A mover class for performing kinematic loop closure on a peptide segment . More...

#include <KinematicMover.hh>

Inheritance diagram for protocols::loops::loop_closure::kinematic_closure::KinematicMover:

Collaboration diagram for protocols::loops::loop_closure::kinematic_closure::KinematicMover:

Public Member Functions
	KinematicMover ()

	~KinematicMover ()

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

void	set_vary_bondangles (bool vary)

bool	get_vary_bondangles ()

void	set_sample_nonpivot_torsions (bool sample)

bool	get_sample_nonpivot_torsions ()

Size	start_res () const

Size	middle_res () const

Size	end_res () const

Size	segment_length () const

Size	loop_begin () const

Size	loop_end () const

core::Real	BANGLE_MIN () const

core::Real	BANGLE_SD () const

void	set_sweep_nonpivot_torsions (bool sweep)

void	set_nonpivot_res_to_sweep (utility::vector1< Size > const &resids)

void	set_nonpivot_bb_torsion_id (utility::vector1< Size > const &bbtorids)

void	set_sweep_start_angle (utility::vector1< core::Real > const &angles_in_degrees)

void	set_sweep_step_size (utility::vector1< core::Real > const &angle_steps_in_degrees)

void	set_sweep_nsteps (utility::vector1< Size > const &nsteps)

bool	sweep_incomplete () const

void	set_filters (utility::vector1< protocols::filters::FilterCOP > const &filters_in)

void	add_filter (protocols::filters::FilterCOP filter)

void	clear_filters ()

virtual void	set_rama_check (bool do_rama_check)

virtual bool	get_rama_check ()

virtual void	set_hardsphere_bump_check (bool do_bump_check)

virtual void	set_do_sfxn_eval_every_iteration (bool do_sfxn_eval)

virtual bool	get_hardsphere_bump_check ()

virtual void	set_pivots (Size start_res, Size middle_res, Size end_res)

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

virtual void	set_idealize_loop_first (bool idealize)

virtual bool	get_idealize_loop_first ()

void	set_temperature (core::Real temp_in)

void	set_sfxn (core::scoring::ScoreFunctionCOP sfxn_in)

void	set_loop_begin_and_end (Size loop_begin, Size loop_end)

bool	check_rama (core::Real old_rama_score, core::Real new_rama_score)

bool	last_move_succeeded ()

void	set_perturber (KinematicPerturberOP perturber_in)

core::Real	get_bump_overlap_factor () const

void	set_bump_overlap_factor (core::Real bump_overlap_factor)

void	update_sequence (utility::vector1< core::chemical::AA > const &sequence)
	Taboo Sampling functions. More...

void	insert_sampled_torsion_string_into_taboo_map (std::string const &ts)

bool	is_in_taboo_map (std::string const &ts) const

utility::vector1 < core::chemical::AA >	get_loop_sequence () const

std::string	torsion_features_string (core::pose::Pose const &pose) const
	bin torsion angles as described in http://www.ncbi.nlm.nih.gov/pubmed/19646450 generates a string with the torsion angle bins, using uppercase letters as in the publication above for omega ~ 180, and lowercase letters for omega ~ 0; to be used in loop sampling analysis – same as in the LoopMover implementation... More...

core::Real	frequency_in_taboo_map (core::Size const &pos, char const &torsion_bin) const
	returns the frequency of torsion_bin at position pos in the current taboo map, used for shifting probabilities of sampled torsion bins in later rounds More...

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)

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

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

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...

virtual 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	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
bool	perform_rama_check (core::pose::Pose const &pose, utility::vector1< core::Real > const &t_ang, utility::vector1< Size > const &pivots, Size const start_res, Size const seg_len)

bool	perform_rama_check (core::pose::Pose const &pose, utility::vector1< core::Real > const &t_ang, utility::vector1< Size > const &pivots, Size const start_res, Size const middle_res, Size const end_res)

bool	perform_bump_check (core::pose::Pose const &pose, Size const start_res, Size const end_res)

void	set_defaults ()

Private Attributes
Size	start_res_

Size	middle_res_

Size	end_res_

Size	seg_len_

Size	loop_begin_

Size	loop_end_

KinematicPerturberOP	perturber_

core::Real	idl_C_N_CA_

core::Real	idl_N_CA_C_

core::Real	idl_CA_C_N_

core::Real	idl_C_N_

core::Real	idl_N_CA_

core::Real	idl_CA_C_

core::Real	BANGLE_MEAN_

core::Real	BANGLE_SD_

core::Real	BANGLE_MIN_

core::Real	BANGLE_MAX_

core::Real	OMEGA_MEAN_

core::Real	OMEGA_SCALE_FACTOR_

core::Real	MAX_SAMPLE_ITS_

bool	vary_bond_angles_

bool	sample_nonpivot_torsions_

bool	sweep_nonpivot_torsion_

utility::vector1< core::Size >	nonpivot_res_to_sweep_

utility::vector1< core::Size >	sweep_torsion_ids_

utility::vector1< core::Real >	sweep_nonpivot_torsion_starts_

utility::vector1< core::Real >	sweep_step_sizes_

utility::LexicographicalIterator	sweep_iterator_

bool	idealize_loop_first_

bool	do_rama_check_

bool	do_hardsphere_bump_check_

bool	do_sfxn_eval_every_iteration_

core::scoring::ScoreFunctionCOP	sfxn_

bool	last_move_succeeded_

core::Real	temperature_

core::Real	bump_overlap_factor_

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

std::map< std::string, bool >	taboo_map_

core::Real	taboo_map_max_capacity_

std::map< utility::vector1 < core::chemical::AA > , std::map< std::string, bool > >	taboo_master_map_

utility::vector1 < core::chemical::AA >	sequence_

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

A mover class for performing kinematic loop closure on a peptide segment .

Definition at line 47 of file KinematicMover.hh.

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::KinematicMover::KinematicMover ( )

Definition at line 78 of file KinematicMover.cc.

References perturber_, and set_defaults().

protocols::loops::loop_closure::kinematic_closure::KinematicMover::~KinematicMover ( )

Definition at line 126 of file KinematicMover.cc.

Member Function Documentation

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::add_filter ( protocols::filters::FilterCOP filter)

inline

Definition at line 98 of file KinematicMover.hh.

References filters_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 284 of file KinematicMover.cc.

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::BANGLE_MIN ( ) const

inline

Definition at line 79 of file KinematicMover.hh.

References BANGLE_MIN_.

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::BANGLE_SD ( ) const

inline

Definition at line 82 of file KinematicMover.hh.

References BANGLE_SD_.

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::check_rama	(	core::Real	old_rama_score,
		core::Real	new_rama_score
	)

Definition at line 269 of file KinematicMover.cc.

References protocols::loops::loop_closure::kinematic_closure::RG(), and temperature_.

Referenced by perform_rama_check().

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::clear_filters ( )

inline

Definition at line 101 of file KinematicMover.hh.

References filters_.

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::end_res ( ) const

inline

Definition at line 67 of file KinematicMover.hh.

References end_res_.

Referenced by perform_bump_check(), and set_pivots().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::frequency_in_taboo_map	(	core::Size const &	pos,
		char const &	torsion_bin
	)		const

returns the frequency of torsion_bin at position pos in the current taboo map, used for shifting probabilities of sampled torsion bins in later rounds

Definition at line 906 of file KinematicMover.cc.

References sequence_, taboo_map_, and protocols::loops::loop_closure::kinematic_closure::TR().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_bump_overlap_factor ( ) const

inline

Definition at line 119 of file KinematicMover.hh.

References bump_overlap_factor_.

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_hardsphere_bump_check ( )

virtual

Definition at line 203 of file KinematicMover.cc.

References do_hardsphere_bump_check_.

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_idealize_loop_first ( )

virtual

Definition at line 183 of file KinematicMover.cc.

References idealize_loop_first_.

utility::vector1< core::chemical::AA > protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_loop_sequence ( ) const

Definition at line 881 of file KinematicMover.cc.

References sequence_.

std::string protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 558 of file KinematicMover.cc.

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_rama_check ( )

virtual

Definition at line 193 of file KinematicMover.cc.

References do_rama_check_.

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_sample_nonpivot_torsions ( )

Definition at line 173 of file KinematicMover.cc.

References sample_nonpivot_torsions_.

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_vary_bondangles ( )

Definition at line 156 of file KinematicMover.cc.

References vary_bond_angles_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::insert_sampled_torsion_string_into_taboo_map ( std::string const & ts)

Definition at line 887 of file KinematicMover.cc.

References sequence_, taboo_map_, taboo_map_max_capacity_, and protocols::loops::loop_closure::kinematic_closure::TR().

Referenced by apply().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::is_in_taboo_map ( std::string const & ts) const

Definition at line 898 of file KinematicMover.cc.

