![]() |
Rosetta
2020.50
|
Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent. More...
#include <CCDLoopClosureMover.hh>
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... | |
![]() | |
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 void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
static 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 std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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 | |
![]() | |
typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
![]() | |
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... | |
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.
protocols::loops::loop_closure::ccd::CCDLoopClosureMover::CCDLoopClosureMover | ( | ) |
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 | ||
) |
|
overridedefault |
|
inline |
Get the number of cycles used to close the loop.
References actual_cycles_.
|
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().
|
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().
|
private |
<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 |
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().
|
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().
|
inline |
Set whether or not closure moves are checked using the rama scores and the Metropolis criterion.
References check_rama_scores_.
|
overridevirtual |
Return the name of the Mover.
Reimplemented from protocols::moves::Mover.
|
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().
|
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().
|
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=().
|
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().
|
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.
|
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().
|
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().
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
|
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().
|
private |
Referenced by get_torsion_axis().
|
private |
References check_rama_scores_, protocols::loops::loop_closure::ccd::coil, deviation_, protocols::loops::loop_closure::ccd::helix, init_options(), loop(), loop_, MALARKEY, max_cycles_, max_per_move_torsion_delta_, max_total_torsion_delta_, movemap(), movemap_, protocols::loops::loop_closure::ccd::n_secondary_structure_types, rama_, protocols::loops::loop_closure::ccd::strand, tolerance_, protocols::moves::Mover::type(), use_rama_2b_, and verbose_.
Referenced by CCDLoopClosureMover().
|
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 | ) |
|
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().
|
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_.
|
inline |
Set the maximum change in torsion angle a residue is allowed per closure move for each of the three secondary structure types.
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().
|
inline |
Get the maximum change in torsion angle a residue is allowed for a single move for one of the three secondary structure types.
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).
<sectruct> | 'H', 'E', or 'L' |
References max_per_move_torsion_delta_per_residue(), and sec_struc_char_to_enum_map().
|
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.
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).
<sectruct> | 'H', 'E', or 'L' |
References max_total_torsion_delta_per_residue(), and sec_struc_char_to_enum_map().
|
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.
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_.
|
static |
CCDLoopClosureMover & protocols::loops::loop_closure::ccd::CCDLoopClosureMover::operator= | ( | CCDLoopClosureMover const & | object_to_copy | ) |
References copy_data().
|
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().
|
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().
|
inline |
Get the average change in rama score for the residues in the loop after completion of loop closure.
References average_change_in_rama_score_.
|
static |
Register options with the option system.
References protocols::loops::loop_closure::ccd::RamaCheckBase::register_options(), and protocols::evaluation::register_options().
|
staticprivate |
|
inline |
|
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().
|
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().
|
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_.
|
inline |
Get the average change in the main-chain torsion angles of the loop after completion of loop closure.
References average_change_in_torsion_angle_.
|
inline |
Are two-body (neighbor-dependent) Ramachandran maps being used?
References use_rama_2b_.
Referenced by init_options(), parse_my_tag(), and rama().
|
inline |
Set whether or not two-body (neighbor-dependent) Ramachandran maps should be used.
References use_rama_2b_.
|
private |
Referenced by actual_cycles(), apply(), and copy_data().
|
private |
Referenced by apply(), compute_closure_metrics(), copy_data(), and rama_delta().
|
private |
Referenced by apply(), compute_closure_metrics(), copy_data(), and torsion_delta().
|
staticprivate |
|
private |
Referenced by check_rama_scores(), copy_data(), init(), and show().
|
private |
Referenced by apply(), calculate_ccd_angle(), copy_data(), deviation(), and init().
|
private |
|
staticprivate |
Referenced by init().
|
private |
Referenced by apply(), copy_data(), init(), max_cycles(), and show().
|
private |
Referenced by copy_data(), init(), max_per_move_torsion_delta_per_residue(), and parse_my_tag().
|
private |
Referenced by copy_data(), init(), max_total_torsion_delta_per_residue(), and parse_my_tag().
|
private |
Referenced by adjust_residue_to_minimize_deviation(), close_loop_in_single_direction(), copy_data(), init(), movemap(), and show().
|
mutableprivate |
Referenced by copy_data(), init(), and rama().
|
private |
|
staticprivate |
Referenced by calculate_ccd_angle(), and close_loop_in_single_direction().
|
private |
Referenced by apply(), copy_data(), init(), show(), success(), and tolerance().
|
private |
Referenced by copy_data(), init(), and use_rama_2B().
|
private |
Referenced by apply(), init(), and set_verbose().