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protocols::kinematic_closure::KicMover Class Reference

Find a new backbone conformation for some region of a protein. More...

#include <KicMover.hh>

Inheritance diagram for protocols::kinematic_closure::KicMover:
Inheritance graph
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Public Member Functions

 KicMover ()
 Default constructor. More...
 
 ~KicMover () override
 Default destructor. More...
 
void get_children_names (utility::vector1< std::string > &names, std::string indent="") const override
 Return the name of this mover. More...
 
pivot_pickers::PivotPickerOP get_pivot_picker ()
 Return the PivotPicker being used by this mover. More...
 
solution_pickers::SolutionPickerOP get_solution_picker ()
 Return the SolutionPicker being used by this mover. More...
 
void add_perturber (perturbers::PerturberOP perturber)
 Specify how the non-pivot torsions should be sampled. More...
 
void clear_perturbers ()
 Forget any perturbers that had been previously added. More...
 
void set_pivot_picker (pivot_pickers::PivotPickerOP picker)
 Specify how the pivot residues should be chosen. More...
 
void set_solution_picker (solution_pickers::SolutionPickerOP picker)
 Specify how a solution should be chosen. More...
 
protocols::loop_modeling::FoldTreeRequest request_fold_tree () const override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::loop_modeling::LoopMover
 LoopMover ()
 Default constructor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Configure from a RosettaScripts tag. More...
 
void apply (Pose &pose) override
 Sample the pose in the regions specified by get_loops(). More...
 
string get_name () const override
 Return the name of this mover. More...
 
bool was_successful () const
 Return true if the previous move was successful. More...
 
void was_successful (bool value)
 Set the success status of a loop mover. More...
 
LoopsOP get_loops ()
 Return the loops to be sampled on the next call to apply(). More...
 
LoopsCOP get_loops () const
 Return the loops to be sampled on the next call to apply(). More...
 
Loop const & get_loop (core::Size index) const
 Return the specified loop. More...
 
void set_loops (LoopsOP loops)
 Set the loops to be sampled on the next call to apply(). More...
 
void set_loops (Loops const &loops)
 Set the loops to be sampled on the next call to apply(). More...
 
void set_loop (Loop const &loop)
 Set the loop to be sampled on the next call to apply(). More...
 
template<typename ToolTypeOP >
ToolTypeOP get_tool (std::string key) const
 Request a tool from this mover or any of its parents. More...
 
template<typename ToolTypeOP >
ToolTypeOP get_tool (std::string key, ToolTypeOP fallback) const
 Request a tool from this mover or any of its parents. More...
 
template<typename ToolTypeOP >
ToolTypeOP set_tool (std::string key, ToolTypeOP value)
 Provide a tool for this mover or any of its children to use. More...
 
void trust_fold_tree ()
 Promise that the calling code will setup a fold tree compatible with request_fold_tree(). If this method is not called, this mover will setup a fold tree on its own every time apply() is called. 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
 
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...
 

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::loop_modeling::LoopMover
static void setup_fold_tree (Pose &pose, LoopsCOP loops, FoldTreeRequest request)
 Setup the given pose with a fold tree that is compatible with the given loops and requests. More...
 
static void define_composition_schema (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen, utility::tag::XMLSchemaSimpleSubelementList &subelements)
 
- 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

bool do_apply (Pose &pose, Loop const &loop) override
 Sample a new backbone conformation for the given loop. More...
 
- Protected Member Functions inherited from protocols::loop_modeling::LoopMover
virtual bool do_apply (Pose &pose)
 Perform the loop sampling move. This method can be overwritten in child classes. More...
 
template<typename ChildSubclassOP >
ChildSubclassOP add_child (ChildSubclassOP child)
 Add a child to this mover. More...
 
void remove_child (LoopMoverOP child)
 Remove a child from this mover. More...
 
void clear_children ()
 Remove all children from this mover. More...
 
