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protocols::loops::loop_closure::ccd::CCDLoopClosureMover Class Reference

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:
Inheritance graph
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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
 
CCDLoopClosureMoveroperator= (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 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 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::Anglemax_per_move_torsion_delta_
 
utility::vector1< core::Anglemax_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::Realstarting_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
void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply ( core::pose::Pose pose)
overridevirtual
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
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
void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::compute_closure_metrics ( core::pose::Pose const &  pose,
core::pose::Pose const &  starting_pose 
)
private
void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::copy_data ( CCDLoopClosureMover to,
CCDLoopClosureMover const &  from 
) const
private
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
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
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
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
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
Orderof 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
Orderof 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
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
void protocols::loops::loop_closure::ccd::CCDLoopClosureMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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
std::map< char, SecondaryStructureType > const & protocols::loops::loop_closure::ccd::CCDLoopClosureMover::sec_struc_char_to_enum_map ( )
staticprivate
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
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
core::Angle protocols::loops::loop_closure::ccd::CCDLoopClosureMover::average_change_in_torsion_angle_
private
Real const protocols::loops::loop_closure::ccd::CCDLoopClosureMover::BAD_SCORE = 500.0
staticprivate
bool protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores_
private
core::Real protocols::loops::loop_closure::ccd::CCDLoopClosureMover::deviation_
private
protocols::loops::Loop protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop_
private
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
utility::vector1< core::Angle > protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_total_torsion_delta_
private
core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap_
private
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
core::Distance protocols::loops::loop_closure::ccd::CCDLoopClosureMover::tolerance_
private
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: