High-level atom tree minimizer class. More...

#include <NormalModeMinimizer.hh>

Inheritance diagram for protocols::normalmode::NormalModeMinimizer:

Public Types
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::optimization::MinimizerOptionsOP	MinimizerOptionsOP

typedef core::optimization::MinimizerOptionsCOP	MinimizerOptionsCOP

typedef core::Real	Real

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

Public Member Functions
	NormalModeMinimizer ()

	~NormalModeMinimizer () override

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

core::optimization::NumericalDerivCheckResultOP	deriv_check_result () const
	After minimization has concluded, the user may access the deriv-check result, assuming that they have run the NormalModeMinimizer with deriv_check = true;. More...

void	set_modes (utility::vector1< core::Size > const modes_using_in)

void	parse_my_tag (TagCOP, basic::datacache::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

	~Mover () override

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...

	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...

virtual 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
	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...

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
void	deriv_check_local (core::pose::Pose const &pose, protocols::normalmode::NormalModeMultifunc f) const

Private Attributes
utility::vector1< core::Size >	modes_using_

core::select::movemap::MoveMapFactoryCOP	movemap_factory_

ScoreFunctionCOP	scorefxn_

MinimizerOptionsOP	options_

Real	dampen_

core::optimization::NumericalDerivCheckResultOP	deriv_check_result_

Additional Inherited Members
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...

Detailed Description

High-level atom tree minimizer class.

Member Typedef Documentation

typedef core::optimization::MinimizerOptionsCOP protocols::normalmode::NormalModeMinimizer::MinimizerOptionsCOP

typedef core::optimization::MinimizerOptionsOP protocols::normalmode::NormalModeMinimizer::MinimizerOptionsOP

typedef core::Real protocols::normalmode::NormalModeMinimizer::Real

typedef core::scoring::ScoreFunctionCOP protocols::normalmode::NormalModeMinimizer::ScoreFunctionCOP

Constructor & Destructor Documentation

protocols::normalmode::NormalModeMinimizer::NormalModeMinimizer ( )

protocols::normalmode::NormalModeMinimizer::~NormalModeMinimizer ( )

overridedefault

Member Function Documentation

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

overridevirtual

Implements protocols::moves::Mover.

References core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::domain_map(), core::pose::Pose::energies(), core::chemical::element::F, core::scoring::get_score_function(), core::pose::symmetry::is_symmetric(), core::optimization::MinimizerMap::nangles(), protocols::normalmode::nma_tr(), core::optimization::MinimizerMap::reset_jump_rb_deltas(), core::scoring::Energies::reset_nblist(), core::optimization::Minimizer::run(), protocols::normalmode::NormalModeMultifunc::set_modes(), core::scoring::Energies::set_use_nblist(), core::optimization::MinimizerMap::setup(), protocols::normalmode::NormalMode::solve(), and protocols::normalmode::NormalMode::torsion().

protocols::moves::MoverOP protocols::normalmode::NormalModeMinimizer::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.

void protocols::normalmode::NormalModeMinimizer::deriv_check_local	(	core::pose::Pose const &	pose,
		protocols::normalmode::NormalModeMultifunc	f
	)		const

private

References protocols::normalmode::NormalModeMultifunc::dfunc(), protocols::comparative_modeling::features::E, core::chemical::element::F, core::chemical::element::I, core::scoring::sasa::LJ, protocols::normalmode::nma_tr(), and protocols::normalmode::NormalModeMultifunc::nvar().

NumericalDerivCheckResultOP protocols::normalmode::NormalModeMinimizer::deriv_check_result ( ) const

After minimization has concluded, the user may access the deriv-check result, assuming that they have run the NormalModeMinimizer with deriv_check = true;.

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

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::moves::Mover.

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

static

void protocols::normalmode::NormalModeMinimizer::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		Pose const &	pose
	)

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References core::select::movemap::mm_enable, and protocols::rosetta_scripts::parse_movemap_factory_legacy().

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

static

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

void protocols::normalmode::NormalModeMinimizer::set_modes ( utility::vector1< core::Size > const modes_using_in )

inline

References modes_using_.

Member Data Documentation

Real protocols::normalmode::NormalModeMinimizer::dampen_

private

core::optimization::NumericalDerivCheckResultOP protocols::normalmode::NormalModeMinimizer::deriv_check_result_

private

utility::vector1< core::Size > protocols::normalmode::NormalModeMinimizer::modes_using_

private

Referenced by set_modes().

core::select::movemap::MoveMapFactoryCOP protocols::normalmode::NormalModeMinimizer::movemap_factory_

private

MinimizerOptionsOP protocols::normalmode::NormalModeMinimizer::options_

private

ScoreFunctionCOP protocols::normalmode::NormalModeMinimizer::scorefxn_

private

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

src/protocols/normalmode/NormalModeMinimizer.hh
src/protocols/normalmode/NormalModeMinimizer.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation