#include <NormalModeRelaxMover.hh>

Inheritance diagram for protocols::normalmode::NormalModeRelaxMover:

[legend]

Public Member Functions
	NormalModeRelaxMover ()

	NormalModeRelaxMover (core::scoring::ScoreFunctionCOP sfxn, bool const cartesian)

	NormalModeRelaxMover (core::scoring::ScoreFunctionCOP sfxn, bool cartesian, core::kinematics::MoveMapCOP mm, std::string const relaxmode, core::Real const distcut)

	~NormalModeRelaxMover () override

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

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	apply_on_pose (core::pose::Pose &pose, core::kinematics::MoveMapOP movemap)

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

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_default ()

void	set_harmonic_constants (core::Real const k_uniform)
	Setters. More...

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

void	invert_direction ()

void	set_extrapolate_scale (core::Real const scale)

void	set_cst_sdev (core::Real const cst_sdev)

void	set_cartesian_minimize (bool const value)

void	set_minoption (core::optimization::MinimizerOptionsCOP minoption)

void	set_relaxmode (std::string const mode)

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

void	set_mode (core::Size const i_mode)

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

void	refresh_normalmode ()

protocols::normalmode::NormalMode const	NM () const

core::Real	cst_sdev () const

core::Real	get_dynamic_scale () const

std::string	relaxmode () const

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

core::pose::PoseOP	get_additional_output () override
	used by the job distributor and MultiplePoseMover (MPM) to return as many of the potential poses as possible. 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...

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

Static Public Member Functions
static std::string	mover_name ()

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...

Private Member Functions
virtual void	initialize_NM_for_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap const &movemap)

void	gen_coord_constraint (core::pose::Pose &pose, utility::vector1< core::Vector > const &excrd) const

void	set_default_minoption ()

utility::vector1< core::Vector >	extrapolate_mode_on_crd (core::pose::Pose const &pose) const

core::pose::Pose	extrapolate_mode_on_pose (core::pose::Pose const &pose) const

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

Private Attributes
core::Size	nmodes_ = 5

bool	mix_modes_ = false

bool	cartesian_ = true

core::Real	pertscale_ = 1.0

bool	randomselect_ = false

core::Real	selection_kT_ = 1e6

bool	centroid_ = false

core::Size	nsample_ = 5

core::Real	moving_distance_ = 1.0

bool	refresh_normalmode_ = true

core::Real	direction_ = 1.0

core::Real	cst_sdev_ = 1.0

bool	cartesian_minimize_ = false

bool	dump_silent_ = false

std::string	outsilent_

utility::vector1< core::pose::PoseOP >	output_pose_OPs_

std::string	relaxmode_

core::optimization::MinimizerOptionsCOP	minoption_

utility::vector1< core::Size >	mode_using_

utility::vector1< core::Real >	mode_scale_

core::select::movemap::MoveMapFactoryCOP	mmf_

core::kinematics::MoveMapOP	mm_

core::scoring::ScoreFunctionOP	sfxn_

core::scoring::ScoreFunctionOP	sfxn_cen_

protocols::normalmode::NormalMode	NM_

core::Real	scale_dynamic_

utility::vector1< core::Real >	dtor_

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 std::list< std::string >	Strings

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...

Constructor & Destructor Documentation

◆ NormalModeRelaxMover() [1/3]

protocols::normalmode::NormalModeRelaxMover::NormalModeRelaxMover ( )

◆ NormalModeRelaxMover() [2/3]

protocols::normalmode::NormalModeRelaxMover::NormalModeRelaxMover	(	core::scoring::ScoreFunctionCOP	sfxn,
		bool const	cartesian
	)

References cartesian_, mm_, NM_, set_default(), sfxn_, and protocols::normalmode::NormalMode::torsion().

◆ NormalModeRelaxMover() [3/3]

protocols::normalmode::NormalModeRelaxMover::NormalModeRelaxMover	(	core::scoring::ScoreFunctionCOP	sfxn,
		bool	cartesian,
		core::kinematics::MoveMapCOP	mm,
		std::string const	relaxmode,
		core::Real const	distcut
	)

References cartesian_, mm_, NM_, relaxmode(), relaxmode_, set_default(), sfxn_, and protocols::normalmode::NormalMode::torsion().

◆ ~NormalModeRelaxMover()

protocols::normalmode::NormalModeRelaxMover::~NormalModeRelaxMover ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

◆ apply_on_pose()

void protocols::normalmode::NormalModeRelaxMover::apply_on_pose	(	core::pose::Pose &	pose,
		core::kinematics::MoveMapOP	movemap
	)

◆ clone()

protocols::moves::MoverOP protocols::normalmode::NormalModeRelaxMover::clone ( ) const

inlineoverridevirtual

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.

Referenced by fresh_instance().

◆ cst_sdev()

core::Real protocols::normalmode::NormalModeRelaxMover::cst_sdev ( ) const

inline

References cst_sdev_.

Referenced by gen_coord_constraint(), and set_cst_sdev().

◆ extrapolate_mode_on_crd()

utility::vector1< Vector > protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_crd ( core::pose::Pose const & pose ) const

private

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

Referenced by apply_on_pose().

◆ extrapolate_mode_on_pose()

pose::Pose protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_pose ( core::pose::Pose const & pose ) const

private

References core::scoring::CA_rmsd(), direction_, dtor_, protocols::normalmode::NormalMode::get_torID(), mode_scale_, mode_using_, moving_distance_, NM(), protocols::normalmode::NormalMode::ntor(), scale_dynamic_, core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and protocols::TR().

Referenced by apply_on_pose().

◆ fresh_instance()

protocols::moves::MoverOP protocols::normalmode::NormalModeRelaxMover::fresh_instance ( ) const

inlineoverridevirtual

Virtual functions from Mover.

Reimplemented from protocols::moves::Mover.

References clone().

◆ gen_coord_constraint()

void protocols::normalmode::NormalModeRelaxMover::gen_coord_constraint	(	core::pose::Pose &	pose,
		utility::vector1< core::Vector > const &	excrd
	)		const

private

References core::pose::Pose::add_constraint(), cartesian_, cst_sdev(), protocols::normalmode::NormalMode::natm(), NM(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by apply_on_pose().

◆ get_additional_output()

core::pose::PoseOP protocols::normalmode::NormalModeRelaxMover::get_additional_output ( )

overridevirtual

used by the job distributor and MultiplePoseMover (MPM) to return as many of the potential poses as possible.

@detail normal mode relaxed poses are remembered as PoseOPs in a score-sorted fashion. Each time this is called, the best is removed from memory and returned until no more remain. Assumes randomselect_/order of output_pose_OPs_ isn't changed between calls because this would not be reflected in how addnl poses are retrived (sorting/shuffling is done only once)

Reimplemented from protocols::moves::Mover.

References centroid_, core::chemical::element::F, output_pose_OPs_, sfxn_, sfxn_cen_, and protocols::TR().

◆ get_dynamic_scale()

core::Real protocols::normalmode::NormalModeRelaxMover::get_dynamic_scale ( ) const

inline

References scale_dynamic_.

◆ get_name()

std::string protocols::normalmode::NormalModeRelaxMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_RMSD()

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

private

References NM(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by apply_on_pose().

◆ initialize_NM_for_movemap()

void protocols::normalmode::NormalModeRelaxMover::initialize_NM_for_movemap	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMap const &	movemap
	)

privatevirtual

References protocols::normalmode::NormalMode::clear_torsions_using(), core::kinematics::MoveMap::get_bb(), NM_, protocols::normalmode::NormalMode::set_torsions_using(), and core::pose::Pose::size().

Referenced by apply().

◆ invert_direction()

void protocols::normalmode::NormalModeRelaxMover::invert_direction ( )

inline

References direction_.

◆ mover_name()

std::string protocols::normalmode::NormalModeRelaxMover::mover_name ( )

static

Referenced by get_name(), protocols::normalmode::NormalModeRelaxMoverCreator::keyname(), and provide_xml_schema().

◆ NM()

protocols::normalmode::NormalMode const protocols::normalmode::NormalModeRelaxMover::NM ( ) const

inline

References NM_.

Referenced by extrapolate_mode_on_crd(), extrapolate_mode_on_pose(), gen_coord_constraint(), get_RMSD(), set_mode(), and set_random_mode().

◆ parse_my_tag()

void protocols::normalmode::NormalModeRelaxMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References cartesian_, cartesian_minimize_, centroid_, dump_silent_, mix_modes_, mmf_, NM_, nmodes_, nsample_, outsilent_, protocols::rosetta_scripts::parse_movemap_factory_legacy(), pertscale_, randomselect_, relaxmode_, selection_kT_, set_harmonic_constants(), sfxn_, sfxn_cen_, and protocols::normalmode::NormalMode::torsion().

◆ provide_xml_schema()

void protocols::normalmode::NormalModeRelaxMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), mover_name(), protocols::moves::Mover::name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::normalmode::NormalModeRelaxMoverCreator::provide_xml_schema().

◆ refresh_normalmode()

void protocols::normalmode::NormalModeRelaxMover::refresh_normalmode ( )

inline

References refresh_normalmode_.

◆ relaxmode()

std::string protocols::normalmode::NormalModeRelaxMover::relaxmode ( ) const

inline

References relaxmode_.

Referenced by NormalModeRelaxMover().

◆ set_cartesian_minimize()

void protocols::normalmode::NormalModeRelaxMover::set_cartesian_minimize ( bool const value )

inline

References cartesian_minimize_.

◆ set_cst_sdev()

void protocols::normalmode::NormalModeRelaxMover::set_cst_sdev ( core::Real const cst_sdev )

inline

References cst_sdev(), and cst_sdev_.

◆ set_default()

void protocols::normalmode::NormalModeRelaxMover::set_default ( )

References cartesian_, minoption_, relaxmode_, sfxn_, and sfxn_cen_.

Referenced by NormalModeRelaxMover().

◆ set_default_minoption()

void protocols::normalmode::NormalModeRelaxMover::set_default_minoption ( )

private

◆ set_extrapolate_scale()

void protocols::normalmode::NormalModeRelaxMover::set_extrapolate_scale ( core::Real const scale )

inline

References moving_distance_.

Referenced by apply().

◆ set_harmonic_constants() [1/2]

void protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants	(	core::Real const	k_connected,
		core::Real const	k_segment,
		core::Real const	k_long
	)

References NM_, and protocols::normalmode::NormalMode::set_harmonic_constants().

◆ set_harmonic_constants() [2/2]

void protocols::normalmode::NormalModeRelaxMover::set_harmonic_constants ( core::Real const k_uniform )

Setters.

References NM_, and protocols::normalmode::NormalMode::set_harmonic_constants().

Referenced by parse_my_tag().

◆ set_minoption()

void protocols::normalmode::NormalModeRelaxMover::set_minoption ( core::optimization::MinimizerOptionsCOP minoption )

inline

References minoption_.

◆ set_mode() [1/2]

void protocols::normalmode::NormalModeRelaxMover::set_mode ( core::Size const i_mode )

References mode_scale_, and mode_using_.

◆ set_mode() [2/2]

void protocols::normalmode::NormalModeRelaxMover::set_mode	(	utility::vector1< core::Size > const	mode_using,
		utility::vector1< core::Real > const	mode_scales
	)

References mode_scale_, mode_using_, NM(), and protocols::TR().

Referenced by apply().

