#include <DockMCMProtocol.hh>

Inheritance diagram for protocols::docking::DockMCMProtocol:

[legend]

Public Member Functions
	DockMCMProtocol ()
	Default constructor. More...

	DockMCMProtocol (core::Size const rb_jump)
	Constructor with one argument - the jump number. More...

	DockMCMProtocol (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 the docking scorefunction and the third is the packing scorefxn. More...

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

	DockMCMProtocol (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 the docking scorefunction and the third is the packing scorefunction. More...

	~DockMCMProtocol () override

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

void	init ()
	Performs the setup specific to this subclass of DockingHighRes (sets up filters). More...

void	set_filter (DockingHighResFilterOP filter)

void	apply (core::pose::Pose &pose) override

void	set_move_map (core::kinematics::MoveMapOP movemap)

void	set_second_cycle (core::Size const &num)

void	set_first_cycle (core::Size const &num)

core::scoring::ScoreFunctionCOP	scorefxn_docking () const

core::scoring::ScoreFunctionCOP	scorefxn_packing () const

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...

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...

Static Public Member Functions
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 Types
typedef core::Real	Real

Private Attributes
DockingHighResFilterOP	filter_

DockMCMCycleOP	dock_mcm_

bool	movemap_reset_

core::kinematics::MoveMapOP	movemap_

core::Size	num_of_first_cycle_

core::Size	num_of_second_cycle_

Friends
std::ostream &	operator<< (std::ostream &out, const DockMCMProtocol &dmp)

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...

Member Typedef Documentation

◆ Real

typedef core::Real protocols::docking::DockMCMProtocol::Real

private

Constructor & Destructor Documentation

◆ DockMCMProtocol() [1/5]

protocols::docking::DockMCMProtocol::DockMCMProtocol ( )

Default constructor.

References init().

◆ DockMCMProtocol() [2/5]

protocols::docking::DockMCMProtocol::DockMCMProtocol ( core::Size const rb_jump )

Constructor with one argument - the jump number.

References init().

◆ DockMCMProtocol() [3/5]

protocols::docking::DockMCMProtocol::DockMCMProtocol	(	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 the docking scorefunction and the third is the packing scorefxn.

References init().

◆ DockMCMProtocol() [4/5]

protocols::docking::DockMCMProtocol::DockMCMProtocol	(	DockJumps const	movable_jumps,
		core::scoring::ScoreFunctionOP	scorefxn
	)

Constructor with two arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and packing.

References init().

◆ DockMCMProtocol() [5/5]

protocols::docking::DockMCMProtocol::DockMCMProtocol	(	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 the docking scorefunction and the third is the packing scorefunction.

References init().

◆ ~DockMCMProtocol()

protocols::docking::DockMCMProtocol::~DockMCMProtocol ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::docking::DockMCMProtocol::apply ( core::pose::Pose & pose )

overridevirtual

decides what to call according to options

Implements protocols::docking::DockingHighRes.

◆ clone()

protocols::moves::MoverOP protocols::docking::DockMCMProtocol::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.