#include <GreedyOptMutationMover.hh>

Inheritance diagram for protocols::design_opt::GreedyOptMutationMover:

Collaboration diagram for protocols::design_opt::GreedyOptMutationMover:

Public Types
typedef core::pose::Pose	Pose

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

Public Member Functions
	GreedyOptMutationMover ()
	default ctor More...

	GreedyOptMutationMover (core::pack::task::TaskFactoryOP task_factory, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MoverOP relax_mover, utility::vector1< protocols::filters::FilterOP > filters, utility::vector1< std::string > sample_types, utility::vector1< core::Real > filter_deltas, bool dump_pdb=false, bool dump_table=false, bool parallel=false, bool stop_before_condition=false, bool skip_best_check=false, bool rtmin=false, bool shuffle_order=false, protocols::filters::FilterOP stopping_condition=protocols::filters::FilterOP(NULL))

bool	pose_coords_are_same (core::pose::Pose const &pose1, core::pose::Pose const &pose2)

void	filter_seqpos_pareto_opt_ptmuts ()

void	clear_cached_data ()

void	calc_pfront_poses_filter_ranks ()

void	dump_scoring_table (std::string filename, core::pose::Pose const &ref_pose) const

void	apply (Pose &pose)

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

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

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...

void	add_filter (protocols::filters::FilterOP, std::string const sample_type, core::Real filter_delta)

virtual	~GreedyOptMutationMover ()

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP task_factory)

core::scoring::ScoreFunctionOP	scorefxn () const

void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)

utility::vector1 < protocols::filters::FilterOP >	filters () const

void	filters (utility::vector1< protocols::filters::FilterOP > filters)

protocols::moves::MoverOP	relax_mover () const

void	relax_mover (protocols::moves::MoverOP relax_mover)

bool	dump_pdb () const

void	dump_pdb (bool const dump_pdb)

bool	dump_table () const

void	dump_table (bool const dump_table)

bool	parallel () const

void	parallel (bool const parallel)

utility::vector1< std::string >	sample_types () const

void	sample_types (utility::vector1< std::string > const sample_types)

utility::vector1< core::Real >	filter_deltas () const

void	filter_deltas (utility::vector1< core::Real > const filter_deltas)

void	stopping_condition (protocols::filters::FilterOP f)

protocols::filters::FilterOP	stopping_condition () const

bool	stop_before_condition () const

void	stop_before_condition (bool const stop_before_condition)

bool	skip_best_check () const

void	skip_best_check (bool const skip_best_check)

utility::vector1 < protocols::simple_filters::DeltaFilterOP >	delta_filters () const

void	delta_filters (utility::vector1< protocols::simple_filters::DeltaFilterOP > const d)

bool	rtmin () const

void	rtmin (bool const b)

bool	shuffle_order () const

void	shuffle_order (bool const b)

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

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_

core::scoring::ScoreFunctionOP	scorefxn_

utility::vector1 < protocols::filters::FilterOP >	filters_

protocols::moves::MoverOP	relax_mover_

utility::vector1< std::string >	sample_types_

bool	dump_pdb_

bool	dump_table_

bool	parallel_

protocols::filters::FilterOP	stopping_condition_

utility::vector1< std::pair < core::Size, utility::vector1 < std::pair < core::chemical::AA, utility::vector1< core::Real > > > > >	seqpos_aa_vals_vec_

utility::vector1< core::Real >	filter_deltas_

core::pose::Pose	ref_pose_

utility::vector1 < core::pose::Pose >	pfront_poses_

utility::vector1 < utility::vector1< core::Real > >	pfront_poses_filter_vals_

utility::vector1 < utility::vector1< core::Size > >	pfront_poses_filter_ranks_

core::Size	nstruct_iter_

bool	stop_before_condition_

bool	skip_best_check_

utility::vector1 < protocols::simple_filters::DeltaFilterOP >	reset_delta_filters_

bool	rtmin_

core::Real	design_shell_

core::Real	repack_shell_

bool	shuffle_order_

Additional Inherited Members
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...

Detailed Description

Definition at line 34 of file GreedyOptMutationMover.hh.

Member Typedef Documentation

typedef core::pose::Pose protocols::design_opt::GreedyOptMutationMover::Pose

Definition at line 37 of file GreedyOptMutationMover.hh.

Constructor & Destructor Documentation

protocols::design_opt::GreedyOptMutationMover::GreedyOptMutationMover ( )

default ctor

Definition at line 71 of file GreedyOptMutationMover.cc.

Referenced by clone().

protocols::design_opt::GreedyOptMutationMover::GreedyOptMutationMover	(	core::pack::task::TaskFactoryOP	task_factory,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MoverOP	relax_mover,
		utility::vector1< protocols::filters::FilterOP >	filters,
		utility::vector1< std::string >	sample_types,
		utility::vector1< core::Real >	filter_deltas,
		bool	dump_pdb = `false`,
		bool	dump_table = `false`,
		bool	parallel = `false`,
		bool	stop_before_condition = `false`,
		bool	skip_best_check = `false`,
		bool	rtmin = `false`,
		bool	shuffle_order = `false`,
		protocols::filters::FilterOP	stopping_condition = `protocols::filters::FilterOP(NULL)`
	)

protocols::design_opt::GreedyOptMutationMover::~GreedyOptMutationMover ( )

virtual

Definition at line 125 of file GreedyOptMutationMover.cc.

Member Function Documentation

void protocols::design_opt::GreedyOptMutationMover::add_filter	(	protocols::filters::FilterOP	filter,
		std::string const	sample_type,
		core::Real	filter_delta
	)

Definition at line 683 of file GreedyOptMutationMover.cc.

References filter_deltas_, filters_, and sample_types_.

Referenced by parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::apply ( Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 500 of file GreedyOptMutationMover.cc.

References calc_pfront_poses_filter_ranks(), clear_cached_data(), protocols::design_opt::cmp_pair_by_first_vec_val(), protocols::design_opt::cmp_pair_vec_by_first_vec_val(), protocols::jd2::current_output_name(), dump_pdb(), dump_scoring_table(), dump_table(), core::pose::Pose::empty(), protocols::design_opt::filter_pareto_opt_poses(), filter_seqpos_pareto_opt_ptmuts(), filters(), protocols::jd2::jd2_used(), core::conformation::Residue::name1(), nstruct_iter_, parallel(), pfront_poses_, pfront_poses_filter_ranks_, pfront_poses_filter_vals_, pose_coords_are_same(), ref_pose_, relax_mover(), reset_delta_filters_, core::pose::Pose::residue(), protocols::design_opt::RG(), sample_types(), scorefxn(), seqpos_aa_vals_vec_, shuffle_order(), skip_best_check(), protocols::loops::stop, stop_before_condition(), stopping_condition(), and task_factory().

void protocols::design_opt::GreedyOptMutationMover::calc_pfront_poses_filter_ranks ( )

Definition at line 361 of file GreedyOptMutationMover.cc.

References protocols::design_opt::cmp_pair_by_second(), pfront_poses_filter_ranks_, and pfront_poses_filter_vals_.

Referenced by apply().

void protocols::design_opt::GreedyOptMutationMover::clear_cached_data ( )

Definition at line 328 of file GreedyOptMutationMover.cc.

References core::pose::Pose::clear(), pfront_poses_, pfront_poses_filter_ranks_, pfront_poses_filter_vals_, ref_pose_, and seqpos_aa_vals_vec_.

Referenced by apply(), dump_pdb(), dump_table(), filter_deltas(), filters(), relax_mover(), scorefxn(), and task_factory().

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::clone ( ) const

virtual

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.

Definition at line 134 of file GreedyOptMutationMover.cc.

References GreedyOptMutationMover().

utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::design_opt::GreedyOptMutationMover::delta_filters ( ) const

Definition at line 250 of file GreedyOptMutationMover.cc.

References reset_delta_filters_.

void protocols::design_opt::GreedyOptMutationMover::delta_filters ( utility::vector1< protocols::simple_filters::DeltaFilterOP > const d)

Definition at line 255 of file GreedyOptMutationMover.cc.

References reset_delta_filters_.

bool protocols::design_opt::GreedyOptMutationMover::dump_pdb ( ) const

Definition at line 198 of file GreedyOptMutationMover.cc.

References dump_pdb_.

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

void protocols::design_opt::GreedyOptMutationMover::dump_pdb ( bool const dump_pdb)

Definition at line 192 of file GreedyOptMutationMover.cc.

References clear_cached_data(), dump_pdb(), and dump_pdb_.

void protocols::design_opt::GreedyOptMutationMover::dump_scoring_table	(	std::string	filename,
		core::pose::Pose const &	ref_pose
	)		const

Definition at line 471 of file GreedyOptMutationMover.cc.

References core::pose::Pose::aa(), core::pose::Pose::pdb_info(), and seqpos_aa_vals_vec_.

Referenced by apply().

bool protocols::design_opt::GreedyOptMutationMover::dump_table ( ) const

Definition at line 209 of file GreedyOptMutationMover.cc.

References dump_table_.

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

void protocols::design_opt::GreedyOptMutationMover::dump_table ( bool const dump_table)

Definition at line 203 of file GreedyOptMutationMover.cc.

References clear_cached_data(), dump_table(), and dump_table_.

vector1< core::Real > protocols::design_opt::GreedyOptMutationMover::filter_deltas ( ) const

Definition at line 277 of file GreedyOptMutationMover.cc.

References filter_deltas_.

Referenced by filter_deltas().

void protocols::design_opt::GreedyOptMutationMover::filter_deltas ( utility::vector1< core::Real > const filter_deltas)

Definition at line 271 of file GreedyOptMutationMover.cc.

References clear_cached_data(), filter_deltas(), and filter_deltas_.

void protocols::design_opt::GreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts ( )

Definition at line 425 of file GreedyOptMutationMover.cc.

References protocols::design_opt::calc_pareto_front(), and seqpos_aa_vals_vec_.

Referenced by apply().

vector1< protocols::filters::FilterOP > protocols::design_opt::GreedyOptMutationMover::filters ( ) const

Definition at line 174 of file GreedyOptMutationMover.cc.

References filters_.

Referenced by apply(), and filters().

void protocols::design_opt::GreedyOptMutationMover::filters ( utility::vector1< protocols::filters::FilterOP > filters)

Definition at line 169 of file GreedyOptMutationMover.cc.

References clear_cached_data(), filters(), and filters_.

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::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.

Definition at line 65 of file GreedyOptMutationMover.hh.

std::string protocols::design_opt::GreedyOptMutationMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 152 of file GreedyOptMutationMover.cc.

References protocols::design_opt::GreedyOptMutationMoverCreator::mover_name().

bool protocols::design_opt::GreedyOptMutationMover::parallel ( ) const

Definition at line 298 of file GreedyOptMutationMover.cc.

References parallel_.

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

void protocols::design_opt::GreedyOptMutationMover::parallel ( bool const parallel)

Definition at line 293 of file GreedyOptMutationMover.cc.

References parallel(), and parallel_.

void protocols::design_opt::GreedyOptMutationMover::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.

Definition at line 694 of file GreedyOptMutationMover.cc.

References add_filter(), design_shell_, dump_pdb(), dump_table(), filters_, parallel(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), relax_mover(), repack_shell_, reset_delta_filters_, rtmin(), scorefxn(), shuffle_order(), skip_best_check(), stop_before_condition(), stopping_condition(), and task_factory().

bool protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Definition at line 338 of file GreedyOptMutationMover.cc.

References core::pose::Pose::conformation(), core::pose::Pose::residue(), core::conformation::Conformation::sequence_matches(), and core::pose::Pose::total_residue().

Referenced by apply().

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::relax_mover ( ) const

Definition at line 164 of file GreedyOptMutationMover.cc.

References relax_mover_.

Referenced by apply(), and parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::relax_mover ( protocols::moves::MoverOP relax_mover)

Definition at line 158 of file GreedyOptMutationMover.cc.

References clear_cached_data(), and relax_mover_.

bool protocols::design_opt::GreedyOptMutationMover::rtmin ( ) const

Definition at line 239 of file GreedyOptMutationMover.cc.

