#include <LoopHashDiversifier.hh>

Inheritance diagram for protocols::loophash::LoopHashDiversifier:

Collaboration diagram for protocols::loophash::LoopHashDiversifier:

Public Member Functions
	LoopHashDiversifier ()

	LoopHashDiversifier (LoopHashLibraryOP library, core::Real min_inter_ss_bbrms, core::Real max_inter_ss_bbrms, core::Real min_intra_ss_bbrms, core::Real max_intra_ss_bbrms, core::Real min_rms, core::Real max_rms, core::Size start_res, core::Size stop_res, core::Size window_size, core::Size max_radius, core::Size max_struct, core::Size num_iterations, core::Size num_try_div, bool ideal, bool filter_by_phipsi, protocols::filters::FilterOP cenfilter, protocols::filters::FilterOP ranking_cenfilter, core::scoring::ScoreFunctionOP scorefxn_cen_cst, core::scoring::ScoreFunctionOP scorefxn_rama_cst)

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

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

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

virtual	~LoopHashDiversifier ()
	**End Creator Methods**/// More...

Real	min_inter_ss_bbrms () const

void	min_inter_ss_bbrms (Real const min_inter_ss_bbrms)

Real	max_inter_ss_bbrms () const

void	max_inter_ss_bbrms (Real const max_inter_ss_bbrms)

Real	min_intra_ss_bbrms () const

void	min_intra_ss_bbrms (Real const min_intra_ss_bbrms)

Real	max_intra_ss_bbrms () const

void	max_intra_ss_bbrms (Real const max_intra_ss_bbrms)

Real	min_rms () const

void	min_rms (Real const min_rms)

Real	max_rms () const

void	max_rms (Real const max_rms)

Size	num_iterations () const

void	num_iterations (Size const num_iterations)

Size	num_try_div () const

void	num_try_div (Size const num_try_div)

utility::vector1< Size >	loop_sizes () const

void	add_loop_size (Size const loop_size)

void	cenfilter (protocols::filters::FilterOP cenfilter)

void	ranking_cenfilter (protocols::filters::FilterOP filter)

protocols::filters::FilterOP	ranking_cenfilter () const

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	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

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...

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
	this function informs 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
	this function informs 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

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::loophash::LoopHashDiversifier::LoopHashDiversifier ( )

References library_, loop_sizes(), loop_sizes_, and window_size_.

Referenced by clone().

protocols::loophash::LoopHashDiversifier::LoopHashDiversifier	(	LoopHashLibraryOP	library,
		core::Real	min_inter_ss_bbrms,
		core::Real	max_inter_ss_bbrms,
		core::Real	min_intra_ss_bbrms,
		core::Real	max_intra_ss_bbrms,
		core::Real	min_rms,
		core::Real	max_rms,
		core::Size	start_res,
		core::Size	stop_res,
		core::Size	window_size,
		core::Size	max_radius,
		core::Size	max_struct,
		core::Size	num_iterations,
		core::Size	num_try_div,
		bool	ideal,
		bool	filter_by_phipsi,
		protocols::filters::FilterOP	cenfilter,
		protocols::filters::FilterOP	ranking_cenfilter,
		core::scoring::ScoreFunctionOP	scorefxn_cen_cst,
		core::scoring::ScoreFunctionOP	scorefxn_rama_cst
	)

References library_, loop_sizes(), loop_sizes_, and window_size_.

protocols::loophash::LoopHashDiversifier::~LoopHashDiversifier ( )

virtual

****End Creator Methods****///

Member Function Documentation

void protocols::loophash::LoopHashDiversifier::add_loop_size ( Size const loop_size)

References loop_sizes_.

Referenced by parse_my_tag().

void protocols::loophash::LoopHashDiversifier::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

void protocols::loophash::LoopHashDiversifier::cenfilter ( protocols::filters::FilterOP cenfilter)

References cenfilter_.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::clone ( ) const

inlinevirtual

clone has to be overridden only if clone invocation is expected.

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.

References LoopHashDiversifier().

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::fresh_instance ( ) const

inlinevirtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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::loophash::LoopHashDiversifier::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::loophash::LoopHashDiversifierCreator::mover_name().

utility::vector1< Size > protocols::loophash::LoopHashDiversifier::loop_sizes ( ) const

References loop_sizes_.

Referenced by LoopHashDiversifier(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( ) const

References max_inter_ss_bbrms_.

Referenced by apply(), and max_inter_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( Real const max_inter_ss_bbrms)

References max_inter_ss_bbrms(), and max_inter_ss_bbrms_.

Real protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( ) const

References max_intra_ss_bbrms_.

Referenced by apply(), and max_intra_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( Real const max_intra_ss_bbrms)

References max_intra_ss_bbrms(), and max_intra_ss_bbrms_.

Real protocols::loophash::LoopHashDiversifier::max_rms ( ) const

References max_rms_.

Referenced by apply(), and max_rms().

void protocols::loophash::LoopHashDiversifier::max_rms ( Real const max_rms)

References max_rms(), and max_rms_.

Real protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( ) const

References min_inter_ss_bbrms_.

Referenced by apply(), and min_inter_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( Real const min_inter_ss_bbrms)

References min_inter_ss_bbrms(), and min_inter_ss_bbrms_.

Real protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( ) const

References min_intra_ss_bbrms_.

Referenced by apply(), and min_intra_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( Real const min_intra_ss_bbrms)

References min_intra_ss_bbrms(), and min_intra_ss_bbrms_.

Real protocols::loophash::LoopHashDiversifier::min_rms ( ) const

References min_rms_.

Referenced by apply(), and min_rms().

void protocols::loophash::LoopHashDiversifier::min_rms ( Real const min_rms)

References min_rms(), and min_rms_.

Size protocols::loophash::LoopHashDiversifier::num_iterations ( ) const

References num_iterations_.

Referenced by num_iterations().

void protocols::loophash::LoopHashDiversifier::num_iterations ( Size const num_iterations)

References num_iterations(), and num_iterations_.

Size protocols::loophash::LoopHashDiversifier::num_try_div ( ) const

References num_try_div_.

Referenced by num_try_div().

void protocols::loophash::LoopHashDiversifier::num_try_div ( Size const num_try_div)

References num_try_div(), and num_try_div_.

void protocols::loophash::LoopHashDiversifier::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 add_loop_size(), cenfilter(), filter_by_phipsi_, protocols::moves::DataMap::get(), core::pose::get_resnum(), ideal_, library_, loop_sizes(), max_inter_ss_bbrms_, max_intra_ss_bbrms_, max_radius_, max_rms_, max_struct_, min_inter_ss_bbrms_, min_intra_ss_bbrms_, min_rms_, num_iterations_, num_try_div_, protocols::rosetta_scripts::parse_filter(), ranking_cenfilter(), scorefxn_cen_cst_, scorefxn_rama_cst_, start_res_, stop_res_, core::pose::Pose::total_residue(), and window_size_.

void protocols::loophash::LoopHashDiversifier::ranking_cenfilter ( protocols::filters::FilterOP filter)

inline

References ranking_cenfilter_.

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::ranking_cenfilter ( ) const

inline

References ranking_cenfilter_.

Referenced by apply(), and parse_my_tag().

Member Data Documentation

std::vector< std::pair< Real, core::io::silent::SilentStructOP > > protocols::loophash::LoopHashDiversifier::all_structs_

private

Referenced by apply().

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::cenfilter_

private

Referenced by apply(), and cenfilter().

bool protocols::loophash::LoopHashDiversifier::filter_by_phipsi_

private

Referenced by apply(), and parse_my_tag().

bool protocols::loophash::LoopHashDiversifier::ideal_

private

Referenced by apply(), and parse_my_tag().

LoopHashLibraryOP protocols::loophash::LoopHashDiversifier::library_

private

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

utility::vector1< Size > protocols::loophash::LoopHashDiversifier::loop_sizes_

private

Referenced by add_loop_size(), loop_sizes(), and LoopHashDiversifier().

Real protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms_

private

Referenced by max_inter_ss_bbrms(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms_

private

Referenced by max_intra_ss_bbrms(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::max_radius_

private

Referenced by apply(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::max_rms_

private

Referenced by max_rms(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::max_struct_

private

Referenced by apply(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms_

private

Referenced by min_inter_ss_bbrms(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms_

private

Referenced by min_intra_ss_bbrms(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::min_rms_

private

Referenced by min_rms(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::num_iterations_

private

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

Size protocols::loophash::LoopHashDiversifier::num_try_div_

private

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

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::ranking_cenfilter_

private

Referenced by ranking_cenfilter().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashDiversifier::scorefxn_cen_cst_

private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashDiversifier::scorefxn_rama_cst_

private

Referenced by apply(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::start_res_

private

Referenced by apply(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::stop_res_

private

Referenced by apply(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::window_size_

private

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

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

src/protocols/loophash/LoopHashDiversifier.hh
src/protocols/loophash/LoopHashDiversifier.cc

Private Attributes
utility::vector1< Size >	loop_sizes_

LoopHashLibraryOP	library_

Real	min_inter_ss_bbrms_

Real	max_inter_ss_bbrms_

Real	min_intra_ss_bbrms_

Real	max_intra_ss_bbrms_

Real	min_rms_

Real	max_rms_

Size	start_res_

Size	stop_res_

Size	window_size_

Size	max_radius_

Size	max_struct_

Size	num_iterations_

Size	num_try_div_

bool	ideal_

bool	filter_by_phipsi_

protocols::filters::FilterOP	cenfilter_

protocols::filters::FilterOP	ranking_cenfilter_

core::scoring::ScoreFunctionOP	scorefxn_cen_cst_

core::scoring::ScoreFunctionOP	scorefxn_rama_cst_

std::vector< std::pair< Real, core::io::silent::SilentStructOP > >	all_structs_

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation