#include <DockMinMover.hh>

Inheritance diagram for protocols::docking::DockMinMover:

Collaboration diagram for protocols::docking::DockMinMover:

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

	DockMinMover (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn)
	Constructor with two arguments. The first is the DockJumps, the second is a scorefunction to use for minimization. More...

	DockMinMover (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, moves::MonteCarloOP mc)

	DockMinMover (DockJumps const movable_jumps, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, std::string min_type, core::Real min_tolerance, bool nb_list, moves::MonteCarloOP mc)
	Constructor with seven arguments. The first is the DockJumps, the second is a movemap, the third is a scorefunction, the fourth is the minimization type (as a string), the fifth is the tolerance, the sixth is a boolean for the nb_list and the seventh is a MonteCarloOP. More...

	~DockMinMover ()

void	set_default ()
	Sets up the default values for the obejct including the movemap and minimization type. More...

void	set_min_type (std::string min_type)
	setters for member variables More...

void	set_min_tolerance (core::Real min_tolerance)

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

virtual std::string	get_name () const
	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)

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

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 Attributes
core::kinematics::MoveMapOP	movemap_

std::string	min_type_

core::Real	min_tolerance_

bool	nb_list_

moves::MonteCarloOP	mc_

moves::TrialMoverOP	minimize_trial_

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 39 of file DockMinMover.hh.

Constructor & Destructor Documentation

protocols::docking::DockMinMover::DockMinMover ( )

Default constructor.

Definition at line 43 of file DockMinMover.cc.

References mc_, min_tolerance_, min_type_, minimize_trial_, movemap_, nb_list_, protocols::docking::DockingHighRes::scorefxn(), and set_default().

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

Constructor with two arguments. The first is the DockJumps, the second is a scorefunction to use for minimization.

Definition at line 53 of file DockMinMover.cc.

References mc_, min_tolerance_, min_type_, minimize_trial_, movemap_, nb_list_, protocols::docking::DockingHighRes::scorefxn(), and set_default().

protocols::docking::DockMinMover::DockMinMover	(	DockJumps const	movable_jumps,
		core::scoring::ScoreFunctionOP	scorefxn,
		moves::MonteCarloOP	mc
	)

Definition at line 68 of file DockMinMover.cc.

References mc_, min_tolerance_, min_type_, minimize_trial_, movemap_, nb_list_, protocols::docking::DockingHighRes::scorefxn(), and set_default().

protocols::docking::DockMinMover::DockMinMover	(	DockJumps const	movable_jumps,
		core::kinematics::MoveMapOP	movemap,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::string	min_type,
		core::Real	min_tolerance,
		bool	nb_list,
		moves::MonteCarloOP	mc
	)

Constructor with seven arguments. The first is the DockJumps, the second is a movemap, the third is a scorefunction, the fourth is the minimization type (as a string), the fifth is the tolerance, the sixth is a boolean for the nb_list and the seventh is a MonteCarloOP.

Definition at line 85 of file DockMinMover.cc.

References mc_, min_tolerance_, min_type_, minimize_trial_, movemap_, nb_list_, and protocols::docking::DockingHighRes::scorefxn().

protocols::docking::DockMinMover::~DockMinMover ( )

Definition at line 104 of file DockMinMover.cc.