LoopMoverOPs get_children () const
 Return all of this mover's children. More...
 
core::Size count_children () const
 Return the number of children this mover has. 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

perturbers::PerturberSetOP perturbers_
 
pivot_pickers::PivotPickerOP pivot_picker_
 
solution_pickers::SolutionPickerOP solution_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
 

Detailed Description

Find a new backbone conformation for some region of a protein.

The first step in the kinematic closure algorithm is to pick a loop and three pivot residues. Any residues in the loop that are not pivots are called non-pivots. The non-pivot backbone torsions are used to make new conformations, while the pivot torsions are used to ensure that the backbone stays closed. Use set_loops() to specify loops to sample. Use set_pivot_picker() to specify how the pivots should be chosen. Use add_perturber() to specify how the non-pivots should be sampled. By default, the algorithm will pick pivots randomly within the region being sampled and will sample the non-pivot torsions from a rama distribution.

Given a set of pivot residues and nonpivot torsion angles, the algorithm will find up to 16 possible solutions. The set_solution_picker() method allows you to control which solution, if any, is picked. By default, the first solution found which passes both a rama and a bump check is used.

Note
The default kinematic closure algorithm samples both pivot and nonpivot torsions from a rama distribution. Because this algorithm is often used in situations where the score function also contains a rama term, the rama bias is usually double-counted. This is bad, because it means that backbone torsions are normally sampled too narrowly. There are two proper ways to deal with this, but they both have drawbacks. The first would be to sample from a uniform distribution and to let the score function take care of preferring angles that fit the rama distribution. Unfortunately, this would be much less efficient than the current approach, primarily because the rama check is fast and filters out a lot of bad solutions. The second approach would be to sample from a rama distribution and to remove the rama term from the score function. This would be even more efficient than the current approach, but it would be prone to bugs because other parts of the code wouldn't expect the score function to be changing on every invocation of KIC.

Once the algorithm has been setup using the helper methods described above, apply() can be called to actually sample a new backbone conformation.

Constructor & Destructor Documentation

protocols::kinematic_closure::KicMover::KicMover ( )

Default constructor.

protocols::kinematic_closure::KicMover::~KicMover ( )
overridedefault

Default destructor.

Member Function Documentation

void protocols::kinematic_closure::KicMover::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.

void protocols::kinematic_closure::KicMover::clear_perturbers ( )

Forget any perturbers that had been previously added.

bool protocols::kinematic_closure::KicMover::do_apply ( Pose pose,
Loop const &  loop 
)
overrideprotectedvirtual

Sample a new backbone conformation for the given loop.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::kinematic_closure::KicMover::get_children_names ( utility::vector1< std::string > &  names,
std::string  indent = "" 
) const
overridevirtual

Return the name of this mover.

Reimplemented from protocols::loop_modeling::LoopMover.

std::string protocols::kinematic_closure::KicMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

pivot_pickers::PivotPickerOP protocols::kinematic_closure::KicMover::get_pivot_picker ( )

Return the PivotPicker being used by this mover.

solution_pickers::SolutionPickerOP protocols::kinematic_closure::KicMover::get_solution_picker ( )

Return the SolutionPicker being used by this mover.

std::string protocols::kinematic_closure::KicMover::mover_name ( )
static
void protocols::kinematic_closure::KicMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
FoldTreeRequest protocols::kinematic_closure::KicMover::request_fold_tree ( ) const
overridevirtual
void protocols::kinematic_closure::KicMover::set_pivot_picker ( pivot_pickers::PivotPickerOP  picker)

Specify how the pivot residues should be chosen.

void protocols::kinematic_closure::KicMover::set_solution_picker ( solution_pickers::SolutionPickerOP  picker)

Specify how a solution should be chosen.

Member Data Documentation

perturbers::PerturberSetOP protocols::kinematic_closure::KicMover::perturbers_
private
pivot_pickers::PivotPickerOP protocols::kinematic_closure::KicMover::pivot_picker_
private
solution_pickers::SolutionPickerOP protocols::kinematic_closure::KicMover::solution_picker_
private

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