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protocols::abinitio::KinematicTaskControl Class Referenceabstract

#include <KinematicTaskControl.hh>

Inheritance diagram for protocols::abinitio::KinematicTaskControl:
Inheritance graph
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Public Member Functions

 KinematicTaskControl ()
 
 KinematicTaskControl (ProtocolOP sampler)
 
 ~KinematicTaskControl () override
 
virtual KinematicControlOP new_kinematics (core::pose::Pose &pose)=0
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void init (core::pose::Pose const &pose) override
 
KinematicControlOP current_kinematics ()
 
void set_input_pose_is_fa (bool setting=true)
 
ProtocolOP sampling_protocol ()
 
checkpoint::CheckPointerget_checkpoints () override
 
- Public Member Functions inherited from protocols::abinitio::Protocol
 Protocol ()
 
 ~Protocol () override=default
 
void set_evaluation (evaluation::MetaPoseEvaluatorOP ev)
 
void add_evaluation (evaluation::PoseEvaluatorOP ev)
 
void evaluate_pose (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const
 
evaluation::MetaPoseEvaluatorOP evaluator ()
 
virtual void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
void set_kinematics (abinitio::KinematicControlOP kc)
 
abinitio::KinematicControl const & kinematics ()
 
virtual bool start_from_centroid () const
 
virtual bool return_centroid () const
 
virtual void return_centroid (bool setting)
 
void apply (core::pose::Pose &) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_silentout_file_name (std::string str)
 
core::scoring::ScoreFunctionOP fullatom_scorefxn ()
 
core::scoring::ScoreFunctionOP centroid_scorefxn ()
 
- 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 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...
 

Protected Member Functions

virtual bool inner_loop (core::pose::Pose &pose)
 
void set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops) const
 
ResolutionSwitcherres_switch ()
 
- 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...
 

Protected Attributes

KinematicControlOP current_kinematics_
 

Private Attributes

ResolutionSwitcherOP res_switch_
 
ProtocolOP sampling_protocol_
 
bool b_input_is_fullatom_
 

Additional Inherited Members

- Public Types inherited from protocols::abinitio::Protocol
typedef Mover BaseClass
 
- 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::abinitio::Protocol
static void register_options ()
 
- 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...
 

Constructor & Destructor Documentation

protocols::abinitio::KinematicTaskControl::KinematicTaskControl ( )
inline
protocols::abinitio::KinematicTaskControl::KinematicTaskControl ( ProtocolOP  sampler)
inline
protocols::abinitio::KinematicTaskControl::~KinematicTaskControl ( )
overridedefault

Member Function Documentation

void protocols::abinitio::KinematicTaskControl::apply ( core::pose::Pose )
overridevirtual
KinematicControlOP protocols::abinitio::KinematicTaskControl::current_kinematics ( )
inline

References current_kinematics_.

checkpoint::CheckPointer& protocols::abinitio::KinematicTaskControl::get_checkpoints ( )
inlineoverridevirtual

Reimplemented from protocols::abinitio::Protocol.

References sampling_protocol_.

std::string protocols::abinitio::KinematicTaskControl::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::abinitio::LoopJumpFoldCst.

void protocols::abinitio::KinematicTaskControl::init ( core::pose::Pose const &  pose)
overridevirtual

Reimplemented from protocols::abinitio::Protocol.

bool protocols::abinitio::KinematicTaskControl::inner_loop ( core::pose::Pose pose)
protectedvirtual
virtual KinematicControlOP protocols::abinitio::KinematicTaskControl::new_kinematics ( core::pose::Pose pose)
pure virtual
ResolutionSwitcher& protocols::abinitio::KinematicTaskControl::res_switch ( )
inlineprotected

References res_switch_.

ProtocolOP protocols::abinitio::KinematicTaskControl::sampling_protocol ( )
inline

References sampling_protocol_.

void protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops ( core::pose::Pose pose,
loops::Loops  loops 
) const
protected
void protocols::abinitio::KinematicTaskControl::set_input_pose_is_fa ( bool  setting = true)
inline

References b_input_is_fullatom_.

Member Data Documentation

bool protocols::abinitio::KinematicTaskControl::b_input_is_fullatom_
private

Referenced by set_input_pose_is_fa().

KinematicControlOP protocols::abinitio::KinematicTaskControl::current_kinematics_
mutableprotected

Referenced by current_kinematics().

ResolutionSwitcherOP protocols::abinitio::KinematicTaskControl::res_switch_
private

Referenced by res_switch().

ProtocolOP protocols::abinitio::KinematicTaskControl::sampling_protocol_
private

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