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Rosetta
2021.16
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Rosetta
2021.16
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Make a kinematic closure move that obeys detailed balance. More...
#include <BalancedKicMover.hh>
Public Member Functions | |
| BalancedKicMover () | |
| Default constructor. More... | |
| ~BalancedKicMover () override | |
| Default destructor. More... | |
| void | apply (Pose &pose) override |
| Sample the pose in the regions specified by get_loops(). More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | set_loop (Loop const &loop) |
| Set the loop to be sampled on the next call to apply(). More... | |
| void | add_perturber (perturbers::PerturberOP perturber) |
| Specify how the non-pivot torsions should be sampled. More... | |
| void | set_pivot_picker (pivot_pickers::PivotPickerOP picker) |
| Specify how the pivot residues should be chosen. More... | |
| bool | preserve_detailed_balance () const override |
| Return true, because this mover always obeys detailed balance. More... | |
| void | set_preserve_detailed_balance (bool) override |
| This mover always obeys detailed balance, so this is a no-op. More... | |
| Real | last_proposal_density_ratio () override |
| utility::vector1 < core::id::TorsionID_Range > | torsion_id_ranges (Pose &pose) override |
| Indicate that each torsion in the loop may take on any value. More... | |
 Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover | |
| ThermodynamicMover () | |
| Default constructor. More... | |
| ~ThermodynamicMover () override | |
| Default destructor. More... | |
| virtual void | initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) |
| Callback executed before any Monte Carlo trials are attempted. More... | |
| virtual void | observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) |
| Callback executed after the Metropolis criterion is evaluated. More... | |
| virtual void | finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) |
| Callback executed after all Monte Carlo trials are completed. More... | |
| virtual bool | is_multi_trial () |
| Return true if the move performs multiple trials on each apply. More... | |
| virtual core::Real | last_inner_score_delta_over_temperature () |
| If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More... | |
| virtual protocols::canonical_sampling::MetropolisHastingsMoverAP | metropolis_hastings_mover () |
| If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More... | |
| virtual void | set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover) |
| If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More... | |
| virtual utility::vector1 < core::id::DOF_ID_Range > | dof_id_ranges (core::pose::Pose &pose) |
| Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. More... | |
| 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 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 ClosureSolutionCOP | pick_solution (SolutionList const &unperturbed_solutions, SolutionList const &perturbed_solutions) |
| Pick a solution in a way that cancels out the geometrical bias of the kinematic closure algorithm. More... | |
| static bool | is_solution_trivial (ClosureProblemCOP problem, ClosureSolutionCOP solution, SolutionList const &unperturbed_solutions, SolutionList const &perturbed_solutions) |
| Return true if the given solution is the same as the input pose. This allows for a more accurate reporting of Monte Carlo statistics. More... | |
| 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... | |
Private Attributes | |
| bool | is_fold_tree_stale_ |
| protocols::loops::Loop | loop_ |
| perturbers::PerturberSetOP | perturbers_ |
| pivot_pickers::PivotPickerOP | pivot_picker_ |
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 |
| 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... | |
Make a kinematic closure move that obeys detailed balance.
This class is very conceptually similar to KicMover, so check out its documentation for a general overview of the kinematic closure algorithm. Here I will just highlight some details associated with making a balanced version of the move. Detailed balance is a useful property, because it allows a Monte Carlo simulation to recapitulate ensembles with correct equilibrium populations (so long as sampling is good, of course). There are a two reasons why the standard KicMover algorithm does not obey detailed balance. The first is that the geometry of the closure move itself introduces some inherent bias which has to be explicitly canceled out. The second is that care needs to be taken to perturb the non-pivot torsions in a way that also obeys detailed balance, as well.
The add_perturber() method works much like it does in KicMover. The only conceptual difference is that when the added perturbers are used internally within apply(), perturbers::Perturber::perturb_with_balance() is called instead of perturbers::Perturber::perturb(). This makes it easy to make variants of the perturber algorithms which obey detailed balance. The set_pivot_picker() method is no different from the KicMover version.
| protocols::kinematic_closure::BalancedKicMover::BalancedKicMover | ( | ) |
Default constructor.
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overridedefault |
Default destructor.
| void protocols::kinematic_closure::BalancedKicMover::add_perturber | ( | perturbers::PerturberOP | perturber | ) |
Specify how the non-pivot torsions should be sampled.
The KicMover starts off with a default set of perturbers. Then first time this method is called, all of the default perturbers are cleared and only the specified perturber is kept. Subsequent calls to this method simply add the specified perturbers. Nothing you add manually gets erased.
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overridevirtual |
Sample the pose in the regions specified by get_loops().
The parent class apply() method automatically sets up a fold tree (if necessary) and keeps track of whether or not the move succeeded. Child classes should reimplement do_apply() instead of this method.
Implements protocols::moves::Mover.
References protocols::loops::set_single_loop_fold_tree().
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inlineoverridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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static |
Return true if the given solution is the same as the input pose. This allows for a more accurate reporting of Monte Carlo statistics.
In order to obey detailed balance, the set of unperturbed solutions must contain one solution that is identical to the input pose. When this solution is picked and applied, the resulting move will pass the Metropolis criterion and lead to an artificially inflated acceptance rate. This method provides a way to report what really happened in the move, so that an accurate acceptance rate can be conveyed. Note that this is a static method, so it can be used outside the context of this class. The input pose conformation is inferred from the given problem.
References core::kinematics::distance().
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inlineoverridevirtual |
Right now the proposal probabilities are balanced internally, so this ratio will always be unity. This could change eventually, though.
Reimplemented from protocols::canonical_sampling::ThermodynamicMover.
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static |
Pick a solution in a way that cancels out the geometrical bias of the kinematic closure algorithm.
Note that this is a static method, which means that it can be used outside the context of this class. The inputs are two sets of closure solutions. The first set should contain the starting conformation, and the second should contain novel conformations. The first set can be generated by running the KIC algorithm without perturbing the non-pivot torsions. For each solution in these two sets, a jacobian will have to be calculated. The solution that is returned will be free of bias. See apply() for an example of how this method is used.
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inlineoverridevirtual |
Return true, because this mover always obeys detailed balance.
Implements protocols::canonical_sampling::ThermodynamicMover.
| void protocols::kinematic_closure::BalancedKicMover::set_loop | ( | Loop const & | loop | ) |
Set the loop to be sampled on the next call to apply().
| void protocols::kinematic_closure::BalancedKicMover::set_pivot_picker | ( | pivot_pickers::PivotPickerOP | picker | ) |
Specify how the pivot residues should be chosen.
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inlineoverridevirtual |
This mover always obeys detailed balance, so this is a no-op.
Implements protocols::canonical_sampling::ThermodynamicMover.
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overridevirtual |
Indicate that each torsion in the loop may take on any value.
Implements protocols::canonical_sampling::ThermodynamicMover.
References core::id::BB, and core::scoring::omega.
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1.8.7