#include <MatDesGreedyOptMutationMover.hh>

Inheritance diagram for protocols::matdes::MatDesGreedyOptMutationMover:

[legend]

Public Types
typedef core::pose::Pose	Pose

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

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

	MatDesGreedyOptMutationMover (core::pack::task::TaskFactoryOP task_factory, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MoverOP relax_mover, utility::vector1< protocols::filters::FilterOP > filters, utility::vector1< std::pair< std::string, core::Real > > filter_thresholds, utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > set_task_for_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, bool diversify=false, bool incl_nonopt=false, bool force_natro=false, bool keep_trying=false, protocols::filters::FilterOP stopping_condition=protocols::filters::FilterOP(nullptr))

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

void	filter_seqpos_pareto_opt_ptmuts ()

void	filter_pareto_opt_poses ()

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) override
	Main Method. More...

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	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)

void	reset_delta_filter_baselines (Pose &pose)

	~MatDesGreedyOptMutationMover () override

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)

utility::vector1< std::pair< std::string, core::Real > >	filter_thresholds () const

void	filter_thresholds (utility::vector1< std::pair< std::string, core::Real > > filter_thresholds)

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)

utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP >	set_task_for_filters () const

void	set_task_for_filters (utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > set_task_for_filters)

bool	force_natro () const

void	force_natro (bool const f)

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

void	force_natro_for_stored_task_names (utility::vector1< std::string > force_natro_for_stored_task_names)

bool	rtmin () const

void	rtmin (bool const b)

bool	shuffle_order () const

void	shuffle_order (bool const b)

bool	diversify () const

void	diversify (bool const b)

bool	incl_nonopt () const

void	incl_nonopt (bool const b)

core::pose::PoseOP	reference_pose () const

void	reference_pose (core::pose::PoseOP const reference_pose)

bool	keep_trying () const

void	keep_trying (bool const k)

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...

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::pack::task::TaskFactoryOP	task_factory_

core::scoring::ScoreFunctionOP	scorefxn_

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

utility::vector1< std::pair< std::string, core::Real > >	filter_thresholds_

utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP >	set_task_for_filters_

utility::vector1< std::string >	force_natro_for_stored_task_names_

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_

utility::vector1< protocols::filters::CompoundFilterOP >	compound_filters_

utility::vector1< protocols::filters::CombinedFilterOP >	combined_filters_

bool	rtmin_

core::Real	design_shell_

core::Real	repack_shell_

bool	shuffle_order_

bool	diversify_

bool	incl_nonopt_

bool	force_natro_

bool	keep_trying_

core::pose::PoseOP	reference_pose_

Additional Inherited Members
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...

Member Typedef Documentation

◆ Pose

typedef core::pose::Pose protocols::matdes::MatDesGreedyOptMutationMover::Pose

Constructor & Destructor Documentation

◆ MatDesGreedyOptMutationMover() [1/2]

protocols::matdes::MatDesGreedyOptMutationMover::MatDesGreedyOptMutationMover ( )

default ctor

◆ MatDesGreedyOptMutationMover() [2/2]

protocols::matdes::MatDesGreedyOptMutationMover::MatDesGreedyOptMutationMover	(	core::pack::task::TaskFactoryOP	task_factory,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MoverOP	relax_mover,
		utility::vector1< protocols::filters::FilterOP >	filters,
		utility::vector1< std::pair< std::string, core::Real > >	filter_thresholds,
		utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP >	set_task_for_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`,
		bool	diversify = `false`,
		bool	incl_nonopt = `false`,
		bool	force_natro = `false`,
		bool	keep_trying = `false`,
		protocols::filters::FilterOP	stopping_condition = `protocols::filters::FilterOP(nullptr)`
	)

◆ ~MatDesGreedyOptMutationMover()

protocols::matdes::MatDesGreedyOptMutationMover::~MatDesGreedyOptMutationMover ( )

overridedefault

Member Function Documentation

◆ add_filter()

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

References filter_deltas_, filters_, and sample_types_.

Referenced by parse_my_tag().

◆ apply()

void protocols::matdes::MatDesGreedyOptMutationMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References calc_pfront_poses_filter_ranks(), clear_cached_data(), protocols::matdes::cmp_pair_by_first_vec_val(), protocols::matdes::cmp_pair_vec_by_first_vec_val(), protocols::jd2::current_output_name(), dump_pdb(), dump_scoring_table(), dump_table(), core::pose::Pose::empty(), filter_pareto_opt_poses(), filter_seqpos_pareto_opt_ptmuts(), filter_thresholds(), filters(), filters_, force_natro_, force_natro_for_stored_task_names_, protocols::jd2::jd2_used(), keep_trying(), core::conformation::Residue::name1(), nstruct_iter_, parallel(), pfront_poses_, pfront_poses_filter_ranks_, pfront_poses_filter_vals_, pose_coords_are_same(), ref_pose_, reference_pose_, relax_mover(), reset_delta_filter_baselines(), reset_delta_filters_, core::pose::Pose::residue(), core::scoring::rg, sample_types(), scorefxn(), seqpos_aa_vals_vec_, set_task_for_filters(), shuffle_order(), skip_best_check(), core::pose::datacache::CacheableDataType::STM_STORED_TASKS, protocols::loops::stop, stop_before_condition(), stopping_condition(), task_factory(), and protocols::matdes::TR().

◆ calc_pfront_poses_filter_ranks()

void protocols::matdes::MatDesGreedyOptMutationMover::calc_pfront_poses_filter_ranks ( )

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

Referenced by apply().

◆ clear_cached_data()

void protocols::matdes::MatDesGreedyOptMutationMover::clear_cached_data ( )

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(), relax_mover(), scorefxn(), and task_factory().

◆ clone()

protocols::moves::MoverOP protocols::matdes::MatDesGreedyOptMutationMover::clone ( ) const

overridevirtual

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.

◆ delta_filters() [1/2]

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

References reset_delta_filters_.

◆ delta_filters() [2/2]

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

References reset_delta_filters_.

◆ diversify() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::diversify ( ) const

References diversify_.

Referenced by parse_my_tag().

◆ diversify() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::diversify ( bool const b )

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

◆ dump_pdb() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb ( ) const

References dump_pdb_.

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

◆ dump_pdb() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb ( bool const dump_pdb )

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

◆ dump_scoring_table()

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

References core::pose::Pose::aa(), protocols::abinitio::filename(), core::conformation::membrane::out, core::pose::Pose::pdb_info(), seqpos_aa_vals_vec_, and protocols::matdes::TR().

Referenced by apply().

◆ dump_table() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_table ( ) const

References dump_table_.

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

◆ dump_table() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::dump_table ( bool const dump_table )

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

◆ filter_deltas() [1/2]

vector1< core::Real > protocols::matdes::MatDesGreedyOptMutationMover::filter_deltas ( ) const

References filter_deltas_.

◆ filter_deltas() [2/2]

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

◆ filter_pareto_opt_poses()

void protocols::matdes::MatDesGreedyOptMutationMover::filter_pareto_opt_poses ( )

References protocols::matdes::calc_pareto_front(), diversify_, filter_deltas_, pfront_poses_, and pfront_poses_filter_vals_.

Referenced by apply().

◆ filter_seqpos_pareto_opt_ptmuts()

void protocols::matdes::MatDesGreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts ( )

References protocols::matdes::calc_pareto_front(), diversify_, filter_deltas_, incl_nonopt_, and seqpos_aa_vals_vec_.

Referenced by apply().

◆ filter_thresholds() [1/2]

vector1< std::pair< std::string, core::Real > > protocols::matdes::MatDesGreedyOptMutationMover::filter_thresholds ( ) const

References filter_thresholds_.

Referenced by apply(), and parse_my_tag().

◆ filter_thresholds() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::filter_thresholds ( utility::vector1< std::pair< std::string, core::Real > > filter_thresholds )

◆ filters() [1/2]

vector1< protocols::filters::FilterOP > protocols::matdes::MatDesGreedyOptMutationMover::filters ( ) const

References filters_.

Referenced by apply().

◆ filters() [2/2]

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

◆ force_natro() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::force_natro ( ) const

References force_natro_.

◆ force_natro() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::force_natro ( bool const f )

References force_natro_.

◆ force_natro_for_stored_task_names() [1/2]

utility::vector1< std::string > protocols::matdes::MatDesGreedyOptMutationMover::force_natro_for_stored_task_names ( ) const

References force_natro_for_stored_task_names_.

◆ force_natro_for_stored_task_names() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::force_natro_for_stored_task_names ( utility::vector1< std::string > force_natro_for_stored_task_names )

References force_natro_for_stored_task_names_.

◆ fresh_instance()

protocols::moves::MoverOP protocols::matdes::MatDesGreedyOptMutationMover::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_name()

std::string protocols::matdes::MatDesGreedyOptMutationMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ incl_nonopt() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt ( ) const

References incl_nonopt_.

Referenced by parse_my_tag().

◆ incl_nonopt() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt ( bool const b )

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

◆ keep_trying() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::keep_trying ( ) const

References keep_trying_.

Referenced by apply(), and parse_my_tag().

◆ keep_trying() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::keep_trying ( bool const k )

References keep_trying_.

◆ mover_name()

std::string protocols::matdes::MatDesGreedyOptMutationMover::mover_name ( )

static

Referenced by get_name(), protocols::matdes::MatDesGreedyOptMutationMoverCreator::keyname(), and provide_xml_schema().

◆ parallel() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::parallel ( ) const

References parallel_.

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

◆ parallel() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::parallel ( bool const parallel )

References parallel(), and parallel_.

◆ parse_my_tag()

void protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_filter(), combined_filters_, compound_filters_, design_shell_, diversify(), dump_pdb(), dump_table(), filter_thresholds(), filters_, force_natro_, force_natro_for_stored_task_names_, incl_nonopt(), keep_trying(), parallel(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover_or_null(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), reference_pose_, relax_mover(), repack_shell_, reset_delta_filters_, rtmin(), protocols::rosetta_scripts::saved_reference_pose(), scorefxn(), set_task_for_filters_, shuffle_order(), skip_best_check(), stop_before_condition(), stopping_condition(), task_factory(), and protocols::matdes::TR().

◆ pose_coords_are_same()

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

References core::pose::Pose::conformation(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::conformation::Conformation::sequence_matches(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ provide_xml_schema()

void protocols::matdes::MatDesGreedyOptMutationMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::attributes_for_saved_reference_pose(), mover_name(), and protocols::design_opt::GreedyOptMutationMover::root_node_for_greedy_opt().

Referenced by protocols::matdes::MatDesGreedyOptMutationMoverCreator::provide_xml_schema().

◆ reference_pose() [1/2]

pose::PoseOP protocols::matdes::MatDesGreedyOptMutationMover::reference_pose ( ) const

References reference_pose_.

Referenced by reference_pose().

◆ reference_pose() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::reference_pose ( core::pose::PoseOP const reference_pose )

References reference_pose(), and reference_pose_.

◆ relax_mover() [1/2]

protocols::moves::MoverOP protocols::matdes::MatDesGreedyOptMutationMover::relax_mover ( ) const

References relax_mover_.

Referenced by apply(), and parse_my_tag().

◆ relax_mover() [2/2]

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

References clear_cached_data(), and relax_mover_.

◆ reset_delta_filter_baselines()

void protocols::matdes::MatDesGreedyOptMutationMover::reset_delta_filter_baselines ( Pose & pose )

References combined_filters_, compound_filters_, reset_delta_filters_, and protocols::matdes::TR().

Referenced by apply().

◆ rtmin() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::rtmin ( ) const

References rtmin_.

Referenced by parse_my_tag().

◆ rtmin() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::rtmin ( bool const b )

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

◆ sample_types() [1/2]

vector1< std::string > protocols::matdes::MatDesGreedyOptMutationMover::sample_types ( ) const

References sample_types_.

Referenced by apply().

◆ sample_types() [2/2]

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

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::matdes::MatDesGreedyOptMutationMover::scorefxn ( ) const

References scorefxn_.

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

◆ scorefxn() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

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

◆ set_task_for_filters() [1/2]

vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > protocols::matdes::MatDesGreedyOptMutationMover::set_task_for_filters ( ) const

References set_task_for_filters_.

Referenced by apply().

◆ set_task_for_filters() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::set_task_for_filters ( utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > set_task_for_filters )

◆ shuffle_order() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order ( ) const

References shuffle_order_.

Referenced by apply(), and parse_my_tag().

◆ shuffle_order() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order ( bool const b )

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

◆ skip_best_check() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check ( ) const

References skip_best_check_.

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

◆ skip_best_check() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check ( bool const skip_best_check )

References skip_best_check(), and skip_best_check_.

◆ stop_before_condition() [1/2]

bool protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition ( ) const

References stop_before_condition_.

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

◆ stop_before_condition() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition ( bool const stop_before_condition )

References stop_before_condition(), and stop_before_condition_.

◆ stopping_condition() [1/2]

protocols::filters::FilterOP protocols::matdes::MatDesGreedyOptMutationMover::stopping_condition ( ) const

inline

References stopping_condition_.

Referenced by apply(), and parse_my_tag().

◆ stopping_condition() [2/2]

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

inline

References stopping_condition_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::matdes::MatDesGreedyOptMutationMover::task_factory ( ) const

References task_factory_.

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

◆ task_factory() [2/2]

void protocols::matdes::MatDesGreedyOptMutationMover::task_factory ( core::pack::task::TaskFactoryOP task_factory )

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

Member Data Documentation

◆ combined_filters_

utility::vector1<protocols::filters::CombinedFilterOP> protocols::matdes::MatDesGreedyOptMutationMover::combined_filters_

private

Referenced by parse_my_tag(), and reset_delta_filter_baselines().

◆ compound_filters_

utility::vector1<protocols::filters::CompoundFilterOP> protocols::matdes::MatDesGreedyOptMutationMover::compound_filters_

private

Referenced by parse_my_tag(), and reset_delta_filter_baselines().

◆ design_shell_

core::Real protocols::matdes::MatDesGreedyOptMutationMover::design_shell_

private

Referenced by parse_my_tag().

◆ diversify_

bool protocols::matdes::MatDesGreedyOptMutationMover::diversify_

private

Referenced by diversify(), filter_pareto_opt_poses(), and filter_seqpos_pareto_opt_ptmuts().

◆ dump_pdb_

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb_

private

Referenced by dump_pdb().

◆ dump_table_

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_table_

private

Referenced by dump_table().

◆ filter_deltas_

utility::vector1< core::Real > protocols::matdes::MatDesGreedyOptMutationMover::filter_deltas_

private

Referenced by add_filter(), filter_deltas(), filter_pareto_opt_poses(), and filter_seqpos_pareto_opt_ptmuts().

◆ filter_thresholds_

utility::vector1< std::pair< std::string, core::Real > > protocols::matdes::MatDesGreedyOptMutationMover::filter_thresholds_

private

Referenced by filter_thresholds().

◆ filters_

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

private

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

◆ force_natro_

bool protocols::matdes::MatDesGreedyOptMutationMover::force_natro_

private

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

◆ force_natro_for_stored_task_names_

utility::vector1< std::string > protocols::matdes::MatDesGreedyOptMutationMover::force_natro_for_stored_task_names_

private

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

◆ incl_nonopt_

bool protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt_

private

Referenced by filter_seqpos_pareto_opt_ptmuts(), and incl_nonopt().

◆ keep_trying_

bool protocols::matdes::MatDesGreedyOptMutationMover::keep_trying_

private

Referenced by keep_trying().

◆ nstruct_iter_

core::Size protocols::matdes::MatDesGreedyOptMutationMover::nstruct_iter_

private

Referenced by apply().

◆ parallel_

bool protocols::matdes::MatDesGreedyOptMutationMover::parallel_

private

Referenced by parallel().

◆ pfront_poses_

utility::vector1< core::pose::Pose > protocols::matdes::MatDesGreedyOptMutationMover::pfront_poses_

private

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

◆ pfront_poses_filter_ranks_

utility::vector1< utility::vector1< core::Size > > protocols::matdes::MatDesGreedyOptMutationMover::pfront_poses_filter_ranks_

private

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

◆ pfront_poses_filter_vals_

utility::vector1< utility::vector1< core::Real > > protocols::matdes::MatDesGreedyOptMutationMover::pfront_poses_filter_vals_

private

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

◆ ref_pose_

core::pose::Pose protocols::matdes::MatDesGreedyOptMutationMover::ref_pose_

private

Referenced by apply(), and clear_cached_data().

◆ reference_pose_

core::pose::PoseOP protocols::matdes::MatDesGreedyOptMutationMover::reference_pose_

private

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

◆ relax_mover_

protocols::moves::MoverOP protocols::matdes::MatDesGreedyOptMutationMover::relax_mover_

private

Referenced by relax_mover().

◆ repack_shell_

core::Real protocols::matdes::MatDesGreedyOptMutationMover::repack_shell_

private

Referenced by parse_my_tag().

◆ reset_delta_filters_

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

private

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

◆ rtmin_

bool protocols::matdes::MatDesGreedyOptMutationMover::rtmin_

private

Referenced by rtmin().

◆ sample_types_

utility::vector1< std::string > protocols::matdes::MatDesGreedyOptMutationMover::sample_types_

private

Referenced by add_filter(), and sample_types().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::matdes::MatDesGreedyOptMutationMover::scorefxn_

private

Referenced by scorefxn().

◆ seqpos_aa_vals_vec_

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

private

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

◆ set_task_for_filters_

utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > protocols::matdes::MatDesGreedyOptMutationMover::set_task_for_filters_

private

Referenced by parse_my_tag(), and set_task_for_filters().

◆ shuffle_order_

bool protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order_

private

Referenced by shuffle_order().

◆ skip_best_check_

bool protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check_

private

Referenced by skip_best_check().

◆ stop_before_condition_

bool protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition_

private

Referenced by stop_before_condition().

◆ stopping_condition_

protocols::filters::FilterOP protocols::matdes::MatDesGreedyOptMutationMover::stopping_condition_

private

Referenced by stopping_condition().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::matdes::MatDesGreedyOptMutationMover::task_factory_

private

Referenced by task_factory().

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

src/protocols/matdes/MatDesGreedyOptMutationMover.hh
src/protocols/matdes/MatDesGreedyOptMutationMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ Pose

Constructor & Destructor Documentation

◆ MatDesGreedyOptMutationMover() [1/2]

◆ MatDesGreedyOptMutationMover() [2/2]

◆ ~MatDesGreedyOptMutationMover()

Member Function Documentation

◆ add_filter()

◆ apply()

◆ calc_pfront_poses_filter_ranks()

◆ clear_cached_data()

◆ clone()

◆ delta_filters() [1/2]

◆ delta_filters() [2/2]

◆ diversify() [1/2]

◆ diversify() [2/2]

◆ dump_pdb() [1/2]

◆ dump_pdb() [2/2]

◆ dump_scoring_table()

◆ dump_table() [1/2]

◆ dump_table() [2/2]

◆ filter_deltas() [1/2]

◆ filter_deltas() [2/2]

◆ filter_pareto_opt_poses()

◆ filter_seqpos_pareto_opt_ptmuts()

◆ filter_thresholds() [1/2]

◆ filter_thresholds() [2/2]

◆ filters() [1/2]

◆ filters() [2/2]

◆ force_natro() [1/2]

◆ force_natro() [2/2]

◆ force_natro_for_stored_task_names() [1/2]

◆ force_natro_for_stored_task_names() [2/2]

◆ fresh_instance()

◆ get_name()

◆ incl_nonopt() [1/2]

◆ incl_nonopt() [2/2]

◆ keep_trying() [1/2]

◆ keep_trying() [2/2]

◆ mover_name()

◆ parallel() [1/2]

◆ parallel() [2/2]

◆ parse_my_tag()

◆ pose_coords_are_same()

◆ provide_xml_schema()

◆ reference_pose() [1/2]

◆ reference_pose() [2/2]

◆ relax_mover() [1/2]

◆ relax_mover() [2/2]

◆ reset_delta_filter_baselines()

◆ rtmin() [1/2]

◆ rtmin() [2/2]

◆ sample_types() [1/2]

◆ sample_types() [2/2]

◆ scorefxn() [1/2]

◆ scorefxn() [2/2]

◆ set_task_for_filters() [1/2]

◆ set_task_for_filters() [2/2]

◆ shuffle_order() [1/2]

◆ shuffle_order() [2/2]

◆ skip_best_check() [1/2]

◆ skip_best_check() [2/2]

◆ stop_before_condition() [1/2]

◆ stop_before_condition() [2/2]

◆ stopping_condition() [1/2]

◆ stopping_condition() [2/2]

◆ task_factory() [1/2]

◆ task_factory() [2/2]

Member Data Documentation

◆ combined_filters_

◆ compound_filters_

◆ design_shell_

◆ diversify_

◆ dump_pdb_

◆ dump_table_