References taboo_map_.

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::last_move_succeeded ( )

Definition at line 278 of file KinematicMover.cc.

References last_move_succeeded_.

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::loop_begin ( ) const

inline

Definition at line 73 of file KinematicMover.hh.

References loop_begin_.

Referenced by set_loop_begin_and_end().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::loop_end ( ) const

inline

Definition at line 76 of file KinematicMover.hh.

References loop_end_.

Referenced by set_loop_begin_and_end().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::middle_res ( ) const

inline

Definition at line 64 of file KinematicMover.hh.

References middle_res_.

Referenced by set_pivots().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check	(	core::pose::Pose const &	pose,
		Size const	start_res,
		Size const	end_res
	)

private

Definition at line 748 of file KinematicMover.cc.

References core::conformation::Residue::atom_type(), bump_overlap_factor_, core::pose::Pose::conformation(), end_res(), core::conformation::Residue::is_protein(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::conformation::Residue::nheavyatoms(), core::conformation::Conformation::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by apply().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_rama_check	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > const &	t_ang,
		utility::vector1< Size > const &	pivots,
		Size const	start_res,
		Size const	seg_len
	)

private

Definition at line 606 of file KinematicMover.cc.

References check_rama(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::ScoringManager::get_instance(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::scoring::rama, and core::pose::Pose::residue().

Referenced by apply().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_rama_check	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > const &	t_ang,
		utility::vector1< Size > const &	pivots,
		Size const	start_res,
		Size const	middle_res,
		Size const	end_res
	)

private

Definition at line 642 of file KinematicMover.cc.

References check_rama(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::ScoringManager::get_instance(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::scoring::rama, and core::pose::Pose::residue().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::segment_length ( ) const

inline

Definition at line 70 of file KinematicMover.hh.

References seg_len_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_bump_overlap_factor ( core::Real bump_overlap_factor)

inline

Definition at line 123 of file KinematicMover.hh.

References bump_overlap_factor_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_defaults ( )

private

Definition at line 832 of file KinematicMover.cc.

Referenced by KinematicMover().

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_do_sfxn_eval_every_iteration ( bool do_sfxn_eval)

virtual

Definition at line 208 of file KinematicMover.cc.

References do_sfxn_eval_every_iteration_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_filters ( utility::vector1< protocols::filters::FilterCOP > const & filters_in)

inline

Definition at line 95 of file KinematicMover.hh.

References filters_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_hardsphere_bump_check ( bool do_bump_check)

virtual

Definition at line 198 of file KinematicMover.cc.

References do_hardsphere_bump_check_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_idealize_loop_first ( bool idealize)

virtual

Definition at line 178 of file KinematicMover.cc.

References idealize_loop_first_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_loop_begin_and_end	(	Size	loop_begin,
		Size	loop_end
	)

Definition at line 145 of file KinematicMover.cc.

References loop_begin(), loop_begin_, loop_end(), and loop_end_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_nonpivot_bb_torsion_id ( utility::vector1< Size > const & bbtorids)

Definition at line 232 of file KinematicMover.cc.

References nonpivot_res_to_sweep_, and sweep_torsion_ids_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_nonpivot_res_to_sweep ( utility::vector1< Size > const & resids)

This must be set before the other properties (torsion angles, starting angles, step sizes, nsteps) are set.

Definition at line 227 of file KinematicMover.cc.

References nonpivot_res_to_sweep_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_perturber ( KinematicPerturberOP perturber_in)

Definition at line 162 of file KinematicMover.cc.

References perturber_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_pivots	(	Size	start_res,
		Size	middle_res,
		Size	end_res
	)

virtual

Definition at line 128 of file KinematicMover.cc.

References end_res(), end_res_, middle_res(), middle_res_, seg_len_, start_res(), and start_res_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_rama_check ( bool do_rama_check)

virtual

Definition at line 188 of file KinematicMover.cc.

References do_rama_check_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sample_nonpivot_torsions ( bool sample)

Definition at line 168 of file KinematicMover.cc.

References sample_nonpivot_torsions_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sfxn ( core::scoring::ScoreFunctionCOP sfxn_in)

Definition at line 213 of file KinematicMover.cc.

References sfxn_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sweep_nonpivot_torsions ( bool sweep)

Definition at line 220 of file KinematicMover.cc.

References sweep_nonpivot_torsion_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sweep_nsteps ( utility::vector1< Size > const & nsteps)

Initializes the LexicographicalIterator

Definition at line 251 of file KinematicMover.cc.

References nonpivot_res_to_sweep_, and sweep_iterator_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sweep_start_angle ( utility::vector1< core::Real > const & angles_in_degrees)

Definition at line 238 of file KinematicMover.cc.

References nonpivot_res_to_sweep_, and sweep_nonpivot_torsion_starts_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sweep_step_size ( utility::vector1< core::Real > const & angle_steps_in_degrees)

Definition at line 244 of file KinematicMover.cc.

References nonpivot_res_to_sweep_, and sweep_step_sizes_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_temperature ( core::Real temp_in)

Definition at line 264 of file KinematicMover.cc.

References temperature_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_vary_bondangles ( bool vary)

Definition at line 151 of file KinematicMover.cc.

References vary_bond_angles_.

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::start_res ( ) const

inline

Definition at line 61 of file KinematicMover.hh.

References start_res_.

Referenced by set_pivots().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_incomplete ( ) const

returns true as long as the Lexicographical iterator has not covered all angles – useful in a while-loop.

Definition at line 257 of file KinematicMover.cc.

References sweep_iterator_.

std::string protocols::loops::loop_closure::kinematic_closure::KinematicMover::torsion_features_string ( core::pose::Pose const & pose) const

bin torsion angles as described in http://www.ncbi.nlm.nih.gov/pubmed/19646450 generates a string with the torsion angle bins, using uppercase letters as in the publication above for omega ~ 180, and lowercase letters for omega ~ 0; to be used in loop sampling analysis – same as in the LoopMover implementation...

Author: Amelie Stein

Date: April 26, 2012

Definition at line 927 of file KinematicMover.cc.

References core::conformation::get_torsion_bin(), loop_begin_, loop_end_, core::pose::Pose::omega(), core::pose::Pose::phi(), and core::pose::Pose::psi().

Referenced by apply().

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::update_sequence ( utility::vector1< core::chemical::AA > const & sequence)

Taboo Sampling functions.

Author: Amelie Stein

Date: Thu May 17 13:23:52 PDT 2012

Definition at line 844 of file KinematicMover.cc.

References perturber_, sequence_, taboo_map_, and taboo_master_map_.

Member Data Documentation

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::BANGLE_MAX_

private

Definition at line 163 of file KinematicMover.hh.

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::BANGLE_MEAN_

private

Definition at line 160 of file KinematicMover.hh.

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::BANGLE_MIN_

private

Definition at line 162 of file KinematicMover.hh.

Referenced by BANGLE_MIN().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::BANGLE_SD_

private

Definition at line 161 of file KinematicMover.hh.

Referenced by BANGLE_SD().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::bump_overlap_factor_

private

Definition at line 188 of file KinematicMover.hh.

Referenced by get_bump_overlap_factor(), perform_bump_check(), and set_bump_overlap_factor().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::do_hardsphere_bump_check_

private

Definition at line 183 of file KinematicMover.hh.

Referenced by apply(), get_hardsphere_bump_check(), and set_hardsphere_bump_check().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::do_rama_check_

private

Definition at line 181 of file KinematicMover.hh.

Referenced by get_rama_check(), and set_rama_check().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::do_sfxn_eval_every_iteration_

private

Definition at line 184 of file KinematicMover.hh.

Referenced by apply(), and set_do_sfxn_eval_every_iteration().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::end_res_

private

Definition at line 142 of file KinematicMover.hh.

Referenced by apply(), end_res(), and set_pivots().

utility::vector1< protocols::filters::FilterCOP > protocols::loops::loop_closure::kinematic_closure::KinematicMover::filters_

private

Definition at line 191 of file KinematicMover.hh.

Referenced by add_filter(), apply(), clear_filters(), and set_filters().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::idealize_loop_first_

private

Definition at line 180 of file KinematicMover.hh.

Referenced by apply(), get_idealize_loop_first(), and set_idealize_loop_first().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::idl_C_N_

private

Definition at line 155 of file KinematicMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::idl_C_N_CA_

private

Definition at line 152 of file KinematicMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::idl_CA_C_

private

Definition at line 157 of file KinematicMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::idl_CA_C_N_

private

Definition at line 154 of file KinematicMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::idl_N_CA_

private

Definition at line 156 of file KinematicMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::idl_N_CA_C_

private

Definition at line 153 of file KinematicMover.hh.

Referenced by apply().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::last_move_succeeded_

private

Definition at line 186 of file KinematicMover.hh.

Referenced by apply(), and last_move_succeeded().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::loop_begin_

private

Definition at line 145 of file KinematicMover.hh.

Referenced by loop_begin(), set_loop_begin_and_end(), and torsion_features_string().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::loop_end_

private

Definition at line 146 of file KinematicMover.hh.

Referenced by loop_end(), set_loop_begin_and_end(), and torsion_features_string().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::MAX_SAMPLE_ITS_

private

Definition at line 169 of file KinematicMover.hh.

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::middle_res_

private

Definition at line 142 of file KinematicMover.hh.

Referenced by apply(), middle_res(), and set_pivots().

utility::vector1< core::Size > protocols::loops::loop_closure::kinematic_closure::KinematicMover::nonpivot_res_to_sweep_

private

Definition at line 174 of file KinematicMover.hh.

Referenced by set_nonpivot_bb_torsion_id(), set_nonpivot_res_to_sweep(), set_sweep_nsteps(), set_sweep_start_angle(), and set_sweep_step_size().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::OMEGA_MEAN_

private

Definition at line 166 of file KinematicMover.hh.

Referenced by apply().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::OMEGA_SCALE_FACTOR_

private

Definition at line 167 of file KinematicMover.hh.

KinematicPerturberOP protocols::loops::loop_closure::kinematic_closure::KinematicMover::perturber_

private

Definition at line 149 of file KinematicMover.hh.

Referenced by apply(), KinematicMover(), set_perturber(), and update_sequence().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::sample_nonpivot_torsions_

private

Definition at line 171 of file KinematicMover.hh.

Referenced by get_sample_nonpivot_torsions(), and set_sample_nonpivot_torsions().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::seg_len_

private

Definition at line 143 of file KinematicMover.hh.

Referenced by segment_length(), and set_pivots().

utility::vector1< core::chemical::AA > protocols::loops::loop_closure::kinematic_closure::KinematicMover::sequence_

private

Definition at line 197 of file KinematicMover.hh.

Referenced by frequency_in_taboo_map(), get_loop_sequence(), insert_sampled_torsion_string_into_taboo_map(), and update_sequence().

core::scoring::ScoreFunctionCOP protocols::loops::loop_closure::kinematic_closure::KinematicMover::sfxn_

private

Definition at line 185 of file KinematicMover.hh.

Referenced by set_sfxn().

Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::start_res_

private

Definition at line 142 of file KinematicMover.hh.

Referenced by apply(), set_pivots(), and start_res().

utility::LexicographicalIterator protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_iterator_

private

Definition at line 178 of file KinematicMover.hh.

Referenced by set_sweep_nsteps(), and sweep_incomplete().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_nonpivot_torsion_

private

Definition at line 173 of file KinematicMover.hh.

Referenced by set_sweep_nonpivot_torsions().

utility::vector1< core::Real > protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_nonpivot_torsion_starts_

private

Definition at line 176 of file KinematicMover.hh.

Referenced by set_sweep_start_angle().

utility::vector1< core::Real > protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_step_sizes_

private

Definition at line 177 of file KinematicMover.hh.

Referenced by set_sweep_step_size().

utility::vector1< core::Size > protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_torsion_ids_

private

Definition at line 175 of file KinematicMover.hh.

Referenced by set_nonpivot_bb_torsion_id().

std::map< std::string, bool > protocols::loops::loop_closure::kinematic_closure::KinematicMover::taboo_map_

private

Definition at line 194 of file KinematicMover.hh.

Referenced by frequency_in_taboo_map(), insert_sampled_torsion_string_into_taboo_map(), is_in_taboo_map(), and update_sequence().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::taboo_map_max_capacity_

private

Definition at line 195 of file KinematicMover.hh.

Referenced by insert_sampled_torsion_string_into_taboo_map().

std::map< utility::vector1< core::chemical::AA >, std::map< std::string, bool > > protocols::loops::loop_closure::kinematic_closure::KinematicMover::taboo_master_map_

private

Definition at line 196 of file KinematicMover.hh.

Referenced by update_sequence().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::temperature_

private

Definition at line 187 of file KinematicMover.hh.

Referenced by check_rama(), and set_temperature().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::vary_bond_angles_

private

Definition at line 170 of file KinematicMover.hh.

Referenced by get_vary_bondangles(), and set_vary_bondangles().

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