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protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover Class Reference

#include <UnfoldedStateEnergyCalculatorMover.hh>

Inheritance diagram for protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover:
Inheritance graph
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Public Member Functions

 UnfoldedStateEnergyCalculatorMover (UnfoldedStateEnergyCalculatorJobDistributor &job_dist, core::scoring::ScoreFunctionCOP pack_scrfxn, core::scoring::ScoreFunctionCOP score_scrfxn, core::Size frag_length, std::string const &mut_aa, bool repack_fragments, bool native_sequence, std::string const &seq_match_seq, core::Size seq_match_pos, bool seq_match_frags)
 ctor More...
 
 ~UnfoldedStateEnergyCalculatorMover () override
 dtor More...
 
 UnfoldedStateEnergyCalculatorMover (UnfoldedStateEnergyCalculatorMover const &usecm)
 cctor More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void apply (Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool reinitialize_for_each_job () const override
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
bool reinitialize_for_new_input () const override
 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...
 
- 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...
 
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

bool fragment_check (Pose &pose, core::Size frag_start_pos)
 Check fragment residues should be polymeric and on same chain. More...
 
void create_random_fragments (Pose &pose, utility::vector1< Pose > &fragments)
 
void create_sequence_match_fragments (Pose &pose, utility::vector1< Pose > &fragments)
 

Private Attributes

UnfoldedStateEnergyCalculatorJobDistributorjob_dist_
 
core::scoring::ScoreFunctionCOP pack_scrfxn_
 
core::scoring::ScoreFunctionCOP score_scrfxn_
 
core::Size frag_length_
 
std::string mut_aa_
 
bool repack_fragments_
 
bool native_sequence_
 
std::string sequence_match_sequence_
 
core::Size sequence_match_position_
 
bool sequence_matched_fragments_
 

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...
 

Constructor & Destructor Documentation

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::UnfoldedStateEnergyCalculatorMover ( UnfoldedStateEnergyCalculatorJobDistributor job_dist,
core::scoring::ScoreFunctionCOP  pack_scrfxn,
core::scoring::ScoreFunctionCOP  score_scrfxn,
core::Size  frag_length,
std::string const &  mut_aa,
bool  repack_fragments,
bool  native_sequence,
std::string const &  seq_match_seq,
core::Size  seq_match_pos,
bool  seq_match_frags 
)

ctor

alternate ctor

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::~UnfoldedStateEnergyCalculatorMover ( )
overridedefault

dtor

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::UnfoldedStateEnergyCalculatorMover ( UnfoldedStateEnergyCalculatorMover const &  usecm)

cctor

Member Function Documentation

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply ( Pose )
overridevirtual
void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments ( Pose pose,
utility::vector1< Pose > &  fragments 
)
private
void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_sequence_match_fragments ( Pose pose,
utility::vector1< Pose > &  fragments 
)
private
bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check ( Pose pose,
core::Size  frag_start_pos 
)
private
protocols::moves::MoverOP protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::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.

std::string protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::reinitialize_for_each_job ( ) const
overridevirtual

Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::reinitialize_for_new_input ( ) const
overridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

Member Data Documentation

core::Size protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::frag_length_
private
UnfoldedStateEnergyCalculatorJobDistributor& protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::job_dist_
private

Referenced by apply().

std::string protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::mut_aa_
private

Referenced by apply().

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::native_sequence_
private

Referenced by apply().

core::scoring::ScoreFunctionCOP protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::pack_scrfxn_
private

Referenced by apply().

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::repack_fragments_
private

Referenced by apply().

core::scoring::ScoreFunctionCOP protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::score_scrfxn_
private
core::Size protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::sequence_match_position_
private
std::string protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::sequence_match_sequence_
private
bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::sequence_matched_fragments_
private

Referenced by apply().


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