#include <DockMCMProtocol.hh>

Inheritance diagram for protocols::docking::DockMCMProtocol:

Collaboration diagram for protocols::docking::DockMCMProtocol:

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 ()

protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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

void	set_filter (DockingHighResFilterOP filter)

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

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

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

void	set_second_cycle (Size const &num)

void	set_first_cycle (Size const &num)

core::scoring::ScoreFunctionCOP	scorefxn_docking () const

core::scoring::ScoreFunctionCOP	scorefxn_packing () const

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)

virtual	~DockingHighRes ()

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

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)

void	set_interface_definition_task_operation (protocols::toolbox::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	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

Private Types
typedef core::Real	Real

Private Attributes
DockingHighResFilterOP	filter_

DockMCMCycleOP	dock_mcm_

bool	movemap_reset_

core::kinematics::MoveMapOP	movemap_

Size	num_of_first_cycle_

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::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP	tf2 ()

Detailed Description

Definition at line 40 of file DockMCMProtocol.hh.

Member Typedef Documentation

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

private

Definition at line 42 of file DockMCMProtocol.hh.

Constructor & Destructor Documentation

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

Default constructor.

Definition at line 78 of file DockMCMProtocol.cc.

References init().

Referenced by clone().

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

Constructor with one argument - the jump number.

Definition at line 85 of file DockMCMProtocol.cc.

References init().

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.

Definition at line 94 of file DockMCMProtocol.cc.

References init().

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.

Definition at line 105 of file DockMCMProtocol.cc.

References init().

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.

Definition at line 115 of file DockMCMProtocol.cc.

References init().

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

Definition at line 125 of file DockMCMProtocol.cc.

Member Function Documentation

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

virtual

docking high resolution apply function

Detailed:: decides what to call according to options

Implements protocols::docking::DockingHighRes.

Definition at line 164 of file DockMCMProtocol.cc.

protocols::moves::MoverOP protocols::docking::DockMCMProtocol::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 131 of file DockMCMProtocol.cc.

References DockMCMProtocol().

std::string protocols::docking::DockMCMProtocol::get_name ( ) const

virtual

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

Implements protocols::docking::DockingHighRes.

Definition at line 292 of file DockMCMProtocol.cc.

void protocols::docking::DockMCMProtocol::init ( void )

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

Definition at line 136 of file DockMCMProtocol.cc.

References filter_, movemap_reset_, num_of_first_cycle_, num_of_second_cycle_, set_first_cycle(), set_second_cycle(), and protocols::moves::Mover::type().