#include <SnugDockProtocol.hh>

Inheritance diagram for protocols::antibody::snugdock::SnugDockProtocol:

[legend]

Public Member Functions
	SnugDockProtocol ()
	default constructor More...

	SnugDockProtocol (SnugDockProtocol const &rhs)
	copy constructor More...

SnugDockProtocol &	operator= (SnugDockProtocol const &rhs)
	assignment operator More...

	~SnugDockProtocol () override

void	apply (Pose &) override
	Main Method. More...

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

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

protocols::moves::MoverOP	fresh_instance () const override
	fresh_instance returns a default-constructed object for JD2 More...

bool	reinitialize_for_new_input () const override
	This mover retains state such that a fresh version is needed if the input Pose is about to change. More...

bool	auto_generate_kink_constraint () const

void	auto_generate_kink_constraint (bool const setting)

bool	high_res_kink_constraint () const

void	high_res_kink_constraint (bool const setting)

bool	low_res_kink_constraint () const

void	low_res_kink_constraint (bool const setting)

bool	constrain_vlvh_qq () const

void	constrain_vlvh_qq (bool const setting)

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

core::pack::task::TaskFactoryOP	repack_tf_from_residue_sets (Pose const &pose, std::set< core::Size > const &ab_residues, std::set< core::Size > const &ag_residues)

void	setup_ab_ag_foldtree (Pose &pose, AntibodyInfoOP antibody_info)

core::conformation::ResidueOP	place_VRT_at_residue_COM (Pose const &pose, utility::vector1< bool > residues)

core::conformation::ResidueOP	place_VRT_at_residue_COM (Pose const &pose, core::Size start, core::Size stop)

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...

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 SnugDockProtocol 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	setup_objects (Pose &pose)

void	setup_loop_refinement_movers ()

void	update_fold_tree_from_bool_vector ()

void	init ()

void	init_for_equal_operator_and_copy_constructor (SnugDockProtocol &lhs, SnugDockProtocol const &rhs)

void	init_from_options ()

void	set_default ()

docking::DockingProtocolOP	docking () const

protocols::loop_modeler::LoopModelerOP	refine_loop () const

Private Attributes
AntibodyInfoOP	antibody_info_

core::pose::PDBInfoOP	pdb_info_

std::map< protocols::antibody::CDRNameEnum, loops::Loop >	CDR_loops_

bool	ab_has_light_chain_

core::Size	vh_vl_jump_

std::set< core::Size >	ab_residues_

std::set< core::Size >	ag_residues_

core::pack::task::TaskFactoryOP	tf_

protocols::loop_modeler::LoopModelerOP	low_res_refine_cdr_h2_

protocols::loop_modeler::LoopModelerOP	low_res_refine_cdr_h3_

docking::DockingProtocolOP	docking_

bool	auto_generate_kink_constraint_

bool	high_res_kink_constraint_

bool	low_res_kink_constraint_

bool	constrain_vlvh_qq_

Friends
std::ostream &	operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)

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

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...

Constructor & Destructor Documentation

◆ SnugDockProtocol() [1/2]

protocols::antibody::snugdock::SnugDockProtocol::SnugDockProtocol ( )

default constructor

References init().

◆ SnugDockProtocol() [2/2]

protocols::antibody::snugdock::SnugDockProtocol::SnugDockProtocol ( SnugDockProtocol const & rhs )

copy constructor

References init_for_equal_operator_and_copy_constructor().

◆ ~SnugDockProtocol()

protocols::antibody::snugdock::SnugDockProtocol::~SnugDockProtocol ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::antibody::snugdock::SnugDockProtocol::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References antibody_info_, protocols::analysis::InterfaceAnalyzerMover::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), auto_generate_kink_constraint(), CDR_loops_, core::pose::Pose::delete_residue_slow(), docking(), get_name(), core::scoring::get_score_function(), protocols::antibody::h3, core::conformation::Residue::is_virtual_residue(), protocols::antibody::kink_constrain_antibody_H3(), core::pose::Pose::residue(), setup_objects(), show(), protocols::loops::stop, and protocols::antibody::TR().

◆ auto_generate_kink_constraint() [1/2]

bool protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint ( ) const

inline

References auto_generate_kink_constraint_.

Referenced by apply(), init_from_options(), and setup_loop_refinement_movers().

◆ auto_generate_kink_constraint() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint ( bool const setting )

inline

References auto_generate_kink_constraint_.

◆ clone()

protocols::moves::MoverOP protocols::antibody::snugdock::SnugDockProtocol::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.

◆ constrain_vlvh_qq() [1/2]

bool protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq ( ) const

inline

References constrain_vlvh_qq_.

Referenced by init_from_options(), and setup_objects().

◆ constrain_vlvh_qq() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq ( bool const setting )

inline

References constrain_vlvh_qq_.

◆ docking()

docking::DockingProtocolOP protocols::antibody::snugdock::SnugDockProtocol::docking ( ) const

private

References docking_.

Referenced by apply(), and setup_objects().

◆ fresh_instance()

protocols::moves::MoverOP protocols::antibody::snugdock::SnugDockProtocol::fresh_instance ( ) const

overridevirtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::antibody::snugdock::SnugDockProtocol::get_name ( ) const

overridevirtual

Each derived class must specify its name.

Implements protocols::moves::Mover.

References protocols::moves::Mover::type().

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

◆ high_res_kink_constraint() [1/2]

bool protocols::antibody::snugdock::SnugDockProtocol::high_res_kink_constraint ( ) const

inline

References high_res_kink_constraint_.

Referenced by init_from_options(), and setup_objects().

◆ high_res_kink_constraint() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::high_res_kink_constraint ( bool const setting )

inline

References high_res_kink_constraint_.

◆ init()

void protocols::antibody::snugdock::SnugDockProtocol::init ( void )

private

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

Referenced by SnugDockProtocol().

◆ init_for_equal_operator_and_copy_constructor()

void protocols::antibody::snugdock::SnugDockProtocol::init_for_equal_operator_and_copy_constructor	(	SnugDockProtocol &	lhs,
		SnugDockProtocol const &	rhs
	)

private

References antibody_info_, docking_, low_res_refine_cdr_h2_, and low_res_refine_cdr_h3_.

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

◆ init_from_options()

void protocols::antibody::snugdock::SnugDockProtocol::init_from_options ( )

private

References auto_generate_kink_constraint(), constrain_vlvh_qq(), high_res_kink_constraint(), and low_res_kink_constraint().

Referenced by init().

◆ low_res_kink_constraint() [1/2]

bool protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint ( ) const

inline

References low_res_kink_constraint_.

Referenced by init_from_options(), and setup_loop_refinement_movers().

◆ low_res_kink_constraint() [2/2]

void protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint ( bool const setting )

inline

References low_res_kink_constraint_.

◆ operator=()

SnugDockProtocol & protocols::antibody::snugdock::SnugDockProtocol::operator= ( SnugDockProtocol const & rhs )

assignment operator

References init_for_equal_operator_and_copy_constructor().

◆ place_VRT_at_residue_COM() [1/2]

core::conformation::ResidueOP protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM	(	Pose const &	pose,
		core::Size	start,
		core::Size	stop
	)

References core::conformation::ResidueFactory::create_residue(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), protocols::loops::start, protocols::loops::stop, core::pose::virtual_type_for_pose(), and core::conformation::Residue::xyz().

◆ place_VRT_at_residue_COM() [2/2]

core::conformation::ResidueOP protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM	(	Pose const &	pose,
		utility::vector1< bool >	residues
	)

References core::conformation::ResidueFactory::create_residue(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), core::pose::virtual_type_for_pose(), and core::conformation::Residue::xyz().

Referenced by setup_ab_ag_foldtree().

◆ refine_loop()

protocols::loop_modeler::LoopModelerOP protocols::antibody::snugdock::SnugDockProtocol::refine_loop ( ) const

private

Referenced by setup_loop_refinement_movers().

◆ register_options()

void protocols::antibody::snugdock::SnugDockProtocol::register_options ( )

static

Associates relevant options with the SnugDockProtocol class.

References protocols::antibody::snugdock::SnugDock::register_options(), and protocols::docking::DockingProtocol::register_options().

◆ reinitialize_for_new_input()

bool protocols::antibody::snugdock::SnugDockProtocol::reinitialize_for_new_input ( ) const

overridevirtual

This mover retains state such that a fresh version is needed if the input Pose is about to change.

Reimplemented from protocols::moves::Mover.

◆ repack_tf_from_residue_sets()

core::pack::task::TaskFactoryOP protocols::antibody::snugdock::SnugDockProtocol::repack_tf_from_residue_sets	(	Pose const &	pose,
		std::set< core::Size > const &	ab_residues,
		std::set< core::Size > const &	ag_residues
	)

References core::select::util::calc_interacting_vector().

Referenced by setup_objects().

◆ set_default()

void protocols::antibody::snugdock::SnugDockProtocol::set_default ( )

private

References ab_has_light_chain_, auto_generate_kink_constraint_, constrain_vlvh_qq_, high_res_kink_constraint_, and low_res_kink_constraint_.

Referenced by init().

◆ setup_ab_ag_foldtree()

void protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree	(	Pose &	pose,
		AntibodyInfoOP	antibody_info
	)

◆ setup_loop_refinement_movers()

void protocols::antibody::snugdock::SnugDockProtocol::setup_loop_refinement_movers ( )

private

References core::scoring::angle_constraint, antibody_info_, core::scoring::atom_pair_constraint, auto_generate_kink_constraint(), CDR_loops_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, get_name(), protocols::antibody::h2, protocols::antibody::h3, low_res_kink_constraint(), low_res_refine_cdr_h2_, low_res_refine_cdr_h3_, core::scoring::overlap_chainbreak, and refine_loop().

Referenced by setup_objects().

◆ setup_objects()

void protocols::antibody::snugdock::SnugDockProtocol::setup_objects ( Pose & pose )

private

References ab_has_light_chain_, ab_residues_, ag_residues_, antibody_info_, CDR_loops_, constrain_vlvh_qq(), docking(), docking_, get_name(), high_res_kink_constraint(), low_res_refine_cdr_h2_, low_res_refine_cdr_h3_, repack_tf_from_residue_sets(), setup_ab_ag_foldtree(), setup_loop_refinement_movers(), tf_, protocols::antibody::TR(), and vh_vl_jump_.

Referenced by apply().

◆ show()

void protocols::antibody::snugdock::SnugDockProtocol::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

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

Referenced by apply().

◆ update_fold_tree_from_bool_vector()

void protocols::antibody::snugdock::SnugDockProtocol::update_fold_tree_from_bool_vector ( )

private

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		SnugDockProtocol const &	snugdockprotocol
	)

friend

Member Data Documentation

◆ ab_has_light_chain_

bool protocols::antibody::snugdock::SnugDockProtocol::ab_has_light_chain_

private

Referenced by set_default(), setup_ab_ag_foldtree(), and setup_objects().

◆ ab_residues_

std::set< core::Size > protocols::antibody::snugdock::SnugDockProtocol::ab_residues_

private

Referenced by setup_ab_ag_foldtree(), and setup_objects().

◆ ag_residues_

std::set< core::Size > protocols::antibody::snugdock::SnugDockProtocol::ag_residues_

private

Referenced by setup_ab_ag_foldtree(), and setup_objects().

◆ antibody_info_

AntibodyInfoOP protocols::antibody::snugdock::SnugDockProtocol::antibody_info_

private

Referenced by apply(), init_for_equal_operator_and_copy_constructor(), setup_loop_refinement_movers(), and setup_objects().

◆ auto_generate_kink_constraint_

bool protocols::antibody::snugdock::SnugDockProtocol::auto_generate_kink_constraint_

private

Referenced by auto_generate_kink_constraint(), and set_default().

