#include <AnchorMovers.hh>

Inheritance diagram for protocols::anchored_design::AnchoredRefineMover:

Public Member Functions
	AnchoredRefineMover (protocols::anchored_design::AnchorMoversDataOP interface_in)

	~AnchoredRefineMover () override

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

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

bool	get_debug () const
	debugging mode activates a bunch of extra output More...

bool	get_refine_CCD_off () const
	do not perform CCD style closure (use KIC only) More...

bool	get_refine_KIC_off () const
	do not perform KIC style closure (use CCD only) More...

bool	get_nonpivot_torsion_sampling () const
	use nonpivot torsion sampling for KIC? More...

bool	get_vicinity_sampling () const
	KIC use vicinity sampling? More...

core::Real	get_vicinity_degree () const
	KIC vicinity sampling degrees. More...

core::Real	get_refine_temp () const
	MC temperature. More...

core::Size	get_refine_cycles () const
	number of MC cycles More...

std::string const &	get_min_type () const
	what minimizer type to use? More...

core::Size	get_refine_repack_cycles () const
	how many cycles between repack/design opportunities? More...

void	set_debug (bool const debug)
	debugging mode activates a bunch of extra output More...

void	set_refine_CCD_off (bool const refine_CCD_off)
	do not perform CCD style closure (use KIC only) More...

void	set_refine_KIC_off (bool const refine_KIC_off)
	do not perform KIC style closure (use CCD only) More...

void	set_nonpivot_torsion_sampling (bool const nonpivot_torsion_sampling)
	use nonpivot torsion sampling for KIC? More...

void	set_vicinity_sampling (bool const vicinity_sampling)
	KIC use vicinity sampling? More...

void	set_vicinity_degree (core::Size const vicinity_degree)
	KIC vicinity sampling degrees. More...

void	set_refine_temp (core::Real const refine_temp)
	MC temperature. More...

void	set_refine_cycles (core::Size const refine_cycles)
	number of MC cycles More...

void	set_min_type (std::string const &min_type)
	what minimizer type to use? More...

void	set_refine_repack_cycles (core::Size const refine_repack_cycles)
	how many cycles between repack/design opportunities? More...

void	read_options ()
	read in options from the options system 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 MoverOP	clone () const
	Return a clone of the Mover object. 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

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

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...

Private Attributes
protocols::anchored_design::AnchorMoversDataOP	interface_

bool	debug_
	debugging mode activates a bunch of extra output More...

bool	refine_CCD_off_
	do not perform CCD style closure (use KIC only) More...

bool	refine_KIC_off_
	do not perform KIC style closure (use CCD only) More...

bool	nonpivot_torsion_sampling_
	use nonpivot torsion sampling for KIC? More...

bool	vicinity_sampling_
	KIC use vicinity sampling? More...

core::Real	vicinity_degree_
	KIC vicinity sampling degrees. More...

core::Real	refine_temp_
	MC temperature. More...

core::Size	refine_cycles_
	number of MC cycles More...

std::string	min_type_
	what minimizer type to use? More...

core::Size	refine_repack_cycles_
	how many cycles between repack/design opportunities? More...

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

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...

Constructor & Destructor Documentation

protocols::anchored_design::AnchoredRefineMover::AnchoredRefineMover ( protocols::anchored_design::AnchorMoversDataOP interface_in )

References read_options(), and protocols::moves::Mover::type().

protocols::anchored_design::AnchoredRefineMover::~AnchoredRefineMover ( )

overridedefault

Member Function Documentation

void protocols::anchored_design::AnchoredRefineMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References debug_, protocols::anchored_design::debug_dump_pose(), protocols::anchored_design::dump_cutpoint_info(), interface_, core::conformation::Residue::is_terminus(), min_type_, nonpivot_torsion_sampling_, core::pack::task::TaskFactory::push_back(), refine_CCD_off_, refine_cycles_, refine_KIC_off_, refine_repack_cycles_, refine_temp_, core::pose::Pose::residue(), T_perturb(), T_refine(), and vicinity_degree_.

Referenced by protocols::anchored_design::AnchoredDesignMover::apply().

bool protocols::anchored_design::AnchoredRefineMover::get_debug ( ) const

debugging mode activates a bunch of extra output

References debug_.

std::string const & protocols::anchored_design::AnchoredRefineMover::get_min_type ( ) const

what minimizer type to use?

References min_type_.

std::string protocols::anchored_design::AnchoredRefineMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::anchored_design::AnchoredRefineMover::get_nonpivot_torsion_sampling ( ) const

use nonpivot torsion sampling for KIC?

References nonpivot_torsion_sampling_.

bool protocols::anchored_design::AnchoredRefineMover::get_refine_CCD_off ( ) const

do not perform CCD style closure (use KIC only)

References refine_CCD_off_.

core::Size protocols::anchored_design::AnchoredRefineMover::get_refine_cycles ( ) const

number of MC cycles

References refine_cycles_.

bool protocols::anchored_design::AnchoredRefineMover::get_refine_KIC_off ( ) const

do not perform KIC style closure (use CCD only)

References refine_KIC_off_.

core::Size protocols::anchored_design::AnchoredRefineMover::get_refine_repack_cycles ( ) const

how many cycles between repack/design opportunities?

References refine_repack_cycles_.

core::Real protocols::anchored_design::AnchoredRefineMover::get_refine_temp ( ) const

MC temperature.

References refine_temp_.

core::Real protocols::anchored_design::AnchoredRefineMover::get_vicinity_degree ( ) const

KIC vicinity sampling degrees.

References vicinity_degree_.

bool protocols::anchored_design::AnchoredRefineMover::get_vicinity_sampling ( ) const

KIC use vicinity sampling?

References vicinity_sampling_.

void protocols::anchored_design::AnchoredRefineMover::read_options ( )

read in options from the options system

References core::pack::interaction_graph::debug, debug_, min_type_, nonpivot_torsion_sampling_, refine_CCD_off_, refine_cycles_, refine_KIC_off_, refine_repack_cycles_, refine_temp_, vicinity_degree_, and vicinity_sampling_.

Referenced by AnchoredRefineMover().

void protocols::anchored_design::AnchoredRefineMover::set_debug ( bool const debug )

debugging mode activates a bunch of extra output

References core::pack::interaction_graph::debug, and debug_.

void protocols::anchored_design::AnchoredRefineMover::set_min_type ( std::string const & min_type )

what minimizer type to use?

References min_type_.

void protocols::anchored_design::AnchoredRefineMover::set_nonpivot_torsion_sampling ( bool const nonpivot_torsion_sampling )

use nonpivot torsion sampling for KIC?

References nonpivot_torsion_sampling_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_CCD_off ( bool const refine_CCD_off )

do not perform CCD style closure (use KIC only)

References refine_CCD_off_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_cycles ( core::Size const refine_cycles )

number of MC cycles

References refine_cycles_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_KIC_off ( bool const refine_KIC_off )

do not perform KIC style closure (use CCD only)

References refine_KIC_off_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_repack_cycles ( core::Size const refine_repack_cycles )

how many cycles between repack/design opportunities?

References refine_repack_cycles_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_temp ( core::Real const refine_temp )

MC temperature.

References refine_temp_.

void protocols::anchored_design::AnchoredRefineMover::set_vicinity_degree ( core::Size const vicinity_degree )

KIC vicinity sampling degrees.

References vicinity_degree_.

void protocols::anchored_design::AnchoredRefineMover::set_vicinity_sampling ( bool const vicinity_sampling )

KIC use vicinity sampling?

References vicinity_sampling_.

Member Data Documentation

bool protocols::anchored_design::AnchoredRefineMover::debug_

private

debugging mode activates a bunch of extra output

Referenced by apply(), get_debug(), read_options(), and set_debug().

protocols::anchored_design::AnchorMoversDataOP protocols::anchored_design::AnchoredRefineMover::interface_

private

Referenced by apply().

std::string protocols::anchored_design::AnchoredRefineMover::min_type_

private

what minimizer type to use?

Referenced by apply(), get_min_type(), read_options(), and set_min_type().

bool protocols::anchored_design::AnchoredRefineMover::nonpivot_torsion_sampling_

private

use nonpivot torsion sampling for KIC?

Referenced by apply(), get_nonpivot_torsion_sampling(), read_options(), and set_nonpivot_torsion_sampling().

bool protocols::anchored_design::AnchoredRefineMover::refine_CCD_off_

private

do not perform CCD style closure (use KIC only)

Referenced by apply(), get_refine_CCD_off(), read_options(), and set_refine_CCD_off().

core::Size protocols::anchored_design::AnchoredRefineMover::refine_cycles_

private

number of MC cycles

Referenced by apply(), get_refine_cycles(), read_options(), and set_refine_cycles().

bool protocols::anchored_design::AnchoredRefineMover::refine_KIC_off_

private

do not perform KIC style closure (use CCD only)

Referenced by apply(), get_refine_KIC_off(), read_options(), and set_refine_KIC_off().

core::Size protocols::anchored_design::AnchoredRefineMover::refine_repack_cycles_

private

how many cycles between repack/design opportunities?

Referenced by apply(), get_refine_repack_cycles(), read_options(), and set_refine_repack_cycles().

core::Real protocols::anchored_design::AnchoredRefineMover::refine_temp_

private

MC temperature.

Referenced by apply(), get_refine_temp(), read_options(), and set_refine_temp().

core::Real protocols::anchored_design::AnchoredRefineMover::vicinity_degree_

private

KIC vicinity sampling degrees.

Referenced by apply(), get_vicinity_degree(), read_options(), and set_vicinity_degree().

bool protocols::anchored_design::AnchoredRefineMover::vicinity_sampling_

private

KIC use vicinity sampling?

Referenced by get_vicinity_sampling(), read_options(), and set_vicinity_sampling().

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

src/protocols/anchored_design/AnchorMovers.hh
src/protocols/anchored_design/AnchorMovers.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation