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protocols::loops::loop_closure::kinematic_closure::KinematicMover Class Reference

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:
Inheritance graph
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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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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::Sizenonpivot_res_to_sweep_
 
utility::vector1< core::Sizesweep_torsion_ids_
 
utility::vector1< core::Realsweep_nonpivot_torsion_starts_
 
utility::vector1< core::Realsweep_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 .

Constructor & Destructor Documentation

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

References set_defaults().

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

Member Function Documentation

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

References filters_.

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

Main Method.

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::conformation::Conformation::append_residue_by_bond(), core::id::BB, core::conformation::Residue::clone(), core::pose::Pose::conformation(), count_bb_atoms(), count_bb_atoms_in_residue(), do_hardsphere_bump_check_, do_sfxn_eval_every_iteration_, end_res_, filters_, get_bb_atoms_for_residue(), idealize_loop_first_, core::conformation::idealize_position(), idl_beta_C_N_, idl_beta_C_N_CA_, idl_beta_CA_CM_, idl_beta_CA_CM_C_, idl_beta_CM_C_, idl_beta_CM_C_N_, idl_beta_N_CA_, idl_beta_N_CA_CM_, idl_C_N_, idl_C_N_CA_, idl_CA_C_, idl_CA_C_N_, idl_N_CA_, idl_N_CA_C_, insert_sampled_torsion_string_into_taboo_map(), is_beta_aminoacid(), core::chemical::is_canonical_D_aa(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), last_move_succeeded_, middle_res_, OMEGA_MEAN_, protocols::forge::methods::order(), perform_bump_check(), perform_rama_check(), perturber(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::scoring::rg, core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), core::pose::Pose::set_omega(), core::conformation::Conformation::set_torsion(), start_res_, torsion_features_string(), protocols::loops::loop_closure::kinematic_closure::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

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

References BANGLE_MIN_.

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

References BANGLE_SD_.

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

References filters_.

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

Referenced by apply().

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().

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().

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().

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().

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

References bump_overlap_factor_.

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().

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().

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

References idealize_loop_first_.

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

References sequence_.

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.

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

References do_rama_check_.

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

References vary_bond_angles_.

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

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

References taboo_map_.

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

References last_move_succeeded_.

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

References loop_begin_.

Referenced by set_loop_begin_and_end().

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

References loop_end_.

Referenced by set_loop_begin_and_end().

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

References middle_res_.

Referenced by set_pivots().

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
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().

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

References seg_len_.

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

References bump_overlap_factor_.

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

Referenced by KinematicMover().

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_do_sfxn_eval_every_iteration ( bool  do_sfxn_eval)
virtual
void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_filters ( utility::vector1< protocols::filters::FilterCOP > const &  filters_in)
inline

References filters_.

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

References idealize_loop_first_.

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_loop_begin_and_end ( core::Size  loop_begin,
core::Size  loop_end 
)
void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_nonpivot_bb_torsion_id ( utility::vector1< core::Size > const &  bbtorids)
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().

void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_perturber ( KinematicPerturberOP  perturber_in)
void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_pivots ( core::Size  start_res,
core::Size  middle_res,
core::Size  end_res 
)
virtual
void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_rama_check ( bool  do_rama_check)
virtual

References do_rama_check_.

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

References sfxn_.

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

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

References temperature_.

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

References vary_bond_angles_.

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

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.

References sweep_iterator_.

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().

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_.

Member Data Documentation

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

Referenced by BANGLE_MIN().

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

Referenced by BANGLE_SD().

core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::bump_overlap_factor_
private
bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::do_hardsphere_bump_check_
private
bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::do_rama_check_
private

Referenced by get_rama_check(), and set_rama_check().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::do_sfxn_eval_every_iteration_
private
core::Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::end_res_
private

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

utility::vector1< protocols::filters::FilterCOP > protocols::loops::loop_closure::kinematic_closure::KinematicMover::filters_
private
bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::idealize_loop_first_
private
core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::idl_beta_C_N_
private

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply(), and last_move_succeeded().

core::Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::loop_begin_
private
core::Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::loop_end_
private
core::Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::middle_res_
private

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

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

Referenced by apply().

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

Referenced by perturber(), and set_perturber().

bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::sample_nonpivot_torsions_
private
core::Size protocols::loops::loop_closure::kinematic_closure::KinematicMover::seg_len_
private

Referenced by segment_length(), and set_pivots().

utility::vector1< core::chemical::AA > protocols::loops::loop_closure::kinematic_closure::KinematicMover::sequence_
private
core::scoring::ScoreFunctionCOP protocols::loops::loop_closure::kinematic_closure::KinematicMover::sfxn_
private

Referenced by set_sfxn().

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

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

utility::LexicographicalIterator protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_iterator_
private
bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_nonpivot_torsion_
private
utility::vector1< core::Real > protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_nonpivot_torsion_starts_
private

Referenced by set_sweep_start_angle().

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

Referenced by set_sweep_step_size().

utility::vector1< core::Size > protocols::loops::loop_closure::kinematic_closure::KinematicMover::sweep_torsion_ids_
private
std::map< core::conformation::torsion_bin_string, bool > protocols::loops::loop_closure::kinematic_closure::KinematicMover::taboo_map_
private
core::Real protocols::loops::loop_closure::kinematic_closure::KinematicMover::taboo_map_max_capacity_
private
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().

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

Referenced by check_rama(), and set_temperature().

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

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