Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent. More...

#include <CCDLoopClosureMover.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::CCDLoopClosureMover:

Public Member Functions
	CCDLoopClosureMover ()
	Empty constructor. More...

	CCDLoopClosureMover (CCDLoopClosureMover const &object_to_copy)
	Copy constructor. More...

	CCDLoopClosureMover (protocols::loops::Loop const &loop)
	Constructor with Loop input option. More...

	CCDLoopClosureMover (protocols::loops::Loop const &loop, core::kinematics::MoveMapCOP mm)
	Constructor with Loop and MoveMap input options. More...

	~CCDLoopClosureMover () override

CCDLoopClosureMover &	operator= (CCDLoopClosureMover const &object_to_copy)

void	show (std::ostream &output=std::cout) const override
	Generate a string representation of CCDLoopClosureMover for debugging purposes. More...

protocols::moves::MoverOP	clone () const override
	Return the name of the Mover. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	apply (core::pose::Pose &pose) override
	Apply the corresponding move to <pose>. More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. More...

protocols::loops::Loop	loop () const
	Get the Loop to be closed. More...

void	loop (protocols::loops::Loop new_loop)
	Set the Loop to be closed. More...

core::kinematics::MoveMap	movemap () const
	Get the current MoveMap. More...

void	movemap (core::kinematics::MoveMapCOP new_movemap)
	Set the MoveMap. Positions outside of the defined loop will be ignored. More...

void	max_per_move_torsion_delta_per_residue (core::Angle input_max_delta_helix, core::Angle input_max_delta_strand, core::Angle input_max_delta_coil)
	Set the maximum change in torsion angle a residue is allowed per closure move for each of the three secondary structure types. More...

core::Angle	max_per_move_torsion_delta_per_residue (SecondaryStructureType secstruct) const
	Get the maximum change in torsion angle a residue is allowed for a single move for one of the three secondary structure types. More...

core::Angle	max_per_move_torsion_delta_per_residue (char secstruct) const
	Get the maximum allowed torsion angle deviation for the entire closure run for one of the three secondary structure types ( H, E, L). More...

core::Angle	max_total_torsion_delta_per_residue (SecondaryStructureType secstruct) const
	Get the maximum change in torsion angle a residue is allowed for the entire closure run for one of the three secondary structure types. More...

core::Angle	max_total_torsion_delta_per_residue (char secstruct) const
	Get the maximum allowed torsion angle deviation for the entire closure run for one of the three secondary structure types ( H, E, L). More...

void	max_total_torsion_delta_per_residue (core::Angle input_max_delta_helix, core::Angle input_max_delta_strand, core::Angle input_max_delta_coil)
	Set the maximum change in torsion angle a residue is allowed for the entire closure run for each of the three secondary structure types. More...

core::Real	tolerance () const
	Get the tolerance for loop closure in Angstroms. More...

void	tolerance (core::Real input_tolerance)
	Set the tolerance for loop closure in Angstroms. More...

core::Size	max_cycles () const
	Get the maximum number of cycles to attempt if the tolerance is not satisfied. More...

void	max_cycles (core::Size input_ccd_cycles)
	Set the maximum number of cycles to attempt if the tolerance is not satisfied. More...

bool	check_rama_scores () const
	Are closure moves checked using the rama scores and the Metropolis criterion? More...

void	check_rama_scores (bool setting)
	Set whether or not closure moves are checked using the rama scores and the Metropolis criterion. More...

bool	use_rama_2B () const
	Are two-body (neighbor-dependent) Ramachandran maps being used? More...

void	use_rama_2B (bool setting)
	Set whether or not two-body (neighbor-dependent) Ramachandran maps should be used. More...

void	set_verbose (bool setting)
	Set whether or not to output loop start/end points at beginning of Mover apply(). More...

core::Real	deviation () const
	Get the RMS deviation of the target atoms after completion of loop closure. More...

core::Angle	torsion_delta () const
	Get the average change in the main-chain torsion angles of the loop after completion of loop closure. More...

core::Real	rama_delta () const
	Get the average change in rama score for the residues in the loop after completion of loop closure. More...

core::Size	actual_cycles () const
	Get the number of cycles used to close the loop. More...

RamaCheckBaseOP	rama () const
	Get a pointer to the RamaCheck instance being used. More...

bool	success () const
	Return true if the forward and backward RMS deviations are each lower than the tolerance value. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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 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...

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 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 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 void	register_options ()
	Register options with the option system. More...

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...

Private Member Functions
void	init (protocols::loops::Loop const &loop, core::kinematics::MoveMapCOP movemap)

void	init_options ()

void	copy_data (CCDLoopClosureMover &to, CCDLoopClosureMover const &from) const

utility::vector1 < core::PointPosition >	get_anchors (core::conformation::Residue const &residue) const

void	index_pair_in_range (core::uint &pos, core::uint &atom, core::Size const n_mainchain_atoms) const

void	get_torsion_axis (core::pose::Pose const &pose, core::uint const seqpos, core::uint const torsion_num, core::Vector &axis_atom_coords, core::Vector &axis_unit_vector) const

core::Angle	calculate_ccd_angle (core::pose::Pose const &pose, core::uint const pos, core::uint const torsion, ChainDirection const direction)

virtual void	get_maximum_torsion_deltas_for_residue (core::pose::Pose const &pose, core::uint const seqpos, core::Real &per_move_allowed_delta, core::Real &total_allowed_delta) const

virtual void	adjust_residue_to_minimize_deviation (core::pose::Pose &pose, core::pose::Pose const &starting_pose, core::uint const seqpos, ChainDirection const direction, core::Real const max_per_move_torsion_delta, core::Real const max_total_torsion_delta)

void	close_loop_in_single_direction (core::pose::Pose &pose, core::pose::Pose const &starting_pose, ChainDirection const direction)

void	compute_closure_metrics (core::pose::Pose const &pose, core::pose::Pose const &starting_pose)

Static Private Member Functions
static std::map< char, SecondaryStructureType > const &	sec_struc_char_to_enum_map ()

Private Attributes
protocols::loops::Loop	loop_

core::kinematics::MoveMapCOP	movemap_

utility::vector1< core::Angle >	max_per_move_torsion_delta_

utility::vector1< core::Angle >	max_total_torsion_delta_

core::Distance	tolerance_

core::Size	max_cycles_

bool	check_rama_scores_

bool	use_rama_2b_

core::Real	deviation_

core::Angle	average_change_in_torsion_angle_

RamaCheckBaseOP	rama_

utility::vector1< core::Real >	starting_rama_scores_

core::Real	average_change_in_rama_score_

core::Size	actual_cycles_

bool	verbose_

Static Private Attributes
static utility::vector1 < core::SSize > const	STEP_SIZE = utility::tools::make_vector1( 1, -1 )

static core::Distance const	MALARKEY = -1.0

static core::Real const	BAD_SCORE = 500.0

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...

Detailed Description

Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent.

This class was initially a wrapper for fast_ccd_loop_closure(), an exposed method in ccd_closure.cc. Before using this mover: 1) Set a proper foldtree - usually a regular loop foldtree is used. (see protocols::loops::foldtree_from_loops) 2) Add cutpoint variants to the loop cutpoint

The original description of the CCD algorithm in relation to protein loop closure can be found here: Canutescu AA, Dunbrack RL Jr: Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003, 12:963-972.

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::CCDLoopClosureMover::CCDLoopClosureMover ( )

Empty constructor.

By default, all residues within the given Loop will be allowed to move.

References init().

protocols::loops::loop_closure::ccd::CCDLoopClosureMover::CCDLoopClosureMover ( CCDLoopClosureMover const & object_to_copy )

Copy constructor.

References copy_data().

protocols::loops::loop_closure::ccd::CCDLoopClosureMover::CCDLoopClosureMover ( protocols::loops::Loop const & loop )

Constructor with Loop input option.

By default, all residues within the given Loop will be allowed to move.

References init(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

protocols::loops::loop_closure::ccd::CCDLoopClosureMover::CCDLoopClosureMover	(	protocols::loops::Loop const &	loop,
		core::kinematics::MoveMapCOP	mm
	)

Constructor with Loop and MoveMap input options.

References init().

protocols::loops::loop_closure::ccd::CCDLoopClosureMover::~CCDLoopClosureMover ( )

overridedefault

Member Function Documentation

core::Size protocols::loops::loop_closure::ccd::CCDLoopClosureMover::actual_cycles ( ) const

inline

Get the number of cycles used to close the loop.

References actual_cycles_.

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation	(	core::pose::Pose &	pose,
		core::pose::Pose const &	starting_pose,
		core::uint const	seqpos,
		ChainDirection const	direction,
		core::Real const	max_per_move_torsion_delta,
		core::Real const	max_total_torsion_delta
	)

privatevirtual

References core::id::BB, calculate_ccd_angle(), check_rama_scores(), protocols::loops::Loop::cut(), protocols::loops::loop_closure::ccd::forward, core::chemical::is_mainchain_torsion_also_ring_torsion(), loop_, movemap_, rama(), core::pose::Pose::residue(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and protocols::loops::loop_closure::ccd::TR().

Referenced by close_loop_in_single_direction().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply ( core::pose::Pose & pose )

overridevirtual

Apply the corresponding move to <pose>.

Implements protocols::moves::Mover.

References actual_cycles_, average_change_in_rama_score_, average_change_in_torsion_angle_, protocols::loops::loop_closure::ccd::backward, check_rama_scores(), close_loop_in_single_direction(), compute_closure_metrics(), deviation_, protocols::loops::loop_closure::ccd::forward, loop_, max_cycles_, rama(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), success(), tolerance_, protocols::loops::loop_closure::ccd::TR(), and verbose_.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::rbsegment_relax::CCDMoveWrapper::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::loops::ccd_close_loops(), protocols::simple_moves::WobbleMover::ccd_closure(), protocols::LoopRebuild::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops().

Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::calculate_ccd_angle	(	core::pose::Pose const &	pose,
		core::uint const	seqpos,
		core::uint const	torsion_num,
		ChainDirection const	direction
	)

private

Parameters

<F>	the coordinates of the fixed target atoms
<M>	the coordinates of the moving positions to be overlapped with the target atoms
<coords>	all of the coordinates of mainchain atoms from a Pose
<seqpos>	the index of the residue for which we are calculating a torsion angle change
<torsion_num>	: the index of the mainchain torsion for which we are calculating a change

Note: The math (including the variable names used) in this function comes from Canutescu & Dunbrack (2003) Prot. Sci. 12, 963.

References protocols::loops::loop_closure::ccd::backward, protocols::loops::Loop::cut(), deviation_, protocols::loops::loop_closure::ccd::forward, get_anchors(), get_torsion_axis(), loop_, protocols::mean_field::min(), core::pose::Pose::residue(), STEP_SIZE, and protocols::loops::loop_closure::ccd::TR().

Referenced by adjust_residue_to_minimize_deviation().

bool protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores ( ) const

inline

Are closure moves checked using the rama scores and the Metropolis criterion?

References check_rama_scores_.

Referenced by adjust_residue_to_minimize_deviation(), apply(), compute_closure_metrics(), protocols::LoopRebuild::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), init_options(), parse_my_tag(), and show().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores ( bool setting )

inline

Set whether or not closure moves are checked using the rama scores and the Metropolis criterion.

References check_rama_scores_.

protocols::moves::MoverOP protocols::loops::loop_closure::ccd::CCDLoopClosureMover::clone ( ) const

overridevirtual

Return the name of the Mover.

Reimplemented from protocols::moves::Mover.

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::close_loop_in_single_direction	(	core::pose::Pose &	pose,
		core::pose::Pose const &	starting_pose,
		ChainDirection const	direction
	)

private

References adjust_residue_to_minimize_deviation(), protocols::loops::loop_closure::ccd::backward, protocols::loops::Loop::cut(), protocols::loops::loop_closure::ccd::forward, get_maximum_torsion_deltas_for_residue(), loop_, movemap_, protocols::loops::Loop::start(), STEP_SIZE, protocols::loops::Loop::stop(), and protocols::loops::loop_closure::ccd::TR().

Referenced by apply().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::compute_closure_metrics	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	starting_pose
	)

private

References average_change_in_rama_score_, average_change_in_torsion_angle_, core::id::BB, check_rama_scores(), loop_, core::conformation::Residue::mainchain_atoms(), rama(), core::pose::Pose::residue(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::torsion().

Referenced by apply().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::copy_data	(	CCDLoopClosureMover &	to,
		CCDLoopClosureMover const &	from
	)		const

private

References actual_cycles_, average_change_in_rama_score_, average_change_in_torsion_angle_, check_rama_scores_, deviation_, loop_, max_cycles_, max_per_move_torsion_delta_, max_total_torsion_delta_, movemap_, rama_, tolerance_, and use_rama_2b_.

Referenced by CCDLoopClosureMover(), and operator=().

core::Real protocols::loops::loop_closure::ccd::CCDLoopClosureMover::deviation ( ) const

inline

Get the RMS deviation of the target atoms after completion of loop closure.

sqrt( dev / number_of_atoms )

References deviation_.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::simple_moves::WobbleMover::ccd_closure(), and success().

protocols::moves::MoverOP protocols::loops::loop_closure::ccd::CCDLoopClosureMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

utility::vector1< PointPosition > protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors ( core::conformation::Residue const & residue ) const

private

References core::conformation::Residue::atom(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), and core::conformation::Atom::xyz().

Referenced by calculate_ccd_angle().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_maximum_torsion_deltas_for_residue	(	core::pose::Pose const &	pose,
		core::uint const	seqpos,
		core::Real &	per_move_allowed_delta,
		core::Real &	total_allowed_delta
	)		const

privatevirtual

References max_per_move_torsion_delta_per_residue(), max_total_torsion_delta_per_residue(), and core::pose::Pose::secstruct().

Referenced by close_loop_in_single_direction().

std::string protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_torsion_axis	(	core::pose::Pose const &	pose,
		core::uint const	seqpos,
		core::uint const	torsion_num,
		core::Vector &	axis_atom_coords,
		core::Vector &	axis_unit_vector
	)		const

private

References index_pair_in_range(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by calculate_ccd_angle().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::index_pair_in_range	(	core::uint &	pos,
		core::uint &	atom,
		core::Size const	n_mainchain_atoms
	)		const

private

Referenced by get_torsion_axis().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::init	(	protocols::loops::Loop const &	loop,
		core::kinematics::MoveMapCOP	movemap
	)

private

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::init_options ( )

private

References check_rama_scores(), max_cycles(), max_per_move_torsion_delta_per_residue(), max_total_torsion_delta_per_residue(), tolerance(), and use_rama_2B().

Referenced by init().

protocols::loops::Loop protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop ( ) const

Get the Loop to be closed.

References loop_.

Referenced by protocols::loops::ccd_close_loops(), and init().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop ( protocols::loops::Loop new_loop )

Set the Loop to be closed.

References loop_.

core::Size protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_cycles ( ) const

inline

Get the maximum number of cycles to attempt if the tolerance is not satisfied.

Each cycle includes both forward and backward directions.

References max_cycles_.

Referenced by protocols::rbsegment_relax::CCDMoveWrapper::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), init_options(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), and parse_my_tag().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_cycles ( core::Size input_ccd_cycles )

inline

Set the maximum number of cycles to attempt if the tolerance is not satisfied.

Each cycle includes both forward and backward directions.

References max_cycles_.

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_per_move_torsion_delta_per_residue	(	core::Angle	input_max_delta_helix,
		core::Angle	input_max_delta_strand,
		core::Angle	input_max_delta_coil
	)

inline

Set the maximum change in torsion angle a residue is allowed per closure move for each of the three secondary structure types.

Parameters

Order of parameters is helix, strand, coil. Angles are in degrees.

References protocols::loops::loop_closure::ccd::coil, protocols::loops::loop_closure::ccd::helix, max_per_move_torsion_delta_, and protocols::loops::loop_closure::ccd::strand.

Referenced by get_maximum_torsion_deltas_for_residue(), init_options(), and max_per_move_torsion_delta_per_residue().

core::Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_per_move_torsion_delta_per_residue ( SecondaryStructureType secstruct ) const

inline

Get the maximum change in torsion angle a residue is allowed for a single move for one of the three secondary structure types.

Returns: angle in degrees

References max_per_move_torsion_delta_.

Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_per_move_torsion_delta_per_residue ( char secstruct ) const

Get the maximum allowed torsion angle deviation for the entire closure run for one of the three secondary structure types ( H, E, L).

Parameters

<sectruct> 'H', 'E', or 'L'

Returns: angle in degrees

References max_per_move_torsion_delta_per_residue(), and sec_struc_char_to_enum_map().

core::Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_per_residue ( SecondaryStructureType secstruct ) const

inline

Get the maximum change in torsion angle a residue is allowed for the entire closure run for one of the three secondary structure types.

Returns: angle in degrees

References max_total_torsion_delta_.

Referenced by get_maximum_torsion_deltas_for_residue(), init_options(), max_total_torsion_delta_per_residue(), and show().

Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_per_residue ( char secstruct ) const

Get the maximum allowed torsion angle deviation for the entire closure run for one of the three secondary structure types ( H, E, L).

Parameters

<sectruct> 'H', 'E', or 'L'

Returns: angle in degrees

References max_total_torsion_delta_per_residue(), and sec_struc_char_to_enum_map().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_per_residue	(	core::Angle	input_max_delta_helix,
		core::Angle	input_max_delta_strand,
		core::Angle	input_max_delta_coil
	)

inline

Set the maximum change in torsion angle a residue is allowed for the entire closure run for each of the three secondary structure types.

Parameters

Order of parameters is helix, strand, coil. Angles are in degrees.

References protocols::loops::loop_closure::ccd::coil, protocols::loops::loop_closure::ccd::helix, max_total_torsion_delta_, and protocols::loops::loop_closure::ccd::strand.

kinematics::MoveMap protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap ( ) const

Get the current MoveMap.

References movemap_.

Referenced by protocols::loops::ccd_close_loops(), and init().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap ( core::kinematics::MoveMapCOP new_movemap )

Set the MoveMap. Positions outside of the defined loop will be ignored.

References movemap_.

std::string protocols::loops::loop_closure::ccd::CCDLoopClosureMover::mover_name ( )

static

Referenced by get_name(), protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator::keyname(), and provide_xml_schema().

CCDLoopClosureMover & protocols::loops::loop_closure::ccd::CCDLoopClosureMover::operator= ( CCDLoopClosureMover const & object_to_copy )

References copy_data().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Called by MoverFactory when constructing new Movers.

Reimplemented from protocols::moves::Mover.

References check_rama_scores(), protocols::loops::loop_closure::ccd::coil, protocols::loops::loop_closure::ccd::helix, max_cycles(), max_per_move_torsion_delta_, max_total_torsion_delta_, rama(), protocols::loops::loop_closure::ccd::strand, tolerance(), and use_rama_2B().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator::provide_xml_schema().

RamaCheckBaseOP protocols::loops::loop_closure::ccd::CCDLoopClosureMover::rama ( ) const

Get a pointer to the RamaCheck instance being used.

References rama_, and use_rama_2B().

Referenced by adjust_residue_to_minimize_deviation(), apply(), compute_closure_metrics(), parse_my_tag(), and show().

core::Real protocols::loops::loop_closure::ccd::CCDLoopClosureMover::rama_delta ( ) const

inline

Get the average change in rama score for the residues in the loop after completion of loop closure.

Note: This value will only be meaningful if the option for checking the rama score is turned on.; Change this name to match the datum. ~Labonte

References average_change_in_rama_score_.

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::register_options ( )

static

Register options with the option system.

References protocols::loops::loop_closure::ccd::RamaCheckBase::register_options(), and protocols::evaluation::register_options().

std::map< char, SecondaryStructureType > const & protocols::loops::loop_closure::ccd::CCDLoopClosureMover::sec_struc_char_to_enum_map ( )

staticprivate

References protocols::loops::loop_closure::ccd::coil, protocols::loops::loop_closure::ccd::helix, and protocols::loops::loop_closure::ccd::strand.

Referenced by max_per_move_torsion_delta_per_residue(), and max_total_torsion_delta_per_residue().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::set_verbose ( bool setting )

inline

Set whether or not to output loop start/end points at beginning of Mover apply().

References verbose_.

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Generate a string representation of CCDLoopClosureMover for debugging purposes.

Print the CcdLoopMover's basic information, the loop it is working on, and details about the instance's configuration.

Reimplemented from protocols::moves::Mover.

References check_rama_scores(), check_rama_scores_, protocols::loops::loop_closure::ccd::coil, protocols::loops::loop_closure::ccd::helix, loop_, max_cycles_, max_total_torsion_delta_per_residue(), movemap_, rama(), protocols::loops::Loop::show(), protocols::loops::loop_closure::ccd::strand, and tolerance_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

bool protocols::loops::loop_closure::ccd::CCDLoopClosureMover::success ( ) const

Return true if the forward and backward RMS deviations are each lower than the tolerance value.

References deviation(), and tolerance_.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::apply(), apply(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops().

core::Real protocols::loops::loop_closure::ccd::CCDLoopClosureMover::tolerance ( ) const

inline

Get the tolerance for loop closure in Angstroms.

A forward and backward splice of RMS over N, CA, and C (or target atoms) must be less than the tolerance for an early return; otherwise, the algorithm will go through the loop the requested number of cycles. RMS Deviation is calculation as sqrt( dev / number_of_atoms )

References tolerance_.

Referenced by init_options(), and parse_my_tag().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::tolerance ( core::Real input_tolerance )

inline

Set the tolerance for loop closure in Angstroms.

A forward and backward splice of RMS deviation over N, CA, and C (or target atoms)must be less than the tolerance for an early return; otherwise, the algorithm will go through the loop the requested number of cycles. RMS Deviation is calculation as sqrt( dev / number_of_atoms )

References tolerance_.

core::Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::torsion_delta ( ) const

inline

Get the average change in the main-chain torsion angles of the loop after completion of loop closure.

Note: Change this name to match the datum. ~Labonte

References average_change_in_torsion_angle_.

bool protocols::loops::loop_closure::ccd::CCDLoopClosureMover::use_rama_2B ( ) const

inline

Are two-body (neighbor-dependent) Ramachandran maps being used?

References use_rama_2b_.

Referenced by init_options(), parse_my_tag(), and rama().

void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::use_rama_2B ( bool setting )

inline

Set whether or not two-body (neighbor-dependent) Ramachandran maps should be used.

References use_rama_2b_.

Member Data Documentation

core::Size protocols::loops::loop_closure::ccd::CCDLoopClosureMover::actual_cycles_

private

Referenced by actual_cycles(), apply(), and copy_data().

core::Real protocols::loops::loop_closure::ccd::CCDLoopClosureMover::average_change_in_rama_score_

private

Referenced by apply(), compute_closure_metrics(), copy_data(), and rama_delta().

core::Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::average_change_in_torsion_angle_

private

Referenced by apply(), compute_closure_metrics(), copy_data(), and torsion_delta().

Real const protocols::loops::loop_closure::ccd::CCDLoopClosureMover::BAD_SCORE = 500.0

staticprivate

bool protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores_

private

Referenced by check_rama_scores(), copy_data(), init(), and show().

core::Real protocols::loops::loop_closure::ccd::CCDLoopClosureMover::deviation_

private

Referenced by apply(), calculate_ccd_angle(), copy_data(), deviation(), and init().

protocols::loops::Loop protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop_

private

Referenced by adjust_residue_to_minimize_deviation(), apply(), calculate_ccd_angle(), close_loop_in_single_direction(), compute_closure_metrics(), copy_data(), init(), loop(), and show().

Distance const protocols::loops::loop_closure::ccd::CCDLoopClosureMover::MALARKEY = -1.0

staticprivate

Referenced by init().

core::Size protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_cycles_

private

Referenced by apply(), copy_data(), init(), max_cycles(), and show().

utility::vector1< core::Angle > protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_per_move_torsion_delta_

private

Referenced by copy_data(), init(), max_per_move_torsion_delta_per_residue(), and parse_my_tag().

utility::vector1< core::Angle > protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_

private

Referenced by copy_data(), init(), max_total_torsion_delta_per_residue(), and parse_my_tag().

core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap_

private

Referenced by adjust_residue_to_minimize_deviation(), close_loop_in_single_direction(), copy_data(), init(), movemap(), and show().

RamaCheckBaseOP protocols::loops::loop_closure::ccd::CCDLoopClosureMover::rama_

mutableprivate

Referenced by copy_data(), init(), and rama().

utility::vector1< core::Real > protocols::loops::loop_closure::ccd::CCDLoopClosureMover::starting_rama_scores_

private

utility::vector1< SSize > const protocols::loops::loop_closure::ccd::CCDLoopClosureMover::STEP_SIZE = utility::tools::make_vector1( 1, -1 )

staticprivate

Referenced by calculate_ccd_angle(), and close_loop_in_single_direction().

core::Distance protocols::loops::loop_closure::ccd::CCDLoopClosureMover::tolerance_

private

Referenced by apply(), copy_data(), init(), show(), success(), and tolerance().

bool protocols::loops::loop_closure::ccd::CCDLoopClosureMover::use_rama_2b_

private

Referenced by copy_data(), init(), and use_rama_2B().

bool protocols::loops::loop_closure::ccd::CCDLoopClosureMover::verbose_

private

Referenced by apply(), init(), and set_verbose().

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

src/protocols/loops/loop_closure/ccd/CCDLoopClosureMover.hh
src/protocols/loops/loop_closure/ccd/CCDLoopClosureMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation