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protocols::rotamer_recovery::RotamerRecoveryMover Class Reference

#include <RotamerRecoveryMover.hh>

Inheritance diagram for protocols::rotamer_recovery::RotamerRecoveryMover:
Inheritance graph

Public Member Functions

 RotamerRecoveryMover ()
 default constructor More...
 RotamerRecoveryMover (rotamer_recovery::RotamerRecoveryOP rotamer_recovery, core::scoring::ScoreFunctionOP scfxn, core::pack::task::TaskFactoryOP task_factory)
 ~RotamerRecoveryMover () override
 RotamerRecoveryMover (RotamerRecoveryMover const &src)
virtual void register_options () const
void apply (core::pose::Pose &pose) override
 Main Method. More...
moves::MoverOP clone () const override
 make a copy More...
moves::MoverOP fresh_instance () const override
 make a copy but use default constructor More...
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
bool reinitialize_for_each_job () const override
 this function informs 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
 this function informs 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...
core::scoring::ScoreFunctionOP score_function ()
void score_function (core::scoring::ScoreFunctionOP)
virtual void show () const
void show (std::ostream &out) const override
 Outputs details about the Mover, including current settings. 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...
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 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 Attributes

rotamer_recovery::RotamerRecoveryOP rotamer_recovery_
core::scoring::ScoreFunctionOP scfxn_
core::pack::task::TaskFactoryOP task_factory_

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...

Constructor & Destructor Documentation

protocols::rotamer_recovery::RotamerRecoveryMover::RotamerRecoveryMover ( )

default constructor

References task_factory_.

protocols::rotamer_recovery::RotamerRecoveryMover::RotamerRecoveryMover ( rotamer_recovery::RotamerRecoveryOP  rotamer_recovery,
core::scoring::ScoreFunctionOP  scfxn,
core::pack::task::TaskFactoryOP  task_factory 
protocols::rotamer_recovery::RotamerRecoveryMover::~RotamerRecoveryMover ( )
protocols::rotamer_recovery::RotamerRecoveryMover::RotamerRecoveryMover ( RotamerRecoveryMover const &  src)

Member Function Documentation

void protocols::rotamer_recovery::RotamerRecoveryMover::apply ( core::pose::Pose )

Main Method.

Implements protocols::moves::Mover.

References rotamer_recovery_, score_function(), and task_factory_.

MoverOP protocols::rotamer_recovery::RotamerRecoveryMover::clone ( ) const

make a copy

Reimplemented from protocols::moves::Mover.

MoverOP protocols::rotamer_recovery::RotamerRecoveryMover::fresh_instance ( ) const

make a copy but use default constructor

Reimplemented from protocols::moves::Mover.

std::string protocols::rotamer_recovery::RotamerRecoveryMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::rotamer_recovery::RotamerRecoveryMover::mover_name ( )
void protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_comparer(), protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_protocol(), protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_reporter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), rotamer_recovery_, score_function(), and protocols::rotamer_recovery::TR().

void protocols::rotamer_recovery::RotamerRecoveryMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::rotamer_recovery::RotamerRecoveryMover::register_options ( ) const

References rotamer_recovery_.

bool protocols::rotamer_recovery::RotamerRecoveryMover::reinitialize_for_each_job ( ) const

this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.

Reimplemented from protocols::moves::Mover.

bool protocols::rotamer_recovery::RotamerRecoveryMover::reinitialize_for_new_input ( ) const

this function informs 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).

Reimplemented from protocols::moves::Mover.

ScoreFunctionOP protocols::rotamer_recovery::RotamerRecoveryMover::score_function ( )

References core::scoring::get_score_function(), and scfxn_.

Referenced by apply(), and parse_my_tag().

void protocols::rotamer_recovery::RotamerRecoveryMover::score_function ( core::scoring::ScoreFunctionOP  )
void protocols::rotamer_recovery::RotamerRecoveryMover::show ( ) const

References rotamer_recovery_.

void protocols::rotamer_recovery::RotamerRecoveryMover::show ( std::ostream &  output) const

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References rotamer_recovery_.

Member Data Documentation

rotamer_recovery::RotamerRecoveryOP protocols::rotamer_recovery::RotamerRecoveryMover::rotamer_recovery_
core::scoring::ScoreFunctionOP protocols::rotamer_recovery::RotamerRecoveryMover::scfxn_

Referenced by score_function().

core::pack::task::TaskFactoryOP protocols::rotamer_recovery::RotamerRecoveryMover::task_factory_

Referenced by apply(), and RotamerRecoveryMover().

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