References rtmin_.

Referenced by parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::rtmin ( bool const b)

Definition at line 234 of file GreedyOptMutationMover.cc.

References protocols::match::upstream::b, and rtmin_.

vector1< std::string > protocols::design_opt::GreedyOptMutationMover::sample_types ( ) const

Definition at line 266 of file GreedyOptMutationMover.cc.

References sample_types_.

Referenced by apply().

void protocols::design_opt::GreedyOptMutationMover::sample_types ( utility::vector1< std::string > const sample_types)

core::scoring::ScoreFunctionOP protocols::design_opt::GreedyOptMutationMover::scorefxn ( ) const

Definition at line 288 of file GreedyOptMutationMover.cc.

References scorefxn_.

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

void protocols::design_opt::GreedyOptMutationMover::scorefxn ( core::scoring::ScoreFunctionOP scorefxn)

Definition at line 282 of file GreedyOptMutationMover.cc.

References clear_cached_data(), scorefxn(), and scorefxn_.

bool protocols::design_opt::GreedyOptMutationMover::shuffle_order ( ) const

Definition at line 247 of file GreedyOptMutationMover.cc.

References shuffle_order_.

Referenced by apply(), and parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::shuffle_order ( bool const b)

Definition at line 242 of file GreedyOptMutationMover.cc.

References protocols::match::upstream::b, and shuffle_order_.

bool protocols::design_opt::GreedyOptMutationMover::skip_best_check ( ) const

Definition at line 229 of file GreedyOptMutationMover.cc.

References skip_best_check_.

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

void protocols::design_opt::GreedyOptMutationMover::skip_best_check ( bool const skip_best_check)

Definition at line 224 of file GreedyOptMutationMover.cc.

References skip_best_check(), and skip_best_check_.

bool protocols::design_opt::GreedyOptMutationMover::stop_before_condition ( ) const

Definition at line 219 of file GreedyOptMutationMover.cc.

References stop_before_condition_.

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

void protocols::design_opt::GreedyOptMutationMover::stop_before_condition ( bool const stop_before_condition)

Definition at line 214 of file GreedyOptMutationMover.cc.

References stop_before_condition(), and stop_before_condition_.

void protocols::design_opt::GreedyOptMutationMover::stopping_condition ( protocols::filters::FilterOP f)

inline

Definition at line 92 of file GreedyOptMutationMover.hh.

References stopping_condition_.

protocols::filters::FilterOP protocols::design_opt::GreedyOptMutationMover::stopping_condition ( ) const

inline

Definition at line 93 of file GreedyOptMutationMover.hh.

References stopping_condition_.

Referenced by apply(), and parse_my_tag().

core::pack::task::TaskFactoryOP protocols::design_opt::GreedyOptMutationMover::task_factory ( ) const

Definition at line 186 of file GreedyOptMutationMover.cc.

References task_factory_.

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

void protocols::design_opt::GreedyOptMutationMover::task_factory ( core::pack::task::TaskFactoryOP task_factory)

Definition at line 179 of file GreedyOptMutationMover.cc.

References clear_cached_data(), task_factory(), and task_factory_.

Member Data Documentation

core::Real protocols::design_opt::GreedyOptMutationMover::design_shell_

private

Definition at line 127 of file GreedyOptMutationMover.hh.

Referenced by parse_my_tag().

bool protocols::design_opt::GreedyOptMutationMover::dump_pdb_

private

Definition at line 111 of file GreedyOptMutationMover.hh.

Referenced by dump_pdb().

bool protocols::design_opt::GreedyOptMutationMover::dump_table_

private

Definition at line 112 of file GreedyOptMutationMover.hh.

Referenced by dump_table().

utility::vector1< core::Real > protocols::design_opt::GreedyOptMutationMover::filter_deltas_

private

Definition at line 117 of file GreedyOptMutationMover.hh.

Referenced by add_filter(), and filter_deltas().

utility::vector1< protocols::filters::FilterOP > protocols::design_opt::GreedyOptMutationMover::filters_

private

Definition at line 108 of file GreedyOptMutationMover.hh.

Referenced by add_filter(), filters(), and parse_my_tag().

core::Size protocols::design_opt::GreedyOptMutationMover::nstruct_iter_

private

Definition at line 122 of file GreedyOptMutationMover.hh.

Referenced by apply().

bool protocols::design_opt::GreedyOptMutationMover::parallel_

private

Definition at line 113 of file GreedyOptMutationMover.hh.

Referenced by parallel().

utility::vector1< core::pose::Pose > protocols::design_opt::GreedyOptMutationMover::pfront_poses_

private

Definition at line 119 of file GreedyOptMutationMover.hh.

Referenced by apply(), and clear_cached_data().

utility::vector1< utility::vector1< core::Size > > protocols::design_opt::GreedyOptMutationMover::pfront_poses_filter_ranks_

private

Definition at line 121 of file GreedyOptMutationMover.hh.

Referenced by apply(), calc_pfront_poses_filter_ranks(), and clear_cached_data().

utility::vector1< utility::vector1< core::Real > > protocols::design_opt::GreedyOptMutationMover::pfront_poses_filter_vals_

private

Definition at line 120 of file GreedyOptMutationMover.hh.

Referenced by apply(), calc_pfront_poses_filter_ranks(), and clear_cached_data().

core::pose::Pose protocols::design_opt::GreedyOptMutationMover::ref_pose_

private

Definition at line 118 of file GreedyOptMutationMover.hh.

Referenced by apply(), and clear_cached_data().

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::relax_mover_

private

Definition at line 109 of file GreedyOptMutationMover.hh.

Referenced by relax_mover().

core::Real protocols::design_opt::GreedyOptMutationMover::repack_shell_

private

Definition at line 128 of file GreedyOptMutationMover.hh.

Referenced by parse_my_tag().

utility::vector1<protocols::simple_filters::DeltaFilterOP> protocols::design_opt::GreedyOptMutationMover::reset_delta_filters_

private

Definition at line 125 of file GreedyOptMutationMover.hh.

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

bool protocols::design_opt::GreedyOptMutationMover::rtmin_

private

Definition at line 126 of file GreedyOptMutationMover.hh.

Referenced by rtmin().

utility::vector1< std::string > protocols::design_opt::GreedyOptMutationMover::sample_types_

private

Definition at line 110 of file GreedyOptMutationMover.hh.

Referenced by add_filter(), and sample_types().

core::scoring::ScoreFunctionOP protocols::design_opt::GreedyOptMutationMover::scorefxn_

private

Definition at line 107 of file GreedyOptMutationMover.hh.

Referenced by scorefxn().

utility::vector1< std::pair< core::Size, utility::vector1< std::pair< core::chemical::AA, utility::vector1< core::Real > > > > > protocols::design_opt::GreedyOptMutationMover::seqpos_aa_vals_vec_

private

Definition at line 116 of file GreedyOptMutationMover.hh.

Referenced by apply(), clear_cached_data(), dump_scoring_table(), and filter_seqpos_pareto_opt_ptmuts().

bool protocols::design_opt::GreedyOptMutationMover::shuffle_order_

private

Definition at line 129 of file GreedyOptMutationMover.hh.

Referenced by shuffle_order().

bool protocols::design_opt::GreedyOptMutationMover::skip_best_check_

private

Definition at line 124 of file GreedyOptMutationMover.hh.

Referenced by skip_best_check().

bool protocols::design_opt::GreedyOptMutationMover::stop_before_condition_

private

Definition at line 123 of file GreedyOptMutationMover.hh.

Referenced by stop_before_condition().

protocols::filters::FilterOP protocols::design_opt::GreedyOptMutationMover::stopping_condition_

private

Definition at line 114 of file GreedyOptMutationMover.hh.

Referenced by stopping_condition().

core::pack::task::TaskFactoryOP protocols::design_opt::GreedyOptMutationMover::task_factory_

private

Definition at line 106 of file GreedyOptMutationMover.hh.

Referenced by task_factory().

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

src/protocols/design_opt/GreedyOptMutationMover.hh
src/protocols/design_opt/GreedyOptMutationMover.cc

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