MoveSet step of Snugdock as described in: More...

#include <SnugDock.hh>

Inheritance diagram for protocols::antibody::snugdock::SnugDock:

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

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

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

	~SnugDock () override

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

void	debug ()

core::Size	number_of_high_resolution_cycles () const

void	number_of_high_resolution_cycles (core::Size const number_of_high_resolution_cycles)

void	set_antibody_info (AntibodyInfoOP antibody_info)

void	set_CDR_loops (std::map< protocols::antibody::CDRNameEnum, loops::Loop > cdr_loops)

void	set_ab_has_light_chain (bool ab_has_light_chain)

void	set_vh_vl_jump (bool vh_vl_jump)

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

bool	high_res_kink_constraint () const

void	high_res_kink_constraint (bool const setting)

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

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

Public Member Functions inherited from protocols::docking::DockingHighRes
	DockingHighRes ()
	Default constructor. More...

	DockingHighRes (core::Size const rb_jump)
	Constructor with one argument - the jump number to dock over. More...

	DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
	Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing. More...

	DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...

	DockingHighRes (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with three arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...

	DockingHighRes (DockingHighRes const &old_instance)

	~DockingHighRes () override

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

void	set_ignore_default_task (bool ignore_default_task)

bool	ignore_default_task ()

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)

void	set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)

DockJumps &	movable_jumps ()

DockJumps const &	movable_jumps () const

void	set_movable_jumps (DockJumps movable_jumps)

core::pack::task::TaskFactoryCOP	task_factory ()

void	set_sc_min (bool sc_min)

void	set_rt_min (bool rt_min)

void	set_partners (std::string partners)

std::string	get_partners () const

void	set_interface_definition_task_operation (protocols::simple_task_operations::InterfaceTaskOperationOP interface_definition)

void	set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)

void	add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)

utility::vector1 < core::pack::task::operation::TaskOperationOP >	get_additional_task_operarations ()

bool	sc_min ()

bool	rt_min ()

std::string	partners ()

core::scoring::ScoreFunctionOP	scorefxn () const

core::scoring::ScoreFunctionOP	scorefxn_pack () const

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 SnugDock class. More...

static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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 const &pose)

void	set_default ()

void	init ()

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

void	init_from_options ()

protocols::loop_modeler::LoopModelerOP	refine_loop () const

Friends
std::ostream &	operator<< (std::ostream &out, SnugDock const &snugdock)

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::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP	tf2 ()

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

MoveSet step of Snugdock as described in:

Sircar A, Gray JJ (2010) SnugDock: Paratope Structural Optimization duringAntibody-Antigen Docking Compensates for Errors in Antibody Homology Models. PLoS Comput Biol 6(1): e1000644. doi:10.1371/journal.pcbi.1000644

This is the main high resolution step of the overall SnugDock protocol. See the Show method for a complete description of the algorithm.

Constructor & Destructor Documentation

protocols::antibody::snugdock::SnugDock::SnugDock ( )

default constructor

References init().

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

copy constructor

References init_for_equal_operator_and_copy_constructor().

protocols::antibody::snugdock::SnugDock::~SnugDock ( )

overridedefault

Member Function Documentation

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

overridevirtual

Main Method.

Implements protocols::docking::DockingHighRes.

References get_name(), high_resolution_step_, mc_, number_of_high_resolution_cycles_, pre_minimization_, protocols::docking::DockingHighRes::scorefxn(), setup_objects(), show(), and protocols::antibody::TR().

protocols::moves::MoverOP protocols::antibody::snugdock::SnugDock::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.

void protocols::antibody::snugdock::SnugDock::debug ( )

References debug_, and number_of_high_resolution_cycles_.

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

overridevirtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::docking::DockingHighRes.

References mover_name().

Referenced by apply(), and setup_objects().

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

inline

References high_res_kink_constraint_.

Referenced by setup_objects().

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

inline

References high_res_kink_constraint_.

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

private

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

Referenced by SnugDock().

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

private

References antibody_info_, debug_, high_resolution_step_, mc_, number_of_high_resolution_cycles_, and pre_minimization_.

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

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

private

References number_of_high_resolution_cycles().

Referenced by init().

std::string protocols::antibody::snugdock::SnugDock::mover_name ( )

static

Referenced by get_name(), protocols::antibody::snugdock::SnugDockCreator::keyname(), and provide_xml_schema().

Size protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles ( ) const

References number_of_high_resolution_cycles_.

Referenced by init_from_options(), and number_of_high_resolution_cycles().

void protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles ( core::Size const number_of_high_resolution_cycles )

References number_of_high_resolution_cycles(), and number_of_high_resolution_cycles_.

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

assignment operator

References init_for_equal_operator_and_copy_constructor().

void protocols::antibody::snugdock::SnugDock::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::antibody::snugdock::SnugDockCreator::provide_xml_schema().

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

private

Referenced by setup_objects().

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

static

Associates relevant options with the SnugDock class.

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

Referenced by protocols::antibody::snugdock::SnugDockProtocol::register_options().

bool protocols::antibody::snugdock::SnugDock::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.

void protocols::antibody::snugdock::SnugDock::set_ab_has_light_chain ( bool ab_has_light_chain )

References ab_has_light_chain_.

void protocols::antibody::snugdock::SnugDock::set_antibody_info ( AntibodyInfoOP antibody_info )

References antibody_info_.

void protocols::antibody::snugdock::SnugDock::set_CDR_loops ( std::map< protocols::antibody::CDRNameEnum, loops::Loop > cdr_loops )

References CDR_loops_.

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

private

References high_res_kink_constraint_, and number_of_high_resolution_cycles_.

Referenced by init().

void protocols::antibody::snugdock::SnugDock::set_task_factory ( core::pack::task::TaskFactoryCOP tf )

References tf_.

void protocols::antibody::snugdock::SnugDock::set_vh_vl_jump ( bool vh_vl_jump )

References vh_vl_jump_.

void protocols::antibody::snugdock::SnugDock::setup_objects ( Pose const & pose )

private

void protocols::antibody::snugdock::SnugDock::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.

Referenced by apply().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		SnugDock const &	snugdock
	)

friend

Member Data Documentation

bool protocols::antibody::snugdock::SnugDock::ab_has_light_chain_

private

Referenced by set_ab_has_light_chain(), and setup_objects().

AntibodyInfoOP protocols::antibody::snugdock::SnugDock::antibody_info_

private

Referenced by init_for_equal_operator_and_copy_constructor(), and set_antibody_info().

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

private

Referenced by set_CDR_loops(), and setup_objects().

bool protocols::antibody::snugdock::SnugDock::debug_

private

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

bool protocols::antibody::snugdock::SnugDock::high_res_kink_constraint_

private

Referenced by high_res_kink_constraint(), and set_default().

moves::MoverContainerOP protocols::antibody::snugdock::SnugDock::high_resolution_step_

private

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

moves::MonteCarloOP protocols::antibody::snugdock::SnugDock::mc_

private

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

core::Size protocols::antibody::snugdock::SnugDock::number_of_high_resolution_cycles_

private

Referenced by apply(), debug(), init_for_equal_operator_and_copy_constructor(), number_of_high_resolution_cycles(), and set_default().

antibody::CDRsMinPackMinOP protocols::antibody::snugdock::SnugDock::pre_minimization_

private

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

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

private

Referenced by set_task_factory(), and setup_objects().

core::Size protocols::antibody::snugdock::SnugDock::vh_vl_jump_

private

Referenced by set_vh_vl_jump(), and setup_objects().

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

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

Private Attributes
AntibodyInfoOP	antibody_info_

moves::MonteCarloOP	mc_

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

bool	ab_has_light_chain_

core::Size	vh_vl_jump_

core::pack::task::TaskFactoryOP	tf_

moves::MoverContainerOP	high_resolution_step_

antibody::CDRsMinPackMinOP	pre_minimization_

bool	debug_

bool	high_res_kink_constraint_

core::Size	number_of_high_resolution_cycles_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation