protocols::matdes::MatDesGreedyOptMutationMover Class Reference

#include <MatDesGreedyOptMutationMover.hh>

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 protocols::filters::Filters_map	Filters_map
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(NULL))
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)
protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::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)
void	reset_delta_filter_baselines (Pose &pose)
virtual	~MatDesGreedyOptMutationMover ()
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)
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
void	set_type (std::string const &setting)
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
	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...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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
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...

Member Typedef Documentation

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

Constructor & Destructor Documentation

protocols::matdes::MatDesGreedyOptMutationMover::MatDesGreedyOptMutationMover

(

)

default ctor

Referenced by clone().

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( NULL )
	)

References diversify(), diversify_, dump_pdb(), dump_pdb_, dump_table(), dump_table_, filter_thresholds(), filter_thresholds_, filters(), filters_, force_natro(), force_natro_, incl_nonopt(), incl_nonopt_, keep_trying(), keep_trying_, nstruct_iter_, parallel(), parallel_, relax_mover(), relax_mover_, rtmin(), rtmin_, sample_types(), sample_types_, scorefxn(), scorefxn_, set_task_for_filters(), set_task_for_filters_, shuffle_order(), shuffle_order_, skip_best_check(), skip_best_check_, stop_before_condition(), stop_before_condition_, stopping_condition(), stopping_condition_, task_factory(), and task_factory_.

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

virtual

Member Function Documentation

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().

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

virtual

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(), numeric::random::random_permutation(), ref_pose_, reference_pose_, relax_mover(), reset_delta_filter_baselines(), reset_delta_filters_, residue, core::pose::Pose::residue(), protocols::matdes::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(), target_aa, and task_factory().

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().

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(), filter_deltas(), filter_thresholds(), filters(), relax_mover(), sample_types(), scorefxn(), set_task_for_filters(), and task_factory().

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

virtual

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.

References MatDesGreedyOptMutationMover().

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

(

)

const

References reset_delta_filters_.

void protocols::matdes::MatDesGreedyOptMutationMover::delta_filters

(

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

d

)

References reset_delta_filters_.

bool protocols::matdes::MatDesGreedyOptMutationMover::diversify

(

)

const

References diversify_.

Referenced by MatDesGreedyOptMutationMover(), and parse_my_tag().

void protocols::matdes::MatDesGreedyOptMutationMover::diversify

(

bool const

b

)

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

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb

(

)

const

References dump_pdb_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb

(

bool const

dump_pdb

)

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

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

References core::pose::Pose::aa(), utility::io::ozstream::close(), core::pose::Pose::pdb_info(), and seqpos_aa_vals_vec_.

Referenced by apply().

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_table

(

)

const

References dump_table_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::dump_table

(

bool const

dump_table

)

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

vector1< core::Real > protocols::matdes::MatDesGreedyOptMutationMover::filter_deltas

(

)

const

References filter_deltas_.

Referenced by filter_deltas().

void protocols::matdes::MatDesGreedyOptMutationMover::filter_deltas

(

utility::vector1< core::Real > const

filter_deltas

)

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

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().

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().

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

(

)

const

References filter_thresholds_.

Referenced by apply(), filter_thresholds(), MatDesGreedyOptMutationMover(), and parse_my_tag().

void protocols::matdes::MatDesGreedyOptMutationMover::filter_thresholds

(

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

filter_thresholds

)

References clear_cached_data(), filter_thresholds(), and filter_thresholds_.

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

(

)

const

References filters_.

Referenced by apply(), filters(), MatDesGreedyOptMutationMover(), and set_task_for_filters().

void protocols::matdes::MatDesGreedyOptMutationMover::filters

(

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

filters

)

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

bool protocols::matdes::MatDesGreedyOptMutationMover::force_natro

(

)

const

References force_natro_.

Referenced by MatDesGreedyOptMutationMover().

void protocols::matdes::MatDesGreedyOptMutationMover::force_natro

(

bool const

f

)

References force_natro_.

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

(

)

const

References force_natro_for_stored_task_names_.

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_.

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

inlinevirtual

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.

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

virtual

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

Implements protocols::moves::Mover.

References protocols::matdes::MatDesGreedyOptMutationMoverCreator::mover_name().

bool protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt

(

)

const

References incl_nonopt_.

Referenced by MatDesGreedyOptMutationMover(), and parse_my_tag().

void protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt

(

bool const

b

)

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

bool protocols::matdes::MatDesGreedyOptMutationMover::keep_trying

(

)

const

References keep_trying_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::keep_trying

(

bool const

k

)

References keep_trying_.

bool protocols::matdes::MatDesGreedyOptMutationMover::parallel

(

)

const

References parallel_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::parallel

(

bool const

parallel

)

References parallel(), and parallel_.

void protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::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_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(), basic::options::OptionKeys::in::file::native, basic::options::option, parallel(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), core::import_pose::pose_from_pdb(), reference_pose_, relax_mover(), repack_shell_, reset_delta_filters_, rtmin(), runtime_assert, protocols::rosetta_scripts::saved_reference_pose(), scorefxn(), set_task_for_filters_, shuffle_order(), skip_best_check(), stop_before_condition(), stopping_condition(), utility::string_split(), task_factory(), user, and utility_exit_with_message.

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

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

Referenced by apply().

pose::PoseOP protocols::matdes::MatDesGreedyOptMutationMover::reference_pose

(

)

const

References reference_pose_.

Referenced by reference_pose().

void protocols::matdes::MatDesGreedyOptMutationMover::reference_pose

(

core::pose::PoseOP const

reference_pose

)

References reference_pose(), and reference_pose_.

protocols::moves::MoverOP protocols::matdes::MatDesGreedyOptMutationMover::relax_mover

(

)

const

References relax_mover_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::relax_mover

(

protocols::moves::MoverOP

relax_mover

)

References clear_cached_data(), and relax_mover_.

void protocols::matdes::MatDesGreedyOptMutationMover::reset_delta_filter_baselines

(

Pose &

pose

)

References combined_filters_, compound_filters_, and reset_delta_filters_.

Referenced by apply().

bool protocols::matdes::MatDesGreedyOptMutationMover::rtmin

(

)

const

References rtmin_.

Referenced by MatDesGreedyOptMutationMover(), and parse_my_tag().

void protocols::matdes::MatDesGreedyOptMutationMover::rtmin

(

bool const

b

)

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

vector1< std::string > protocols::matdes::MatDesGreedyOptMutationMover::sample_types

(

)

const

References sample_types_.

Referenced by apply(), MatDesGreedyOptMutationMover(), and sample_types().

void protocols::matdes::MatDesGreedyOptMutationMover::sample_types

(

utility::vector1< std::string > const

sample_types

)

References clear_cached_data(), sample_types(), and sample_types_.

core::scoring::ScoreFunctionOP protocols::matdes::MatDesGreedyOptMutationMover::scorefxn

(

)

const

References scorefxn_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

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

vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > protocols::matdes::MatDesGreedyOptMutationMover::set_task_for_filters

(

)

const

References set_task_for_filters_.

Referenced by apply(), and MatDesGreedyOptMutationMover().

void protocols::matdes::MatDesGreedyOptMutationMover::set_task_for_filters

(

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

set_task_for_filters

)

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

bool protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order

(

)

const

References shuffle_order_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order

(

bool const

b

)

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

bool protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check

(

)

const

References skip_best_check_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check

(

bool const

skip_best_check

)

References skip_best_check(), and skip_best_check_.

bool protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition

(

)

const

References stop_before_condition_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition

(

bool const

stop_before_condition

)

References stop_before_condition(), and stop_before_condition_.

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

inline

References stopping_condition_.

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

inline

References stopping_condition_.

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

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

(

)

const

References task_factory_.

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

void protocols::matdes::MatDesGreedyOptMutationMover::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

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

Member Data Documentation

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

private

Referenced by parse_my_tag(), and reset_delta_filter_baselines().

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

private

Referenced by parse_my_tag(), and reset_delta_filter_baselines().

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

private

Referenced by parse_my_tag().

bool protocols::matdes::MatDesGreedyOptMutationMover::diversify_

private

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

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb_

private

Referenced by dump_pdb(), and MatDesGreedyOptMutationMover().

bool protocols::matdes::MatDesGreedyOptMutationMover::dump_table_

private

Referenced by dump_table(), and MatDesGreedyOptMutationMover().

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().

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

private

Referenced by filter_thresholds(), and MatDesGreedyOptMutationMover().

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

private

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

bool protocols::matdes::MatDesGreedyOptMutationMover::force_natro_

private

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

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().

bool protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt_

private

Referenced by filter_seqpos_pareto_opt_ptmuts(), incl_nonopt(), and MatDesGreedyOptMutationMover().

bool protocols::matdes::MatDesGreedyOptMutationMover::keep_trying_

private

Referenced by keep_trying(), and MatDesGreedyOptMutationMover().

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

private

Referenced by apply(), and MatDesGreedyOptMutationMover().

bool protocols::matdes::MatDesGreedyOptMutationMover::parallel_

private

Referenced by MatDesGreedyOptMutationMover(), and parallel().

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

private

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

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().

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().

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

private

Referenced by apply(), and clear_cached_data().

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

private

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

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

private

Referenced by MatDesGreedyOptMutationMover(), and relax_mover().

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

private

Referenced by parse_my_tag().

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().

bool protocols::matdes::MatDesGreedyOptMutationMover::rtmin_

private

Referenced by MatDesGreedyOptMutationMover(), and rtmin().

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

private

Referenced by add_filter(), MatDesGreedyOptMutationMover(), and sample_types().

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

private

Referenced by MatDesGreedyOptMutationMover(), and scorefxn().

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().

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

private

Referenced by MatDesGreedyOptMutationMover(), parse_my_tag(), and set_task_for_filters().

bool protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order_

private

Referenced by MatDesGreedyOptMutationMover(), and shuffle_order().

bool protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check_

private

Referenced by MatDesGreedyOptMutationMover(), and skip_best_check().

bool protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition_

private

Referenced by MatDesGreedyOptMutationMover(), and stop_before_condition().

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

private

Referenced by MatDesGreedyOptMutationMover(), and stopping_condition().

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

private

Referenced by MatDesGreedyOptMutationMover(), and task_factory().

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

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