mover to fit B factors More...

#include <BfactorFittingMover.hh>

Inheritance diagram for protocols::electron_density::BfactorFittingMover:

[legend]

Public Member Functions
	BfactorFittingMover ()

	~BfactorFittingMover () override=default

void	init ()

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

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

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

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

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

void	set_scorescale (core::Real scorescale)

void	set_wt_adp (core::Real wt_adp)

void	set_wt_dens (core::Real wt_dens)

void	set_rmax (core::Real rmax)

void	set_radius_exp (core::Size radius_exp)

void	set_max_iter (core::Size max_iter)

void	set_minimizer (std::string minimizer)

void	set_init (bool init)

void	set_exact (bool exact)

core::Real	get_scorescale ()

core::Real	get_wt_adp ()

core::Real	get_wt_dens ()

core::Real	get_rmax ()

core::Size	get_radius_exp ()

core::Size	get_max_iter ()

std::string	get_minimizer ()

bool	get_init ()

bool	get_exact ()

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 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::Real	scorescale_

core::Real	wt_adp_

core::Real	wt_dens_

core::Real	rmax_

core::Size	radius_exp_

core::Size	max_iter_

std::string	minimizer_

bool	init_

bool	exact_

bool	verbose_

bool	deriv_check_

core::Real	res_low_

core::Real	res_high_

core::Size	nresbins_

utility::vector1< core::Real >	weights_to_scan_

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...

Detailed Description

mover to fit B factors

Constructor & Destructor Documentation

◆ BfactorFittingMover()

protocols::electron_density::BfactorFittingMover::BfactorFittingMover ( )

References init().

◆ ~BfactorFittingMover()

protocols::electron_density::BfactorFittingMover::~BfactorFittingMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::electron_density::BfactorFittingMover::apply ( core::pose::Pose & )

overridevirtual

◆ clone()

moves::MoverOP protocols::electron_density::BfactorFittingMover::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.

◆ fresh_instance()

moves::MoverOP protocols::electron_density::BfactorFittingMover::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.

◆ get_exact()

bool protocols::electron_density::BfactorFittingMover::get_exact ( )

inline

References exact_.

◆ get_init()

bool protocols::electron_density::BfactorFittingMover::get_init ( )

inline

References init_.

◆ get_max_iter()

core::Size protocols::electron_density::BfactorFittingMover::get_max_iter ( )

inline

References max_iter_.

◆ get_minimizer()

std::string protocols::electron_density::BfactorFittingMover::get_minimizer ( )

inline

References minimizer_.

◆ get_name()

std::string protocols::electron_density::BfactorFittingMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_radius_exp()

core::Size protocols::electron_density::BfactorFittingMover::get_radius_exp ( )

inline

References radius_exp_.

◆ get_rmax()

core::Real protocols::electron_density::BfactorFittingMover::get_rmax ( )

inline

References rmax_.

◆ get_scorescale()

core::Real protocols::electron_density::BfactorFittingMover::get_scorescale ( )

inline

References scorescale_.

◆ get_wt_adp()

core::Real protocols::electron_density::BfactorFittingMover::get_wt_adp ( )

inline

References wt_adp_.

◆ get_wt_dens()

core::Real protocols::electron_density::BfactorFittingMover::get_wt_dens ( )

inline

References wt_dens_.

◆ init()

void protocols::electron_density::BfactorFittingMover::init ( void )

References deriv_check_, exact_, init_, max_iter_, minimizer_, radius_exp_, rmax_, scorescale_, verbose_, weights_to_scan_, wt_adp_, and wt_dens_.

Referenced by BfactorFittingMover(), and set_init().

◆ mover_name()

std::string protocols::electron_density::BfactorFittingMover::mover_name ( )

static

Referenced by get_name(), protocols::electron_density::BfactorFittingMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::electron_density::BfactorFittingMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References deriv_check_, exact_, init_, max_iter_, minimizer_, nresbins_, radius_exp_, res_high_, res_low_, rmax_, scorescale_, verbose_, weights_to_scan_, wt_adp_, and wt_dens_.

◆ provide_xml_schema()

void protocols::electron_density::BfactorFittingMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::electron_density::BfactorFittingMoverCreator::provide_xml_schema().

◆ set_exact()

void protocols::electron_density::BfactorFittingMover::set_exact ( bool exact )

inline

References exact_.

◆ set_init()

void protocols::electron_density::BfactorFittingMover::set_init ( bool init )

inline

References init(), and init_.

