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

#include <KinematicMover.hh>

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

[legend]

Public Member Functions
	KinematicMover ()

	~KinematicMover () override

std::string	get_name () const override
	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 ()

core::Size	start_res () const

core::Size	middle_res () const

core::Size	end_res () const

core::Size	segment_length () const

core::Size	loop_begin () const

core::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< core::Size > const &resids)

void	set_nonpivot_bb_torsion_id (utility::vector1< core::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< core::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 (core::Size start_res, core::Size middle_res, core::Size end_res)

void	apply (core::pose::Pose &) override
	Main Method. More...

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 (core::Size loop_begin, core::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)

KinematicPerturberOP	perturber ()

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 (core::conformation::torsion_bin_string const &ts)

bool	is_in_taboo_map (core::conformation::torsion_bin_string const &ts) const

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

core::conformation::torsion_bin_string	torsion_features_string (core::pose::Pose const &pose) const
	bin torsion angles as described in http://www.ncbi.nlm.nih.gov/pubmed/19646450 More...

core::Real	frequency_in_taboo_map (core::Size pos, core::conformation::ppo_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...

bool	is_beta_aminoacid (const core::conformation::Residue &res) const
	Function to determine whether an amino acid is a beta amino acid. Added 23 August 2013 by Vikram K. Mulligan. More...

core::Size	count_bb_atoms_in_residue (const core::pose::Pose &pose, const core::Size position) const
	Function to count the number of backbone atoms in a single residue in the segment that will be closed. Added 23 August 2013 by Vikram K. Mulligan. More...

core::Size	count_bb_atoms (const core::pose::Pose &pose, const core::Size start_res, const core::Size end_res) const
	Function to count the number of backbone atoms in the segment that will be closed. This is needed for segments including residues with nonstandard amino acids (e.g. beta-3-amino acids). Added 23 August 2013 by Vikram K. Mulligan. More...

std::string	get_bb_atoms_for_residue (const core::conformation::Residue &res, const core::Size bb_atom_index) const

std::string	get_bumpcheck_atoms_for_residue (const core::conformation::Residue &rsd, const core::Size bumpcheck_atom_index) const

core::Size	get_bumpcheck_atom_count_for_residue (const core::conformation::Residue &rsd) const

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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

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

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

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

void	set_defaults ()

Private Attributes
core::Size	start_res_

core::Size	middle_res_

core::Size	end_res_

core::Size	seg_len_

core::Size	loop_begin_

core::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	idl_beta_C_N_CA_

core::Real	idl_beta_N_CA_CM_

core::Real	idl_beta_CA_CM_C_

core::Real	idl_beta_CM_C_N_

core::Real	idl_beta_C_N_

core::Real	idl_beta_N_CA_

core::Real	idl_beta_CA_CM_

core::Real	idl_beta_CM_C_

core::Real	BANGLE_MEAN_

core::Real	BANGLE_SD_

core::Real	BANGLE_MIN_

core::Real	OMEGA_MEAN_

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< core::conformation::torsion_bin_string, bool >	taboo_map_

core::Real	taboo_map_max_capacity_

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

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

Additional Inherited Members
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

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...

Detailed Description

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

Constructor & Destructor Documentation

◆ KinematicMover()

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

References set_defaults().

◆ ~KinematicMover()

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

overridedefault

Member Function Documentation

◆ add_filter()

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

inline

References filters_.

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ BANGLE_MIN()

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

inline

References BANGLE_MIN_.

◆ BANGLE_SD()

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

inline

References BANGLE_SD_.

◆ check_rama()

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

References protocols::mean_field::max(), protocols::simple_moves::bb_sampler::probability, core::scoring::rg, and temperature_.

◆ clear_filters()

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

inline

References filters_.

◆ count_bb_atoms()

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

Function to count the number of backbone atoms in the segment that will be closed. This is needed for segments including residues with nonstandard amino acids (e.g. beta-3-amino acids). Added 23 August 2013 by Vikram K. Mulligan.

References count_bb_atoms_in_residue(), end_res(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), and start_res().

Referenced by apply().

◆ count_bb_atoms_in_residue()

core::Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::count_bb_atoms_in_residue	(	const core::pose::Pose &	pose,
		const core::Size	position
	)		const

Function to count the number of backbone atoms in a single residue in the segment that will be closed. Added 23 August 2013 by Vikram K. Mulligan.

References is_beta_aminoacid(), and core::pose::Pose::residue().

Referenced by apply(), and count_bb_atoms().

◆ end_res()

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

inline

References end_res_.

Referenced by count_bb_atoms(), perform_bump_check(), and set_pivots().

◆ frequency_in_taboo_map()

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::frequency_in_taboo_map	(	core::Size	pos,
		core::conformation::ppo_torsion_bin	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.

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

◆ get_bb_atoms_for_residue()

std::string protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_bb_atoms_for_residue	(	const core::conformation::Residue &	res,
		const core::Size	bb_atom_index
	)		const

References is_beta_aminoacid().

Referenced by apply().

◆ get_bump_overlap_factor()

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

inline

References bump_overlap_factor_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ get_bumpcheck_atom_count_for_residue()

core::Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_bumpcheck_atom_count_for_residue ( const core::conformation::Residue & rsd ) const

References is_beta_aminoacid().

Referenced by perform_bump_check().

◆ get_bumpcheck_atoms_for_residue()

std::string protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_bumpcheck_atoms_for_residue	(	const core::conformation::Residue &	rsd,
		const core::Size	bumpcheck_atom_index
	)		const

References is_beta_aminoacid().

Referenced by perform_bump_check().

◆ get_hardsphere_bump_check()

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

virtual

References do_hardsphere_bump_check_.

◆ get_idealize_loop_first()

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

virtual

References idealize_loop_first_.

◆ get_loop_sequence()

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

References sequence_.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_rama_check()

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

virtual

References do_rama_check_.

◆ get_sample_nonpivot_torsions()

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

References sample_nonpivot_torsions_.

◆ get_vary_bondangles()

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

References vary_bond_angles_.

◆ insert_sampled_torsion_string_into_taboo_map()

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::insert_sampled_torsion_string_into_taboo_map ( core::conformation::torsion_bin_string const & ts )

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

Referenced by apply().

◆ is_beta_aminoacid()

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::is_beta_aminoacid ( const core::conformation::Residue & res ) const

Function to determine whether an amino acid is a beta amino acid. Added 23 August 2013 by Vikram K. Mulligan.

References core::conformation::Residue::has().

Referenced by apply(), count_bb_atoms_in_residue(), get_bb_atoms_for_residue(), get_bumpcheck_atom_count_for_residue(), and get_bumpcheck_atoms_for_residue().

◆ is_in_taboo_map()

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::is_in_taboo_map ( core::conformation::torsion_bin_string const & ts ) const

References taboo_map_.

◆ last_move_succeeded()

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

References last_move_succeeded_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ loop_begin()

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

inline

References loop_begin_.

Referenced by set_loop_begin_and_end().

◆ loop_end()

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

inline

References loop_end_.

Referenced by set_loop_begin_and_end().

◆ middle_res()

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

inline

References middle_res_.

Referenced by set_pivots().

◆ perform_bump_check()

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

private

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_type(), bump_overlap_factor_, core::pose::Pose::conformation(), end_res(), get_bumpcheck_atom_count_for_residue(), get_bumpcheck_atoms_for_residue(), core::conformation::Residue::has(), 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::size(), start_res(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ perform_rama_check() [1/2]

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< core::Size > const &	pivots,
		core::Size const	start_res,
		core::Size const	middle_res,
		core::Size const	end_res
	)

private

◆ perform_rama_check() [2/2]

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< core::Size > const &	pivots,
		core::Size const	start_res,
		core::Size const	seg_len
	)

private

Referenced by apply().

◆ perturber()

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

References protocols::moves::Mover::get_self_ptr(), and perturber_.

Referenced by apply(), and update_sequence().

◆ segment_length()

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

inline

References seg_len_.

◆ set_bump_overlap_factor()

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

inline

References bump_overlap_factor_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_defaults()

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

private

Referenced by KinematicMover().

◆ set_do_sfxn_eval_every_iteration()

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

virtual

References do_sfxn_eval_every_iteration_.

◆ set_filters()

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

inline

References filters_.

◆ set_hardsphere_bump_check()

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

virtual

References do_hardsphere_bump_check_.

◆ set_idealize_loop_first()

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

virtual

References idealize_loop_first_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_loop_begin_and_end()

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

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

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_nonpivot_bb_torsion_id()

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

References nonpivot_res_to_sweep_, and sweep_torsion_ids_.

◆ set_nonpivot_res_to_sweep()

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

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

References nonpivot_res_to_sweep_, and core::select::resids().

◆ set_perturber()

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

References protocols::moves::Mover::get_self_ptr(), and perturber_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_pivots()

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

virtual

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

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_rama_check()

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

virtual

References do_rama_check_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_sample_nonpivot_torsions()

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

References sample_nonpivot_torsions_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_sfxn()

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

References sfxn_.

◆ set_sweep_nonpivot_torsions()

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

References sweep_nonpivot_torsion_.

◆ set_sweep_nsteps()

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

Initializes the LexicographicalIterator

References nonpivot_res_to_sweep_, and sweep_iterator_.

◆ set_sweep_start_angle()

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

References nonpivot_res_to_sweep_, and sweep_nonpivot_torsion_starts_.

◆ set_sweep_step_size()

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

References nonpivot_res_to_sweep_, and sweep_step_sizes_.

◆ set_temperature()

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

References temperature_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ set_vary_bondangles()

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

References vary_bond_angles_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

◆ start_res()

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

inline

References start_res_.

Referenced by count_bb_atoms(), perform_bump_check(), and set_pivots().

◆ sweep_incomplete()

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.

References sweep_iterator_.

◆ torsion_features_string()

core::conformation::torsion_bin_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

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().

◆ update_sequence()

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

References perturber(), sequence_, taboo_map_, and taboo_master_map_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

Member Data Documentation

◆ BANGLE_MEAN_

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

private

◆ BANGLE_MIN_

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

private

Referenced by BANGLE_MIN().

◆ BANGLE_SD_

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

private

Referenced by BANGLE_SD().

◆ bump_overlap_factor_

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

private

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

◆ do_hardsphere_bump_check_

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

private

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

◆ do_rama_check_

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

private

Referenced by get_rama_check(), and set_rama_check().

◆ do_sfxn_eval_every_iteration_

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

private

Referenced by apply(), and set_do_sfxn_eval_every_iteration().

◆ end_res_

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

private

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

◆ filters_

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

private

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

◆ idealize_loop_first_

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

private

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

◆ idl_beta_C_N_

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

private

Referenced by apply().

◆ idl_beta_C_N_CA_

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

private

Referenced by apply().

◆ idl_beta_CA_CM_

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

private

Referenced by apply().

◆ idl_beta_CA_CM_C_

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

private

Referenced by apply().

◆ idl_beta_CM_C_

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

private

Referenced by apply().

◆ idl_beta_CM_C_N_

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

private

Referenced by apply().

◆ idl_beta_N_CA_

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

private

Referenced by apply().

◆ idl_beta_N_CA_CM_

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

private

Referenced by apply().

◆ idl_C_N_

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

private

Referenced by apply().

◆ idl_C_N_CA_

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

private

Referenced by apply().

◆ idl_CA_C_

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

private

Referenced by apply().

◆ idl_CA_C_N_

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

private

Referenced by apply().

◆ idl_N_CA_

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

private

Referenced by apply().

◆ idl_N_CA_C_

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

private

Referenced by apply().

◆ last_move_succeeded_

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

private

Referenced by apply(), and last_move_succeeded().

◆ loop_begin_

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

private

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

◆ loop_end_

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

private

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

◆ middle_res_

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

private

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

◆ nonpivot_res_to_sweep_

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

private

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

◆ OMEGA_MEAN_

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

private

Referenced by apply().

◆ perturber_

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

private

Referenced by perturber(), and set_perturber().

◆ sample_nonpivot_torsions_

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

private

Referenced by get_sample_nonpivot_torsions(), and set_sample_nonpivot_torsions().

◆ seg_len_

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

private

Referenced by segment_length(), and set_pivots().

◆ sequence_

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

private

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

◆ sfxn_

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

private

Referenced by set_sfxn().

◆ start_res_

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

private

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

◆ sweep_iterator_

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

private

Referenced by set_sweep_nsteps(), and sweep_incomplete().

◆ sweep_nonpivot_torsion_

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

private

Referenced by set_sweep_nonpivot_torsions().

◆ sweep_nonpivot_torsion_starts_

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

private

Referenced by set_sweep_start_angle().

◆ sweep_step_sizes_

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

private

Referenced by set_sweep_step_size().

◆ sweep_torsion_ids_

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

private

Referenced by set_nonpivot_bb_torsion_id().

◆ taboo_map_

std::map< core::conformation::torsion_bin_string, bool > protocols::loops::loop_closure::kinematic_closure::KinematicMover::taboo_map_

private

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

◆ taboo_map_max_capacity_

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

private

Referenced by insert_sampled_torsion_string_into_taboo_map().

◆ taboo_master_map_

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

private

Referenced by update_sequence().

◆ temperature_

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

private

Referenced by check_rama(), and set_temperature().

◆ vary_bond_angles_

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

private

Referenced by get_vary_bondangles(), and set_vary_bondangles().

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

src/protocols/loops/loop_closure/kinematic_closure/KinematicMover.hh
src/protocols/loops/loop_closure/kinematic_closure/KinematicMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ KinematicMover()

◆ ~KinematicMover()

Member Function Documentation

◆ add_filter()

◆ apply()

◆ BANGLE_MIN()

◆ BANGLE_SD()

◆ check_rama()

◆ clear_filters()

◆ count_bb_atoms()

◆ count_bb_atoms_in_residue()

◆ end_res()

◆ frequency_in_taboo_map()

◆ get_bb_atoms_for_residue()

◆ get_bump_overlap_factor()

◆ get_bumpcheck_atom_count_for_residue()

◆ get_bumpcheck_atoms_for_residue()

◆ get_hardsphere_bump_check()

◆ get_idealize_loop_first()

◆ get_loop_sequence()

◆ get_name()

◆ get_rama_check()

◆ get_sample_nonpivot_torsions()

◆ get_vary_bondangles()

◆ insert_sampled_torsion_string_into_taboo_map()

◆ is_beta_aminoacid()

◆ is_in_taboo_map()

◆ last_move_succeeded()

◆ loop_begin()

◆ loop_end()

◆ middle_res()

◆ perform_bump_check()

◆ perform_rama_check() [1/2]

◆ perform_rama_check() [2/2]

◆ perturber()

◆ segment_length()

◆ set_bump_overlap_factor()

◆ set_defaults()

◆ set_do_sfxn_eval_every_iteration()

◆ set_filters()

◆ set_hardsphere_bump_check()

◆ set_idealize_loop_first()

◆ set_loop_begin_and_end()

◆ set_nonpivot_bb_torsion_id()

◆ set_nonpivot_res_to_sweep()

◆ set_perturber()

◆ set_pivots()

◆ set_rama_check()

◆ set_sample_nonpivot_torsions()

◆ set_sfxn()

◆ set_sweep_nonpivot_torsions()

◆ set_sweep_nsteps()

◆ set_sweep_start_angle()

◆ set_sweep_step_size()

◆ set_temperature()

◆ set_vary_bondangles()

◆ start_res()

◆ sweep_incomplete()

◆ torsion_features_string()

◆ update_sequence()

Member Data Documentation

◆ BANGLE_MEAN_

◆ BANGLE_MIN_

◆ BANGLE_SD_

◆ bump_overlap_factor_

◆ do_hardsphere_bump_check_

◆ do_rama_check_

◆ do_sfxn_eval_every_iteration_

◆ end_res_

◆ filters_

◆ idealize_loop_first_

◆ idl_beta_C_N_

◆ idl_beta_C_N_CA_

◆ idl_beta_CA_CM_