#include <RotamerTrialsMover.hh>

Inheritance diagram for protocols::minimization_packing::EnergyCutRotamerTrialsMover:

Public Member Functions
	EnergyCutRotamerTrialsMover ()

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

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

	~EnergyCutRotamerTrialsMover () override

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

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

Public Member Functions inherited from protocols::minimization_packing::RotamerTrialsMover
	RotamerTrialsMover ()

	RotamerTrialsMover (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...

	RotamerTrialsMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in)
	constructor with TaskFactory More...

	RotamerTrialsMover (RotamerTrialsMover const &rval)
	copy constructor More...

	~RotamerTrialsMover () override
	destructor More...

protocols::moves::MoverOP	clone () const override
	clone this object More...

protocols::moves::MoverOP	fresh_instance () const override
	create this type of object More...

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

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

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

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml More...

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...

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

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...

Protected 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...

protocols::moves::MonteCarloOP	mc ()

Protected Member Functions inherited from protocols::minimization_packing::RotamerTrialsMover
ScoreFunctionCOP	scorefxn () const
	read access for derived classes More...

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

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...

Private Attributes
protocols::moves::MonteCarloOP	mc_

core::Real	energycut_

Additional Inherited Members
Public Types inherited from protocols::minimization_packing::RotamerTrialsMover
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

typedef protocols::moves::MoverOP	MoverOP

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

Static Public Member Functions inherited from protocols::minimization_packing::RotamerTrialsMover
static std::string	mover_name ()

static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_rotamer_trials_mover (utility::tag::XMLSchemaDefinition &xsd)

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...

Constructor & Destructor Documentation

protocols::minimization_packing::EnergyCutRotamerTrialsMover::EnergyCutRotamerTrialsMover ( )

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

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

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

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

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

protocols::minimization_packing::EnergyCutRotamerTrialsMover::~EnergyCutRotamerTrialsMover ( )

overridedefault

Member Function Documentation

void protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply ( core::pose::Pose & pose )

overridevirtual

apply this mover to a pose

Reimplemented from protocols::minimization_packing::RotamerTrialsMover.

References protocols::minimization_packing::RotamerTrialsMover::clone(), core::pose::symmetry::is_symmetric(), mc_, core::pack::rotamer_trials(), protocols::minimization_packing::RotamerTrialsMover::scorefxn(), setup_energycut_task(), core::pack::symmetric_rotamer_trials(), and protocols::minimization_packing::RotamerTrialsMover::task().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::rigidbody_monte_carlo_minimize(), and protocols::flexpep_docking::FlexPepDockingProtocol::torsions_monte_carlo_minimize().

std::string protocols::minimization_packing::EnergyCutRotamerTrialsMover::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::minimization_packing::RotamerTrialsMover.

Reimplemented in protocols::minimization_packing::symmetry::SymEnergyCutRotamerTrialsMover.

protocols::moves::MonteCarloOP protocols::minimization_packing::EnergyCutRotamerTrialsMover::mc ( )

protected

References mc_.

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

protected

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_energy(), core::pack::task::PackerTask::restrict_to_repacking(), core::pose::Pose::size(), and core::scoring::total_score.

Referenced by apply().

Member Data Documentation

core::Real protocols::minimization_packing::EnergyCutRotamerTrialsMover::energycut_

private

Referenced by setup_energycut_task().

protocols::moves::MonteCarloOP protocols::minimization_packing::EnergyCutRotamerTrialsMover::mc_

private

Referenced by apply(), and mc().

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

src/protocols/minimization_packing/RotamerTrialsMover.hh
src/protocols/minimization_packing/RotamerTrialsMover.cc

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation