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protocols::loops::loop_closure::kinematic_closure::KinematicWrapper Class Reference

#include <KinematicWrapper.hh>

Inheritance diagram for protocols::loops::loop_closure::kinematic_closure::KinematicWrapper:
Inheritance graph
[legend]

Public Member Functions

 KinematicWrapper (KinematicMoverOP kinmover_in, protocols::loops::Loop loop, core::Size cycles=0)
 ctor with Loop More...
 
 KinematicWrapper (KinematicMoverOP kinmover_in, core::Size loop_begin, core::Size loop_end, core::Size cycles=0)
 ctor with explicit loop begin/end More...
 
 ~KinematicWrapper () override
 
void apply (core::pose::Pose &pose) override
 re-applies KinematicMover with different pivots until success More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void respect_this_movemap (core::kinematics::MoveMapCOP mm)
 this function derives the allowed_positions_ vector from mm and the loop begin/end More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual 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...
 

Private Member Functions

void ctor ()
 two ctors have same functions, just different initialization lists; de-duplicated here More...
 
void init_allowed_pos ()
 initializes allowed positions - for constructors and resetting More...
 

Private Attributes

KinematicMoverOP kinmover_
 OP for KinematicMover. More...
 
core::Size const loop_begin_
 the loop this object-instance remodels More...
 
core::Size const loop_end_
 the loop this object-instance remodels More...
 
core::Size const limit_
 a limit on the number of cycles the mover will run More...
 
utility::vector1< core::Sizeallowed_positions_
 vector of positions allowed as pivots More...
 

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
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 
- Protected Member Functions 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

This class extends KinematicMover by composition (has-a KinematicMover). The idea is to make KinematicMover useful when ONLY the apply() function is available (as in MoverContainers, etc.). It will reapply KinematicMover until the KinematicMover reports a success. This class uses searches through loop begin/middle/end points while searching for solutions. You can pass a MoveMap; it will refuse to put pivots where the MoveMap is not mobile.

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::KinematicWrapper ( KinematicMoverOP  kinmover_in,
protocols::loops::Loop  loop,
core::Size  cycles = 0 
)

ctor with Loop

References ctor().

protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::KinematicWrapper ( KinematicMoverOP  kinmover_in,
core::Size  loop_begin,
core::Size  loop_end,
core::Size  cycles = 0 
)

ctor with explicit loop begin/end

References ctor().

protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::~KinematicWrapper ( )
overridedefault

Member Function Documentation

void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply ( core::pose::Pose pose)
overridevirtual
void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::ctor ( )
private

two ctors have same functions, just different initialization lists; de-duplicated here

trivial wrapper around stuff needed in two ctors (de-duplicating the code)

References init_allowed_pos(), loop_begin_, and loop_end_.

Referenced by KinematicWrapper().

std::string protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::init_allowed_pos ( )
private

initializes allowed positions - for constructors and resetting

initializes the allowed_positions vector with every position in the loop as an allowed pivot

References allowed_positions_, loop_begin_, and loop_end_.

Referenced by ctor(), and respect_this_movemap().

void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::respect_this_movemap ( core::kinematics::MoveMapCOP  mm)

this function derives the allowed_positions_ vector from mm and the loop begin/end

this function compares positions in the allowed_positions vector with the movemap, and removes non-mobile positions

References allowed_positions_, init_allowed_pos(), and protocols::loops::loop_closure::kinematic_closure::TR().

Member Data Documentation

utility::vector1<core::Size> protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::allowed_positions_
private

vector of positions allowed as pivots

Referenced by apply(), init_allowed_pos(), and respect_this_movemap().

KinematicMoverOP protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::kinmover_
private

OP for KinematicMover.

Referenced by apply().

core::Size const protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::limit_
private

a limit on the number of cycles the mover will run

Referenced by apply().

core::Size const protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::loop_begin_
private

the loop this object-instance remodels

Referenced by ctor(), and init_allowed_pos().

core::Size const protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::loop_end_
private

the loop this object-instance remodels

Referenced by ctor(), and init_allowed_pos().


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