
	Associates relevant options with the AntibodyModeler class. More...

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...

Private Member Functions
void	finalize_setup (core::pose::Pose &pose)

void	init ()

void	setup_objects ()

void	init_from_options ()

Private Attributes
bool	graft_l1_

bool	graft_l2_

bool	graft_l3_

bool	graft_h1_

bool	graft_h2_

bool	graft_h3_

bool	h3_no_stem_graft_

bool	packonly_after_graft_

bool	camelid_

bool	camelid_constraints_

bool	sc_min_

bool	rt_min_

bool	benchmark_

bool	stem_optimize_

core::Real	cst_weight_

core::scoring::ScoreFunctionOP	scorefxn_pack_

AntibodyInfoOP	ab_info_

Ab_TemplateInfoOP	ab_t_info_

core::pack::task::TaskFactoryOP	tf_

protocols::moves::SequenceMoverOP	graft_sequence_

protocols::moves::SequenceMoverOP	optimize_sequence_

CDRsMinPackMinOP	cdrs_min_pack_min_

Friends
std::ostream &	operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2)

Additional Inherited Members
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...

Member Typedef Documentation

◆ GraftMap

typedef std::map< std::string, bool > protocols::antibody::GraftCDRLoopsProtocol::GraftMap

Constructor & Destructor Documentation

◆ GraftCDRLoopsProtocol()

protocols::antibody::GraftCDRLoopsProtocol::GraftCDRLoopsProtocol ( )

References init().

◆ ~GraftCDRLoopsProtocol()

protocols::antibody::GraftCDRLoopsProtocol::~GraftCDRLoopsProtocol ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ab_info_, protocols::antibody::align_to_native(), camelid_constraints_, cdrs_min_pack_min_, display_constraint_residues(), core::pose::Pose::dump_pdb(), finalize_setup(), protocols::moves::Mover::get_native_pose(), graft_sequence_, optimize_sequence_, core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::set_ss_from_phipsi(), core::pose::Pose::size(), stem_optimize_, and protocols::antibody::TR().

◆ clone()

protocols::moves::MoverOP protocols::antibody::GraftCDRLoopsProtocol::clone ( ) const

overridevirtual

Return a clone of the Mover object.

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.

◆ display_constraint_residues()

void protocols::antibody::GraftCDRLoopsProtocol::display_constraint_residues ( core::pose::Pose & pose )

References ab_info_, protocols::antibody::Extended, protocols::antibody::h3, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::loops::stop, and protocols::antibody::TR().

Referenced by apply().

◆ finalize_setup()

void protocols::antibody::GraftCDRLoopsProtocol::finalize_setup ( core::pose::Pose & pose )

private

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ init()

void protocols::antibody::GraftCDRLoopsProtocol::init ( void )

private

References init_from_options(), register_options(), set_default(), setup_objects(), and protocols::moves::Mover::type().

Referenced by GraftCDRLoopsProtocol().

◆ init_from_options()

void protocols::antibody::GraftCDRLoopsProtocol::init_from_options ( )

private

◆ register_options()

void protocols::antibody::GraftCDRLoopsProtocol::register_options ( )

static

Associates relevant options with the AntibodyModeler class.

Referenced by init().

◆ set_benchmark()

void protocols::antibody::GraftCDRLoopsProtocol::set_benchmark ( bool benchmark )

inline

References benchmark_.

Referenced by init_from_options().

◆ set_camelid()

void protocols::antibody::GraftCDRLoopsProtocol::set_camelid ( bool camelid )

inline

References camelid_.

Referenced by init_from_options().

◆ set_camelid_constraints()

void protocols::antibody::GraftCDRLoopsProtocol::set_camelid_constraints ( bool camelid_constraints )

inline

References camelid_constraints_.

Referenced by init_from_options().

◆ set_cst_weight()

void protocols::antibody::GraftCDRLoopsProtocol::set_cst_weight ( core::Real cst_weight )

inline

References cst_weight_.

Referenced by init_from_options().

◆ set_default()

void protocols::antibody::GraftCDRLoopsProtocol::set_default ( )

Assigns default values to primitive members.

References benchmark_, camelid_, camelid_constraints_, cst_weight_, graft_h1_, graft_h2_, graft_h3_, graft_l1_, graft_l2_, graft_l3_, h3_no_stem_graft_, packonly_after_graft_, rt_min_, sc_min_, stem_optimize_, and protocols::antibody::TR().

Referenced by init().

◆ set_graft_h1()

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_h1 ( bool graft_h1 )

inline

References graft_h1_.

Referenced by init_from_options().

◆ set_graft_h2()

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_h2 ( bool graft_h2 )

inline

References graft_h2_.

Referenced by init_from_options().

◆ set_graft_h3()

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_h3 ( bool graft_h3 )

inline

References graft_h3_.

Referenced by init_from_options().

◆ set_graft_l1()

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_l1 ( bool graft_l1 )

inline

References graft_l1_.

Referenced by init_from_options().

◆ set_graft_l2()

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_l2 ( bool graft_l2 )

inline

References graft_l2_.

Referenced by init_from_options().

◆ set_graft_l3()

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_l3 ( bool graft_l3 )

inline

References graft_l3_.

Referenced by init_from_options().

◆ set_h3_stem_graft()

void protocols::antibody::GraftCDRLoopsProtocol::set_h3_stem_graft ( bool h3_stem_graft )

inline

References h3_no_stem_graft_.

Referenced by init_from_options().

◆ set_packonly_after_graft()

void protocols::antibody::GraftCDRLoopsProtocol::set_packonly_after_graft ( bool setting )

inline

References packonly_after_graft_.

Referenced by init_from_options().

◆ set_rt_min()

void protocols::antibody::GraftCDRLoopsProtocol::set_rt_min ( bool rtmin )

inline

References rt_min_.

◆ set_sc_min()

void protocols::antibody::GraftCDRLoopsProtocol::set_sc_min ( bool scmin )

inline

References sc_min_.

◆ set_stem_optimize()

void protocols::antibody::GraftCDRLoopsProtocol::set_stem_optimize ( bool setting )

inline

References stem_optimize_.

Referenced by init_from_options().

◆ setup_objects()

void protocols::antibody::GraftCDRLoopsProtocol::setup_objects ( )

private

References ab_info_, ab_t_info_, core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::scoring::get_score_function(), graft_sequence_, core::scoring::overlap_chainbreak, scorefxn_pack_, and tf_.

Referenced by init().

◆ show()

void protocols::antibody::GraftCDRLoopsProtocol::show ( std::ostream & out = std::cout ) const

overridevirtual

Show the complete setup of the docking protocol

Reimplemented from protocols::moves::Mover.

References core::conformation::membrane::out.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		const GraftCDRLoopsProtocol &	ab_m_2
	)

friend

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::GraftCDRLoopsProtocol::ab_info_

private

Referenced by apply(), display_constraint_residues(), finalize_setup(), and setup_objects().

◆ ab_t_info_

Ab_TemplateInfoOP protocols::antibody::GraftCDRLoopsProtocol::ab_t_info_

private

Referenced by finalize_setup(), and setup_objects().

◆ benchmark_

bool protocols::antibody::GraftCDRLoopsProtocol::benchmark_

private

Referenced by finalize_setup(), set_benchmark(), and set_default().

◆ camelid_

bool protocols::antibody::GraftCDRLoopsProtocol::camelid_

private

Referenced by finalize_setup(), init_from_options(), set_camelid(), and set_default().

◆ camelid_constraints_

bool protocols::antibody::GraftCDRLoopsProtocol::camelid_constraints_

private

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

◆ cdrs_min_pack_min_

CDRsMinPackMinOP protocols::antibody::GraftCDRLoopsProtocol::cdrs_min_pack_min_

private

Referenced by apply(), and finalize_setup().

◆ cst_weight_

core::Real protocols::antibody::GraftCDRLoopsProtocol::cst_weight_

private

Referenced by finalize_setup(), set_cst_weight(), and set_default().

◆ graft_h1_

bool protocols::antibody::GraftCDRLoopsProtocol::graft_h1_

private

Referenced by finalize_setup(), set_default(), and set_graft_h1().

◆ graft_h2_

bool protocols::antibody::GraftCDRLoopsProtocol::graft_h2_

private

Referenced by finalize_setup(), set_default(), and set_graft_h2().

◆ graft_h3_

bool protocols::antibody::GraftCDRLoopsProtocol::graft_h3_

private

Referenced by finalize_setup(), set_default(), and set_graft_h3().

◆ graft_l1_

bool protocols::antibody::GraftCDRLoopsProtocol::graft_l1_

private

Referenced by finalize_setup(), init_from_options(), set_default(), and set_graft_l1().

◆ graft_l2_

bool protocols::antibody::GraftCDRLoopsProtocol::graft_l2_

private

Referenced by finalize_setup(), init_from_options(), set_default(), and set_graft_l2().

◆ graft_l3_

bool protocols::antibody::GraftCDRLoopsProtocol::graft_l3_

private

Referenced by finalize_setup(), init_from_options(), set_default(), and set_graft_l3().

◆ graft_sequence_

protocols::moves::SequenceMoverOP protocols::antibody::GraftCDRLoopsProtocol::graft_sequence_

private

Referenced by apply(), finalize_setup(), and setup_objects().

◆ h3_no_stem_graft_

bool protocols::antibody::GraftCDRLoopsProtocol::h3_no_stem_graft_

private

Referenced by finalize_setup(), set_default(), and set_h3_stem_graft().

◆ optimize_sequence_

protocols::moves::SequenceMoverOP protocols::antibody::GraftCDRLoopsProtocol::optimize_sequence_

private

Referenced by apply(), and finalize_setup().

◆ packonly_after_graft_

bool protocols::antibody::GraftCDRLoopsProtocol::packonly_after_graft_

private

Referenced by finalize_setup(), set_default(), and set_packonly_after_graft().

◆ rt_min_

bool protocols::antibody::GraftCDRLoopsProtocol::rt_min_

private

Referenced by finalize_setup(), set_default(), and set_rt_min().

◆ sc_min_

bool protocols::antibody::GraftCDRLoopsProtocol::sc_min_

private

Referenced by finalize_setup(), set_default(), and set_sc_min().

◆ scorefxn_pack_

core::scoring::ScoreFunctionOP protocols::antibody::GraftCDRLoopsProtocol::scorefxn_pack_

private

Referenced by setup_objects().

◆ stem_optimize_

bool protocols::antibody::GraftCDRLoopsProtocol::stem_optimize_

private

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

◆ tf_

core::pack::task::TaskFactoryOP protocols::antibody::GraftCDRLoopsProtocol::tf_

private

Referenced by finalize_setup(), and setup_objects().

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

src/protocols/antibody/GraftCDRLoopsProtocol.hh
src/protocols/antibody/GraftCDRLoopsProtocol.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Member Typedef Documentation

◆ GraftMap

Constructor & Destructor Documentation

◆ GraftCDRLoopsProtocol()

◆ ~GraftCDRLoopsProtocol()

Member Function Documentation

◆ apply()

◆ clone()

◆ display_constraint_residues()

◆ finalize_setup()

◆ get_name()

◆ init()

◆ init_from_options()

◆ register_options()

◆ set_benchmark()

◆ set_camelid()

◆ set_camelid_constraints()

◆ set_cst_weight()

◆ set_default()

◆ set_graft_h1()

◆ set_graft_h2()

◆ set_graft_h3()

◆ set_graft_l1()

◆ set_graft_l2()

◆ set_graft_l3()

◆ set_h3_stem_graft()

◆ set_packonly_after_graft()

◆ set_rt_min()

◆ set_sc_min()

◆ set_stem_optimize()

◆ setup_objects()

◆ show()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ ab_info_

◆ ab_t_info_

◆ benchmark_

◆ camelid_

◆ camelid_constraints_

◆ cdrs_min_pack_min_

◆ cst_weight_

◆ graft_h1_

◆ graft_h2_

◆ graft_h3_

◆ graft_l1_

◆ graft_l2_

◆ graft_l3_

◆ graft_sequence_

◆ h3_no_stem_graft_

◆ optimize_sequence_

◆ packonly_after_graft_

◆ rt_min_

◆ sc_min_

◆ scorefxn_pack_

◆ stem_optimize_

◆ tf_