#include <LocalRelax.hh>

Inheritance diagram for protocols::relax::LocalRelax:

[legend]

Public Member Functions
	LocalRelax ()

void	optimization_loop (Pose &pose, core::pack::task::PackerTaskOP ptask, core::kinematics::MoveMapOP mm, core::Real, core::Real)
	one cycle of local optimization More...

utility::vector1< utility::vector1< bool > >	get_neighbor_graph (Pose const &pose)
	get matrix of interacting residues More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	RS integration. More...

protocols::moves::MoverOP	clone () const override
	return a fresh instance of this class in an owning pointer More...

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

void	set_pack_sfxn (core::scoring::ScoreFunctionOP const &sf)

void	set_min_sfxn (core::scoring::ScoreFunctionOP const &sf)

void	set_sfxn (core::scoring::ScoreFunctionOP const &sf)

void	set_K (core::Real const K)

void	set_max_iter (core::Real const max_iter)

void	set_ncyc (core::Size const ncyc)

void	set_nexp (core::Size const nexp)

core::scoring::ScoreFunctionOP	get_pack_sfxn () const

core::scoring::ScoreFunctionOP	get_min_sfxn () const

core::Real	get_K () const

core::Real	get_max_iter () const

core::Size	get_ncyc () const

core::Size	get_nexp () const

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 ()

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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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 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 Attributes
core::Size	NCYC_

core::Size	NEXP_

core::Real	K_

core::Real	max_iter_

bool	ramp_cart_

bool	verbose_

utility::vector1< core::Real >	ramp_schedule_

core::scoring::ScoreFunctionOP	pack_sfxn_

core::scoring::ScoreFunctionOP	min_sfxn_

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

◆ LocalRelax()

protocols::relax::LocalRelax::LocalRelax ( )

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), and core::scoring::get_score_function().

Member Function Documentation

◆ apply()

void protocols::relax::LocalRelax::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::chemical::FULL_ATOM_t, core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::pack::task::ResidueLevelTask_::restrict_to_repacking(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), and protocols::relax::TR().

◆ clone()

protocols::moves::MoverOP protocols::relax::LocalRelax::clone ( ) const

inlineoverridevirtual

return a fresh instance of this class in an owning pointer

Reimplemented from protocols::moves::Mover.

◆ get_K()

core::Real protocols::relax::LocalRelax::get_K ( ) const

inline

References K_.

◆ get_max_iter()

core::Real protocols::relax::LocalRelax::get_max_iter ( ) const

inline

References max_iter_.

◆ get_min_sfxn()

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::get_min_sfxn ( ) const

inline

References min_sfxn_.

◆ get_name()

std::string protocols::relax::LocalRelax::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_ncyc()

core::Size protocols::relax::LocalRelax::get_ncyc ( ) const

inline

References NCYC_.

◆ get_neighbor_graph()

utility::vector1< utility::vector1< bool > > protocols::relax::LocalRelax::get_neighbor_graph ( Pose const & pose )

get matrix of interacting residues

References core::conformation::Residue::atom(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

◆ get_nexp()

core::Size protocols::relax::LocalRelax::get_nexp ( ) const

inline

References NEXP_.

◆ get_pack_sfxn()

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::get_pack_sfxn ( ) const

inline

References pack_sfxn_.

◆ mover_name()

std::string protocols::relax::LocalRelax::mover_name ( )

static

Referenced by protocols::relax::LocalRelaxCreator::keyname().

◆ optimization_loop()

void protocols::relax::LocalRelax::optimization_loop	(	Pose &	pose,
		core::pack::task::PackerTaskOP	ptask,
		core::kinematics::MoveMapOP	mm,
		core::Real	fa_rep_scale,
		core::Real	min_tol
	)

one cycle of local optimization

References core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, core::pose::Pose::dump_pdb(), core::scoring::fa_rep, protocols::mean_field::max(), core::optimization::MinimizerOptions::max_iter(), core::pack::pack_rotamers(), core::optimization::CartesianMinimizer::run(), core::id::to_string(), and protocols::relax::TR().

◆ parse_my_tag()

void protocols::relax::LocalRelax::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

RS integration.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

void protocols::relax::LocalRelax::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::relax::LocalRelaxCreator::provide_xml_schema().

◆ set_K()

void protocols::relax::LocalRelax::set_K ( core::Real const K )

inline

References core::chemical::element::K, and K_.

◆ set_max_iter()

void protocols::relax::LocalRelax::set_max_iter ( core::Real const max_iter )

inline

References max_iter_.

◆ set_min_sfxn()

void protocols::relax::LocalRelax::set_min_sfxn ( core::scoring::ScoreFunctionOP const & sf )

inline

References min_sfxn_.

◆ set_ncyc()

void protocols::relax::LocalRelax::set_ncyc ( core::Size const ncyc )

inline

References NCYC_.

◆ set_nexp()

void protocols::relax::LocalRelax::set_nexp ( core::Size const nexp )

inline

References NEXP_.

◆ set_pack_sfxn()

void protocols::relax::LocalRelax::set_pack_sfxn ( core::scoring::ScoreFunctionOP const & sf )

inline

References pack_sfxn_.

◆ set_sfxn()

void protocols::relax::LocalRelax::set_sfxn ( core::scoring::ScoreFunctionOP const & sf )

inline

References min_sfxn_, and pack_sfxn_.

Member Data Documentation

◆ K_

core::Real protocols::relax::LocalRelax::K_

private

Referenced by get_K(), and set_K().

◆ max_iter_

core::Real protocols::relax::LocalRelax::max_iter_

private

Referenced by get_max_iter(), and set_max_iter().

◆ min_sfxn_

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::min_sfxn_

private

Referenced by get_min_sfxn(), set_min_sfxn(), and set_sfxn().

◆ NCYC_

core::Size protocols::relax::LocalRelax::NCYC_

private

Referenced by get_ncyc(), and set_ncyc().

◆ NEXP_

core::Size protocols::relax::LocalRelax::NEXP_

private

Referenced by get_nexp(), and set_nexp().

◆ pack_sfxn_

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::pack_sfxn_

private

Referenced by get_pack_sfxn(), set_pack_sfxn(), and set_sfxn().

◆ ramp_cart_

bool protocols::relax::LocalRelax::ramp_cart_

private

◆ ramp_schedule_

utility::vector1< core::Real > protocols::relax::LocalRelax::ramp_schedule_

private

◆ verbose_

bool protocols::relax::LocalRelax::verbose_

private

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

src/protocols/relax/LocalRelax.hh
src/protocols/relax/LocalRelax.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ LocalRelax()

Member Function Documentation

◆ apply()

◆ clone()

◆ get_K()

◆ get_max_iter()

◆ get_min_sfxn()

◆ get_name()

◆ get_ncyc()

◆ get_neighbor_graph()

◆ get_nexp()

◆ get_pack_sfxn()

◆ mover_name()

◆ optimization_loop()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_K()

◆ set_max_iter()

◆ set_min_sfxn()

◆ set_ncyc()

◆ set_nexp()

◆ set_pack_sfxn()

◆ set_sfxn()

Member Data Documentation

◆ K_

◆ max_iter_

◆ min_sfxn_

◆ NCYC_

◆ NEXP_

◆ pack_sfxn_

◆ ramp_cart_

◆ ramp_schedule_

◆ verbose_