#include <LoopMover_KIC.hh>
Public Member Functions | |
| LoopMover_Perturb_KIC () | |
| LoopMover_Perturb_KIC (protocols::loops::LoopsOP loops_in) | |
| LoopMover_Perturb_KIC (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn) | |
| ~LoopMover_Perturb_KIC () override | |
| void | show (std::ostream &output=std::cout) const override |
| Outputs details about the Mover, including current settings. More... | |
| void | set_extended_torsions (core::pose::Pose &pose, Loop const &loop) override |
| Extend a loop. More... | |
| void | set_default_settings () |
| core::Size | get_max_kic_build_attempts () const |
| void | set_max_kic_build_attempts (core::Size max_kic_build_attempts) |
| protocols::moves::MoverOP | clone () const override |
| Clone this object. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 Public Member Functions inherited from protocols::loops::loop_mover::IndependentLoopMover | |
| IndependentLoopMover () | |
| IndependentLoopMover (LoopsOP loops_in) | |
| IndependentLoopMover (utility::vector1< bool > const &selection) | |
| IndependentLoopMover (LoopsFileData const &lfd) | |
| IndependentLoopMover (GuardedLoopsFromFileOP guarded_loops) | |
| ~IndependentLoopMover () override | |
| void | set_defaults () |
| void | apply (core::pose::Pose &pose) override |
| Apply the loop-build protocol to the input pose. More... | |
| void | set_build_attempts_ (int value) |
| Accessors: More... | |
| void | set_grow_attempts_ (int value) |
| void | set_accept_aborted_loops_ (bool value) |
| void | set_strict_loops (bool value) |
| void | set_random_order_ (bool value) |
| void | set_build_all_loops_ (bool value) |
| void | set_loop_combine_rate_ (core::Real value) |
| int | get_build_attempts () const |
| int | get_grow_attempts () const |
| bool | get_accept_aborted_loops () const |
| bool | get_strict_loops () const |
| bool | get_random_order () const |
| bool | get_build_all_loops () const |
| bool | get_loop_combine_rate () const |
| bool | get_all_loops_closed () const |
| LoopResult | get_last_LoopResult () const |
| Public Member Functions inherited from protocols::loops::loop_mover::LoopMover | |
| LoopMover () | |
| LoopMover (protocols::loops::LoopsOP loops_in) | |
| LoopMover (protocols::loops::LoopsFileData const &loops_from_file) | |
| LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops) | |
| LoopMover (LoopMover const &rhs) | |
| copy ctor More... | |
| LoopMover & | operator= (LoopMover const &rhs) |
| assignment operator More... | |
| ~LoopMover () override | |
| void | set_guarded_loops_not_in_charge () |
| Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More... | |
| void | set_scorefxn (const core::scoring::ScoreFunctionOP score_in) |
| const core::scoring::ScoreFunctionOP & | scorefxn () const |
| void | loops (protocols::loops::LoopsOP lptr) |
| Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More... | |
| void | loops (LoopsFileData const &loop_file_data) |
| Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More... | |
| void | loops (protocols::loops::loops_definers::LoopsDefinerOP setting) |
| void | loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops) |
| Set the guarded_loops pointer. More... | |
| protocols::loops::LoopsCOP | loops () const |
| Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More... | |
| protocols::loops::LoopsOP | loops () |
| non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More... | |
| const utility::vector1< core::fragment::FragSetOP > & | frag_libs () const |
| core::conformation::torsion_bin_string | torsion_features_string (core::pose::Pose const &pose) const |
| create a string representing the torsion bins (ABEGX) for the loops defined in the guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there's only one Loop object in the guarded_loops_ object). More... | |
| void | add_fragments (core::fragment::FragSetOP fragset) |
| add a fragment set More... | |
| void | clear_fragments () |
| clear the list of fragment sets More... | |
| MoveMapOP const & | false_movemap () const |
| explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More... | |
| void | false_movemap (MoveMapOP const &mm) |
| explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More... | |
| checkpoint::CheckPointerOP & | get_checkpoints () |
| 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 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 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... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| 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 | |
| loop_mover::LoopResult | model_loop (core::pose::Pose &pose, protocols::loops::Loop const &loop) override |
| basic::Tracer & | tr () const override |
| Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover | |
| core::Size | enforce_false_movemap (MoveMapOP &mm) const |
| import the false_movemap's explicit False settings into the given MoveMap More... | |
| void | set_loops_from_pose_observer_cache (core::pose::Pose const &pose) |
| allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More... | |
| bool | use_loops_from_observer_cache () const |
| void | set_use_loops_from_observer_cache (bool const loops_from_observer_cache) |
| void | resolve_loop_indices (core::pose::Pose const &p) |
| Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. 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... | |
Private Attributes | |
| core::Size | max_seglen_ |
| bool | recover_low_ |
| core::Size | max_kic_build_attempts_ |
| core::Size | remodel_kic_attempts_ |
Additional Inherited Members | |
| Public Types inherited from protocols::loops::loop_mover::LoopMover | |
| typedef core::kinematics::MoveMapOP | MoveMapOP |
| 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 |
Constructor & Destructor Documentation
◆ LoopMover_Perturb_KIC() [1/3]
| protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::LoopMover_Perturb_KIC | ( | ) |
◆ LoopMover_Perturb_KIC() [2/3]
| protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::LoopMover_Perturb_KIC | ( | protocols::loops::LoopsOP | loops_in | ) |
◆ LoopMover_Perturb_KIC() [3/3]
| protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::LoopMover_Perturb_KIC | ( | protocols::loops::LoopsOP | loops_in, |
| core::scoring::ScoreFunctionOP | scorefxn | ||
| ) |
◆ ~LoopMover_Perturb_KIC()
|
overridedefault |
Member Function Documentation
◆ clone()
|
overridevirtual |
Clone this object.
Reimplemented from protocols::moves::Mover.
◆ get_max_kic_build_attempts()
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inline |
References max_kic_build_attempts_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::loops::loop_mover::IndependentLoopMover.
References mover_name().
◆ model_loop()
|
overrideprotectedvirtual |
Uses kinematic_mover to remodel a protein segment. If the 'extended' flag in the loop definition for the segment is set to '1', will idealize all bond lengths, bond angles, and phi, psi, and omega torsions before modeling. This stage is carried out entirely with a centroid representation. Applies to only one loop, given as an argument.
Implements protocols::loops::loop_mover::IndependentLoopMover.
References core::pose::Pose::aa(), protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::moves::MonteCarlo::boltzmann(), core::scoring::cart_bonded, protocols::loops::loop_mover::CriticalFailure, protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, protocols::moves::FAIL_RETRY, protocols::loops::loop_mover::Failure, core::pose::Pose::fold_tree(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::get_bump_overlap_factor(), protocols::moves::Mover::get_native_pose(), core::kinematics::FoldTree::is_cutpoint(), protocols::loops::Loop::is_extended(), core::pose::symmetry::is_symmetric(), protocols::loops::Loop::is_terminal(), protocols::moves::MonteCarlo::last_accepted_pose(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::last_move_succeeded(), protocols::loops::loop_rmsd(), protocols::loops::loops_set_move_map(), protocols::moves::MonteCarlo::lowest_score_pose(), core::pose::symmetry::make_symmetric_movemap(), core::conformation::map_string_to_torsion_bin_string(), protocols::mean_field::max(), max_kic_build_attempts_, max_seglen_, protocols::mean_field::min(), protocols::moves::MS_SUCCESS, protocols::moves::Mover::name(), core::conformation::membrane::out, protocols::moves::MonteCarlo::recover_low(), recover_low_, remodel_kic_attempts_, core::scoring::rg, protocols::loops::loop_mover::LoopMover::scorefxn(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_bump_overlap_factor(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_idealize_loop_first(), protocols::moves::Mover::set_last_move_status(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_loop_begin_and_end(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_perturber(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_pivots(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_rama_check(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_sample_nonpivot_torsions(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_temperature(), protocols::moves::MonteCarlo::set_temperature(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_vary_bondangles(), protocols::moves::MonteCarlo::show_scores(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::loop_mover::Success, core::id::to_string(), protocols::loops::loop_mover::LoopMover::torsion_features_string(), core::scoring::Energies::total_energies(), tr(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::update_sequence(), and core::scoring::EMapVector::weighted_string_of().
◆ mover_name()
|
static |
◆ provide_xml_schema()
|
static |
◆ set_default_settings()
| void protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::set_default_settings | ( | ) |
References max_kic_build_attempts_, max_seglen_, recover_low_, remodel_kic_attempts_, and protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops().
Referenced by LoopMover_Perturb_KIC().
◆ set_extended_torsions()
|
overridevirtual |
Extend a loop.
Set a loop to extended torsion angles.
Reimplemented from protocols::loops::loop_mover::LoopMover.
◆ set_max_kic_build_attempts()
|
inline |
References max_kic_build_attempts_.
◆ show()
|
overridevirtual |
Outputs details about the Mover, including current settings.
Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.
Reimplemented from protocols::moves::Mover.
References max_kic_build_attempts_, max_seglen_, recover_low_, and remodel_kic_attempts_.
Referenced by protocols::loops::loop_mover::perturb::operator<<().
◆ tr()
|
overrideprotectedvirtual |
Implements protocols::loops::loop_mover::LoopMover.
References protocols::loops::loop_mover::perturb::TR().
Referenced by model_loop().
Member Data Documentation
◆ max_kic_build_attempts_
|
private |
Referenced by get_max_kic_build_attempts(), model_loop(), set_default_settings(), set_max_kic_build_attempts(), and show().
◆ max_seglen_
|
private |
Referenced by model_loop(), set_default_settings(), and show().
◆ recover_low_
|
private |
Referenced by model_loop(), set_default_settings(), and show().
◆ remodel_kic_attempts_
|
private |
Referenced by model_loop(), set_default_settings(), and show().
The documentation for this class was generated from the following files:
- src/protocols/loops/loop_mover/perturb/LoopMover_KIC.hh
- src/protocols/loops/loop_mover/perturb/LoopMover_KIC.cc