◆ CDR_loops_

std::map<protocols::antibody::CDRNameEnum,loops::Loop> protocols::antibody::snugdock::SnugDockProtocol::CDR_loops_

private

Referenced by apply(), setup_ab_ag_foldtree(), setup_loop_refinement_movers(), and setup_objects().

◆ constrain_vlvh_qq_

bool protocols::antibody::snugdock::SnugDockProtocol::constrain_vlvh_qq_

private

Referenced by constrain_vlvh_qq(), and set_default().

◆ docking_

docking::DockingProtocolOP protocols::antibody::snugdock::SnugDockProtocol::docking_

mutableprivate

Referenced by docking(), init_for_equal_operator_and_copy_constructor(), and setup_objects().

◆ high_res_kink_constraint_

bool protocols::antibody::snugdock::SnugDockProtocol::high_res_kink_constraint_

private

Referenced by high_res_kink_constraint(), and set_default().

◆ low_res_kink_constraint_

bool protocols::antibody::snugdock::SnugDockProtocol::low_res_kink_constraint_

private

Referenced by low_res_kink_constraint(), and set_default().

◆ low_res_refine_cdr_h2_

protocols::loop_modeler::LoopModelerOP protocols::antibody::snugdock::SnugDockProtocol::low_res_refine_cdr_h2_

private

Referenced by init_for_equal_operator_and_copy_constructor(), setup_loop_refinement_movers(), and setup_objects().

◆ low_res_refine_cdr_h3_

protocols::loop_modeler::LoopModelerOP protocols::antibody::snugdock::SnugDockProtocol::low_res_refine_cdr_h3_

private

Referenced by init_for_equal_operator_and_copy_constructor(), setup_loop_refinement_movers(), and setup_objects().

◆ pdb_info_

core::pose::PDBInfoOP protocols::antibody::snugdock::SnugDockProtocol::pdb_info_

private

◆ tf_

core::pack::task::TaskFactoryOP protocols::antibody::snugdock::SnugDockProtocol::tf_

private

Referenced by setup_objects().

◆ vh_vl_jump_

core::Size protocols::antibody::snugdock::SnugDockProtocol::vh_vl_jump_

private

Referenced by setup_ab_ag_foldtree(), and setup_objects().

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

src/protocols/antibody/snugdock/SnugDockProtocol.hh
src/protocols/antibody/snugdock/SnugDockProtocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ SnugDockProtocol() [1/2]

◆ SnugDockProtocol() [2/2]

◆ ~SnugDockProtocol()

Member Function Documentation

◆ apply()

◆ auto_generate_kink_constraint() [1/2]

◆ auto_generate_kink_constraint() [2/2]

◆ clone()

◆ constrain_vlvh_qq() [1/2]

◆ constrain_vlvh_qq() [2/2]

◆ docking()

◆ fresh_instance()

◆ get_name()

◆ high_res_kink_constraint() [1/2]

◆ high_res_kink_constraint() [2/2]

◆ init()

◆ init_for_equal_operator_and_copy_constructor()

◆ init_from_options()

◆ low_res_kink_constraint() [1/2]

◆ low_res_kink_constraint() [2/2]

◆ operator=()

◆ place_VRT_at_residue_COM() [1/2]

◆ place_VRT_at_residue_COM() [2/2]

◆ refine_loop()

◆ register_options()

◆ reinitialize_for_new_input()

◆ repack_tf_from_residue_sets()

◆ set_default()

◆ setup_ab_ag_foldtree()

◆ setup_loop_refinement_movers()

◆ setup_objects()

◆ show()

◆ update_fold_tree_from_bool_vector()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ ab_has_light_chain_

◆ ab_residues_

◆ ag_residues_

◆ antibody_info_

◆ auto_generate_kink_constraint_

◆ CDR_loops_

◆ constrain_vlvh_qq_

◆ docking_

◆ high_res_kink_constraint_

◆ low_res_kink_constraint_

◆ low_res_refine_cdr_h2_

◆ low_res_refine_cdr_h3_

◆ pdb_info_

◆ tf_

◆ vh_vl_jump_