◆ set_random_mode()

void protocols::normalmode::NormalModeRelaxMover::set_random_mode	(	std::string const	select_option = `"probabilistic"`,
		core::Real const	importance_portion = `1.0`
	)

References protocols::normalmode::NormalMode::get_importance(), mode_scale_, mode_using_, NM(), nmodes_, core::scoring::rg, and protocols::TR().

◆ set_relaxmode()

void protocols::normalmode::NormalModeRelaxMover::set_relaxmode ( std::string const mode )

inline

References relaxmode_.

Member Data Documentation

◆ cartesian_

bool protocols::normalmode::NormalModeRelaxMover::cartesian_ = true

private

Referenced by apply_on_pose(), gen_coord_constraint(), NormalModeRelaxMover(), parse_my_tag(), and set_default().

◆ cartesian_minimize_

bool protocols::normalmode::NormalModeRelaxMover::cartesian_minimize_ = false

private

Referenced by apply_on_pose(), parse_my_tag(), and set_cartesian_minimize().

◆ centroid_

bool protocols::normalmode::NormalModeRelaxMover::centroid_ = false

private

Referenced by apply(), get_additional_output(), and parse_my_tag().

◆ cst_sdev_

core::Real protocols::normalmode::NormalModeRelaxMover::cst_sdev_ = 1.0

private

Referenced by cst_sdev(), and set_cst_sdev().

◆ direction_

core::Real protocols::normalmode::NormalModeRelaxMover::direction_ = 1.0

private

Referenced by extrapolate_mode_on_crd(), extrapolate_mode_on_pose(), and invert_direction().

◆ dtor_

utility::vector1< core::Real > protocols::normalmode::NormalModeRelaxMover::dtor_

mutableprivate

Referenced by extrapolate_mode_on_pose().

◆ dump_silent_

bool protocols::normalmode::NormalModeRelaxMover::dump_silent_ = false

private

Referenced by apply(), and parse_my_tag().

◆ minoption_

core::optimization::MinimizerOptionsCOP protocols::normalmode::NormalModeRelaxMover::minoption_

private

Referenced by apply_on_pose(), set_default(), and set_minoption().

◆ mix_modes_

bool protocols::normalmode::NormalModeRelaxMover::mix_modes_ = false

private

Referenced by apply(), and parse_my_tag().

◆ mm_

core::kinematics::MoveMapOP protocols::normalmode::NormalModeRelaxMover::mm_

private

Referenced by apply(), and NormalModeRelaxMover().

◆ mmf_

core::select::movemap::MoveMapFactoryCOP protocols::normalmode::NormalModeRelaxMover::mmf_

private

Referenced by apply(), and parse_my_tag().

◆ mode_scale_

utility::vector1< core::Real > protocols::normalmode::NormalModeRelaxMover::mode_scale_

private

Referenced by apply(), extrapolate_mode_on_crd(), extrapolate_mode_on_pose(), set_mode(), and set_random_mode().

◆ mode_using_

utility::vector1< core::Size > protocols::normalmode::NormalModeRelaxMover::mode_using_

private

Referenced by extrapolate_mode_on_crd(), extrapolate_mode_on_pose(), set_mode(), and set_random_mode().

◆ moving_distance_

core::Real protocols::normalmode::NormalModeRelaxMover::moving_distance_ = 1.0

private

Referenced by extrapolate_mode_on_crd(), extrapolate_mode_on_pose(), and set_extrapolate_scale().

◆ NM_

protocols::normalmode::NormalMode protocols::normalmode::NormalModeRelaxMover::NM_

private

Referenced by apply_on_pose(), initialize_NM_for_movemap(), NM(), NormalModeRelaxMover(), parse_my_tag(), and set_harmonic_constants().

◆ nmodes_

core::Size protocols::normalmode::NormalModeRelaxMover::nmodes_ = 5

private

Referenced by apply(), parse_my_tag(), and set_random_mode().

◆ nsample_

core::Size protocols::normalmode::NormalModeRelaxMover::nsample_ = 5

private

Referenced by apply(), and parse_my_tag().

◆ output_pose_OPs_

utility::vector1< core::pose::PoseOP > protocols::normalmode::NormalModeRelaxMover::output_pose_OPs_

private

Referenced by apply(), and get_additional_output().

◆ outsilent_

std::string protocols::normalmode::NormalModeRelaxMover::outsilent_

private

Referenced by apply(), and parse_my_tag().

◆ pertscale_

core::Real protocols::normalmode::NormalModeRelaxMover::pertscale_ = 1.0

private

Referenced by apply(), and parse_my_tag().

◆ randomselect_

bool protocols::normalmode::NormalModeRelaxMover::randomselect_ = false

private

Referenced by apply(), and parse_my_tag().

◆ refresh_normalmode_

bool protocols::normalmode::NormalModeRelaxMover::refresh_normalmode_ = true

private

Referenced by apply_on_pose(), and refresh_normalmode().

◆ relaxmode_

std::string protocols::normalmode::NormalModeRelaxMover::relaxmode_

private

Referenced by apply_on_pose(), NormalModeRelaxMover(), parse_my_tag(), relaxmode(), set_default(), and set_relaxmode().

◆ scale_dynamic_

core::Real protocols::normalmode::NormalModeRelaxMover::scale_dynamic_

mutableprivate

Referenced by extrapolate_mode_on_crd(), extrapolate_mode_on_pose(), and get_dynamic_scale().

◆ selection_kT_

core::Real protocols::normalmode::NormalModeRelaxMover::selection_kT_ = 1e6

private

Referenced by parse_my_tag().

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::normalmode::NormalModeRelaxMover::sfxn_

private

Referenced by apply(), apply_on_pose(), get_additional_output(), NormalModeRelaxMover(), parse_my_tag(), and set_default().

◆ sfxn_cen_

core::scoring::ScoreFunctionOP protocols::normalmode::NormalModeRelaxMover::sfxn_cen_

private

Referenced by apply(), get_additional_output(), parse_my_tag(), and set_default().

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

src/protocols/normalmode/NormalModeRelaxMover.hh
src/protocols/normalmode/NormalModeRelaxMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ NormalModeRelaxMover() [1/3]

◆ NormalModeRelaxMover() [2/3]

◆ NormalModeRelaxMover() [3/3]

◆ ~NormalModeRelaxMover()

Member Function Documentation

◆ apply()

◆ apply_on_pose()

◆ clone()

◆ cst_sdev()

◆ extrapolate_mode_on_crd()

◆ extrapolate_mode_on_pose()

◆ fresh_instance()

◆ gen_coord_constraint()

◆ get_additional_output()

◆ get_dynamic_scale()

◆ get_name()

◆ get_RMSD()

◆ initialize_NM_for_movemap()

◆ invert_direction()

◆ mover_name()

◆ NM()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ refresh_normalmode()

◆ relaxmode()

◆ set_cartesian_minimize()

◆ set_cst_sdev()

◆ set_default()

◆ set_default_minoption()

◆ set_extrapolate_scale()

◆ set_harmonic_constants() [1/2]

◆ set_harmonic_constants() [2/2]

◆ set_minoption()

◆ set_mode() [1/2]

◆ set_mode() [2/2]

◆ set_random_mode()

◆ set_relaxmode()

Member Data Documentation

◆ cartesian_

◆ cartesian_minimize_

◆ centroid_

◆ cst_sdev_

◆ direction_

◆ dtor_

◆ dump_silent_

◆ minoption_

◆ mix_modes_

◆ mm_

◆ mmf_

◆ mode_scale_

◆ mode_using_

◆ moving_distance_

◆ NM_

◆ nmodes_

◆ nsample_

◆ output_pose_OPs_

◆ outsilent_

◆ pertscale_

◆ randomselect_

◆ refresh_normalmode_

◆ relaxmode_

◆ scale_dynamic_

◆ selection_kT_

◆ sfxn_

◆ sfxn_cen_