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

#include <KicMover.hh>

Public Member Functions
	KicMover ()
	Default constructor. More...

	~KicMover ()
	Default destructor. More...

std::string	get_name () const
	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

Public Member Functions inherited from protocols::loop_modeling::LoopMover
	LoopMover ()
	Default constructor. More...

	~LoopMover ()
	Default destructor. More...

void	apply (Pose &pose)
	Sample the pose in the regions specified by get_loops(). More...

bool	was_successful () const
	Return true if the previous move was successful. More...

Loops	get_loops () const
	Return the loops to be sampled on the next call to apply(). More...

core::scoring::ScoreFunctionCOP	get_score_function () const
	Return the score function to be used on the next call to apply(). More...

core::scoring::ScoreFunctionOP	get_score_function ()
	Return the score function to be used on the next call to apply() (non-const access). More...

void	set_loop (Loop const &loop)
	Set the loop 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_score_function (core::scoring::ScoreFunctionOP sfxn)
	Set the score function to be used on the next call to apply(). 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, most movers will setup a fold tree on their own the first time apply() is called. More...

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...

Protected Member Functions
bool	do_apply (Pose &pose, Loop const &loop)
	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...

void	dont_manage_score_function ()
	Disable all the LoopMover score function related methods. More...

template<class LoopMoverSubclassOP >
LoopMoverSubclassOP	register_nested_loop_mover (LoopMoverSubclassOP mover)
	Indicate that the given loop mover is used within do_apply(). More...

void	deregister_nested_loop_movers ()
	Drop association with any currently registered loop movers. More...

vector1< LoopMoverOP > const &	get_nested_loop_movers () const
	Return a reference to the list of nested loop movers. 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 protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::loop_modeling::LoopMover
static void	setup_fold_tree (Pose &pose, Loops const &loops, FoldTreeRequest request)
	Setup the given pose with a fold tree that is compatible with the given loops and requests. 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...

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.

References protocols::kinematic_closure::perturbers::PerturberSet::add().

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

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
	)

protectedvirtual

Sample a new backbone conformation for the given loop.

Reimplemented from protocols::loop_modeling::LoopMover.

References option, and type.

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

inlinevirtual

Return the name of this mover.

Reimplemented from protocols::loop_modeling::LoopMover.

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.

FoldTreeRequest protocols::kinematic_closure::KicMover::request_fold_tree ( ) const

virtual

Reimplemented from protocols::loop_modeling::LoopMover.

References protocols::loop_modeling::FTR_LOOPS_WITH_CUTS.

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:

src/protocols/kinematic_closure/KicMover.hh
src/protocols/kinematic_closure/KicMover.cc

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation