#include <NormalModeRelaxMover.hh>

Public Member Functions
	CartesianNormalModeMover (core::pose::Pose const &, core::scoring::ScoreFunctionCOP sfxn, std::string const relaxmode)

	CartesianNormalModeMover (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP sfxn, core::kinematics::MoveMapCOP mm, std::string const mode="CA", Real const distcut=10.0, std::string const relaxmode="min")

	~CartesianNormalModeMover ()

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

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

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

virtual void	gen_coord_constraint (pose::Pose &pose, utility::vector1< Vector > const &excrd)
	Pure virtual functions inside NMmover. More...

virtual void	set_default_minoption ()

Public Member Functions inherited from protocols::normalmode::NormalModeRelaxMover
	NormalModeRelaxMover ()

	~NormalModeRelaxMover ()

virtual protocols::moves::MoverOP	fresh_instance () const
	Virtual functions from Mover. More...

virtual void	set_movemap (core::pose::Pose const &pose, core::kinematics::MoveMapCOP movemap)

void	set_harmonic_constants (Real const k_uniform)
	Common options. More...

void	set_harmonic_constants (Real const k_connected, Real const k_segment, Real const k_long)

void	invert_direction ()

void	set_extrapolate_scale (Real const scale)

void	set_cst_sdev (Real const cst_sdev)

void	set_mode (utility::vector1< Size > const mode_using, utility::vector1< Real > const mode_scales)

void	set_mode (Size const i_mode)

void	set_cartesian_minimize (bool const value)

void	set_random_mode (Size const nmode, std::string const select_option="probabilistic", Real const importance_portion=1.0)

void	set_minoption (optimization::MinimizerOptionsCOP minoption)

void	refresh_normalmode ()

protocols::normalmode::NormalMode	NM ()

Real	cst_sdev ()

Real	get_dynamic_scale ()

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

void	set_type (std::string const &setting)

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 (TagCOP tag, basic::datacache::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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Member Functions
utility::vector1< Vector >	extrapolate_mode (pose::Pose const &pose)

Real	get_RMSD (utility::vector1< Vector > const excrd, pose::Pose const &pose)

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 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. 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...

Protected Attributes inherited from protocols::normalmode::NormalModeRelaxMover
Real	direction_

Real	moving_distance_

Real	cst_sdev_

bool	refresh_normalmode_

bool	cartesian_minimize_

optimization::MinimizerOptionsCOP	minoption_

Real	scale_dynamic_

std::string	relaxmode_

utility::vector1< Size >	mode_using_

utility::vector1< Real >	mode_scale_

core::kinematics::MoveMapOP	mm_

core::scoring::ScoreFunctionOP	sfxn_

core::scoring::ScoreFunctionOP	sfxn_cen_

protocols::normalmode::NormalMode	NM_

Constructor & Destructor Documentation

protocols::normalmode::CartesianNormalModeMover::CartesianNormalModeMover	(	core::pose::Pose const &	,
		core::scoring::ScoreFunctionCOP	sfxn,
		std::string const	relaxmode
	)

protocols::normalmode::CartesianNormalModeMover::CartesianNormalModeMover	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	sfxn,
		core::kinematics::MoveMapCOP	mm,
		std::string const	mode = `"CA"`,
		Real const	distcut = `10.0`,
		std::string const	relaxmode = `"min"`
	)

protocols::normalmode::CartesianNormalModeMover::~CartesianNormalModeMover ( )

Member Function Documentation

void protocols::normalmode::CartesianNormalModeMover::apply ( core::pose::Pose & pose )

virtual

virtual protocols::moves::MoverOP protocols::normalmode::CartesianNormalModeMover::clone ( ) const

inlinevirtual

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.

utility::vector1< Vector > protocols::normalmode::CartesianNormalModeMover::extrapolate_mode ( pose::Pose const & pose )

private

References protocols::normalmode::NormalModeRelaxMover::direction_, protocols::normalmode::NormalModeRelaxMover::mode_scale_, protocols::normalmode::NormalModeRelaxMover::mode_using_, protocols::normalmode::NormalModeRelaxMover::moving_distance_, protocols::normalmode::NormalMode::natm(), protocols::normalmode::NormalModeRelaxMover::NM(), core::pose::Pose::residue(), rmsd, protocols::normalmode::NormalModeRelaxMover::scale_dynamic_, protocols::TR, and core::conformation::Residue::xyz().