Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant. More...

#include <RotamerTrialsMinMover.hh>

Inheritance diagram for protocols::simple_moves::EnergyCutRotamerTrialsMinMover:

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Collaboration diagram for protocols::simple_moves::EnergyCutRotamerTrialsMinMover:

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Public Member Functions
	EnergyCutRotamerTrialsMinMover ()

	EnergyCutRotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, PackerTask &task_in, protocols::moves::MonteCarloOP mc_in, core::Real energycut_in)

	EnergyCutRotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in, protocols::moves::MonteCarloOP mc_in, core::Real energycut_in)

virtual	~EnergyCutRotamerTrialsMinMover ()

virtual void	apply (core::pose::Pose &pose)
	apply this mover to a pose More...

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

Public Member Functions inherited from protocols::simple_moves::RotamerTrialsMinMover
	RotamerTrialsMinMover ()

	RotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, PackerTask &task_in)
	constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE More...

	RotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in)
	constructor with TaskFactory for producing the packer task More...

void	init ()

virtual	~RotamerTrialsMinMover ()

void	score_function (core::scoring::ScoreFunctionCOP sf)

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

virtual void	parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	Parse XML for RosettaScripts. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	Return a new mover instance (for RosettaScripts) More...

virtual protocols::moves::MoverOP	clone () const
	Return a copy of this mover instance (for RosettaScripts) More...

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)

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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	setup_energycut_task (core::pose::Pose const &pose, protocols::moves::MonteCarlo const &mc, core::pack::task::PackerTask &task_in) const
	selects a subset of residues to repack based on the per residue energies of the last accepted pose in the MC object. More...

Private Attributes
protocols::moves::MonteCarloOP	mc_

core::Real	energycut_

Additional Inherited Members
Public Types inherited from protocols::simple_moves::RotamerTrialsMinMover
typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::PackerTaskOP	PackerTaskOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

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::simple_moves::RotamerTrialsMinMover
ScoreFunctionCOP	scorefxn () const
	read access for derived classes More...

PackerTaskOP	task (core::pose::Pose const &pose) const
	read access for derived classes, pose needed to run TaskFactory More...

Detailed Description

Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant.

Constructor & Destructor Documentation

protocols::simple_moves::EnergyCutRotamerTrialsMinMover::EnergyCutRotamerTrialsMinMover ( )

References protocols::simple_moves::RotamerTrialsMinMover::init(), and protocols::moves::Mover::type().

protocols::simple_moves::EnergyCutRotamerTrialsMinMover::EnergyCutRotamerTrialsMinMover	(	ScoreFunctionCOP	scorefxn_in,
		PackerTask &	task_in,
		protocols::moves::MonteCarloOP	mc_in,
		core::Real	energycut_in
	)

References protocols::simple_moves::RotamerTrialsMinMover::init(), and protocols::moves::Mover::type().

protocols::simple_moves::EnergyCutRotamerTrialsMinMover::EnergyCutRotamerTrialsMinMover	(	ScoreFunctionCOP	scorefxn_in,
		TaskFactoryCOP	factory_in,
		protocols::moves::MonteCarloOP	mc_in,
		core::Real	energycut_in
	)

References protocols::simple_moves::RotamerTrialsMinMover::init(), and protocols::moves::Mover::type().

protocols::simple_moves::EnergyCutRotamerTrialsMinMover::~EnergyCutRotamerTrialsMinMover ( )

virtual

Member Function Documentation

void protocols::simple_moves::EnergyCutRotamerTrialsMinMover::apply ( core::pose::Pose & pose)

virtual

apply this mover to a pose

Reimplemented from protocols::simple_moves::RotamerTrialsMinMover.

References mc_, core::pack::RTMin::rtmin(), protocols::simple_moves::RotamerTrialsMinMover::scorefxn(), setup_energycut_task(), and protocols::simple_moves::RotamerTrialsMinMover::task().

std::string protocols::simple_moves::EnergyCutRotamerTrialsMinMover::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::RotamerTrialsMinMover.

void protocols::simple_moves::EnergyCutRotamerTrialsMinMover::setup_energycut_task	(	core::pose::Pose const &	pose,
		protocols::moves::MonteCarlo const &	mc,
		core::pack::task::PackerTask &	task_in
	)		const

private

selects a subset of residues to repack based on the per residue energies of the last accepted pose in the MC object.

starting from a fresh task, it reduces the number of residues to be repacked to only those whose energy has increased by energycut_ since the application of the last move.

References core::pose::Pose::energies(), energycut_, protocols::moves::MonteCarlo::lowest_score_pose(), core::pack::task::PackerTask::nonconst_residue_task(), core::pack::task::ResidueLevelTask::prevent_repacking(), core::scoring::Energies::residue_total_energies(), core::pack::task::PackerTask::restrict_to_repacking(), core::pose::Pose::total_residue(), and core::scoring::total_score.

Referenced by apply().