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Rosetta Protocols
2014.35
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Rosetta Protocols
2014.35
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A mover class for performing kinematic loop closure on a peptide segment . More...
#include <KinematicMover.hh>
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 (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 | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| void | set_type (std::string const &setting) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| void | set_current_tag (std::string const &new_tag) |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| void | type (const std::string &type_in) |
| virtual MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::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 |
| 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
Private 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 () |
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 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. 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... | |
A mover class for performing kinematic loop closure on a peptide segment .
| protocols::loops::loop_closure::kinematic_closure::KinematicMover::KinematicMover | ( | ) |
References kic_bump_overlap_factor, loops, option, options, perturber_, and set_defaults().
| protocols::loops::loop_closure::kinematic_closure::KinematicMover::~KinematicMover | ( | ) |
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References filters_.
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Implements protocols::moves::Mover.
References core::conformation::Residue::aa(), core::conformation::Conformation::append_residue_by_bond(), bridgeObjects(), chainTORS(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), count_bb_atoms(), count_bb_atoms_in_residue(), numeric::conversions::degrees(), do_hardsphere_bump_check_, do_sfxn_eval_every_iteration_, end_res_, filter, filters_, get_bb_atoms_for_residue(), idealize_loop_first_, 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_, printMatrix(), numeric::conversions::radians(), numeric::random::random_permutation(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), numeric::random::RG, protocols::loops::loop_closure::kinematic_closure::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(), numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().
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References BANGLE_MIN_.
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References BANGLE_SD_.
| bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::check_rama | ( | core::Real | old_rama_score, |
| core::Real | new_rama_score | ||
| ) |
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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().
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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().
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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().
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References do_hardsphere_bump_check_.
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References idealize_loop_first_.
| utility::vector1< core::chemical::AA > protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_loop_sequence | ( | ) | const |
References sequence_.
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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References do_rama_check_.
| bool protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_sample_nonpivot_torsions | ( | ) |
References 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 | ) |
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_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_.
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References loop_begin_.
Referenced by set_loop_begin_and_end().
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References loop_end_.
Referenced by set_loop_begin_and_end().
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References middle_res_.
Referenced by set_pivots().
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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::total_residue(), and core::conformation::Residue::xyz().
Referenced by apply().
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Referenced by apply().
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References seg_len_.
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References bump_overlap_factor_.
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Referenced by KinematicMover().
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References do_sfxn_eval_every_iteration_.
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References filters_.
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References do_hardsphere_bump_check_.
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References idealize_loop_first_.
| void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_loop_begin_and_end | ( | Size | loop_begin, |
| Size | loop_end | ||
| ) |
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 | ) |
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.
References nonpivot_res_to_sweep_.
| void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_perturber | ( | KinematicPerturberOP | perturber_in | ) |
References perturber_.
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References end_res(), end_res_, middle_res(), middle_res_, runtime_assert, seg_len_, start_res(), and start_res_.
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References do_rama_check_.
| void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sample_nonpivot_torsions | ( | bool | sample | ) |
References sample_nonpivot_torsions_.
| 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 | ) |
References sweep_nonpivot_torsion_.
| void protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sweep_nsteps | ( | utility::vector1< Size > const & | nsteps | ) |
Initializes the LexicographicalIterator
References nonpivot_res_to_sweep_, utility::LexicographicalIterator::set_dimension_sizes(), and sweep_iterator_.
| 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_.
| 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_.
| 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_.
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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 utility::LexicographicalIterator::at_end(), and 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...
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.
References perturber_, sequence_, taboo_map_, and taboo_master_map_.
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Referenced by BANGLE_MIN().
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Referenced by BANGLE_SD().
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Referenced by get_bump_overlap_factor(), perform_bump_check(), and set_bump_overlap_factor().
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Referenced by apply(), get_hardsphere_bump_check(), and set_hardsphere_bump_check().
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Referenced by get_rama_check(), and set_rama_check().
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Referenced by apply(), and set_do_sfxn_eval_every_iteration().
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Referenced by apply(), end_res(), and set_pivots().
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Referenced by add_filter(), apply(), clear_filters(), and set_filters().
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Referenced by apply(), get_idealize_loop_first(), and set_idealize_loop_first().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply().
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Referenced by apply(), and last_move_succeeded().
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Referenced by loop_begin(), set_loop_begin_and_end(), and torsion_features_string().
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Referenced by loop_end(), set_loop_begin_and_end(), and torsion_features_string().
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Referenced by apply(), middle_res(), and set_pivots().
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Referenced by apply().
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Referenced by apply(), KinematicMover(), set_perturber(), and update_sequence().
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Referenced by get_sample_nonpivot_torsions(), and set_sample_nonpivot_torsions().
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Referenced by segment_length(), and set_pivots().
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Referenced by set_sfxn().
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Referenced by apply(), set_pivots(), and start_res().
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Referenced by set_sweep_nsteps(), and sweep_incomplete().
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Referenced by set_sweep_nonpivot_torsions().
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Referenced by set_sweep_start_angle().
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Referenced by set_sweep_step_size().
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Referenced by set_nonpivot_bb_torsion_id().
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Referenced by insert_sampled_torsion_string_into_taboo_map().
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Referenced by update_sequence().
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Referenced by check_rama(), and set_temperature().
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Referenced by get_vary_bondangles(), and set_vary_bondangles().
1.8.7