◆ set_max_iter()

void protocols::electron_density::BfactorFittingMover::set_max_iter ( core::Size max_iter )

inline

References max_iter_.

◆ set_minimizer()

void protocols::electron_density::BfactorFittingMover::set_minimizer ( std::string minimizer )

inline

References minimizer_.

◆ set_radius_exp()

void protocols::electron_density::BfactorFittingMover::set_radius_exp ( core::Size radius_exp )

inline

References radius_exp_.

◆ set_rmax()

void protocols::electron_density::BfactorFittingMover::set_rmax ( core::Real rmax )

inline

References rmax_.

◆ set_scorescale()

void protocols::electron_density::BfactorFittingMover::set_scorescale ( core::Real scorescale )

inline

References scorescale_.

◆ set_wt_adp()

void protocols::electron_density::BfactorFittingMover::set_wt_adp ( core::Real wt_adp )

inline

References wt_adp_.

◆ set_wt_dens()

void protocols::electron_density::BfactorFittingMover::set_wt_dens ( core::Real wt_dens )

inline

References wt_dens_.

Member Data Documentation

◆ deriv_check_

bool protocols::electron_density::BfactorFittingMover::deriv_check_

private

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

◆ exact_

bool protocols::electron_density::BfactorFittingMover::exact_

private

Referenced by apply(), get_exact(), init(), parse_my_tag(), and set_exact().

◆ init_

bool protocols::electron_density::BfactorFittingMover::init_

private

Referenced by apply(), get_init(), init(), parse_my_tag(), and set_init().

◆ max_iter_

core::Size protocols::electron_density::BfactorFittingMover::max_iter_

private

Referenced by apply(), get_max_iter(), init(), parse_my_tag(), and set_max_iter().

◆ minimizer_

std::string protocols::electron_density::BfactorFittingMover::minimizer_

private

Referenced by apply(), get_minimizer(), init(), parse_my_tag(), and set_minimizer().

◆ nresbins_

core::Size protocols::electron_density::BfactorFittingMover::nresbins_

private

Referenced by parse_my_tag().

◆ radius_exp_

core::Size protocols::electron_density::BfactorFittingMover::radius_exp_

private

Referenced by apply(), get_radius_exp(), init(), parse_my_tag(), and set_radius_exp().

◆ res_high_

core::Real protocols::electron_density::BfactorFittingMover::res_high_

private

Referenced by parse_my_tag().

◆ res_low_

core::Real protocols::electron_density::BfactorFittingMover::res_low_

private

Referenced by parse_my_tag().

◆ rmax_

core::Real protocols::electron_density::BfactorFittingMover::rmax_

private

Referenced by apply(), get_rmax(), init(), parse_my_tag(), and set_rmax().

◆ scorescale_

core::Real protocols::electron_density::BfactorFittingMover::scorescale_

private

Referenced by apply(), get_scorescale(), init(), parse_my_tag(), and set_scorescale().

◆ verbose_

bool protocols::electron_density::BfactorFittingMover::verbose_

private

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

◆ weights_to_scan_

utility::vector1< core::Real > protocols::electron_density::BfactorFittingMover::weights_to_scan_

private

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

◆ wt_adp_

core::Real protocols::electron_density::BfactorFittingMover::wt_adp_

private

Referenced by apply(), get_wt_adp(), init(), parse_my_tag(), and set_wt_adp().

◆ wt_dens_

core::Real protocols::electron_density::BfactorFittingMover::wt_dens_

private

Referenced by apply(), get_wt_dens(), init(), parse_my_tag(), and set_wt_dens().

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

src/protocols/electron_density/BfactorFittingMover.hh
src/protocols/electron_density/BfactorFittingMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BfactorFittingMover()

◆ ~BfactorFittingMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_exact()

◆ get_init()

◆ get_max_iter()

◆ get_minimizer()

◆ get_name()

◆ get_radius_exp()

◆ get_rmax()

◆ get_scorescale()

◆ get_wt_adp()

◆ get_wt_dens()

◆ init()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_exact()

◆ set_init()

◆ set_max_iter()

◆ set_minimizer()

◆ set_radius_exp()

◆ set_rmax()

◆ set_scorescale()

◆ set_wt_adp()

◆ set_wt_dens()

Member Data Documentation

◆ deriv_check_

◆ exact_

◆ init_

◆ max_iter_

◆ minimizer_

◆ nresbins_

◆ radius_exp_

◆ res_high_

◆ res_low_

◆ rmax_

◆ scorescale_

◆ verbose_

◆ weights_to_scan_

◆ wt_adp_

◆ wt_dens_