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protocols::symmetry::SetupNCSMover Class Reference

#include <SetupNCSMover.hh>

Inheritance diagram for protocols::symmetry::SetupNCSMover:
Inheritance graph
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Public Member Functions

 SetupNCSMover ()
 
 SetupNCSMover (std::string src, std::string tgt)
 
 SetupNCSMover (std::string src, utility::vector1< std::string > tgt)
 
 SetupNCSMover (utility::vector1< std::string > src, utility::vector1< std::string > tgt)
 
 ~SetupNCSMover () override
 
void add_group (std::string src, std::string tgt)
 
void add_groupE (std::string src, std::string tgt)
 
void add_groupD (std::string src, std::string tgt)
 
void set_defaults ()
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_bb (bool bb_in)
 
bool bb ()
 
void set_chi (bool chi_in)
 
bool chi ()
 
void set_symmetric_sequence (bool symmetric_sequence_in)
 
bool symmetric_sequence ()
 
bool distance_pair ()
 
void set_limit (core::Real limit_in)
 
core::Real limit ()
 
void set_weight (core::Real wt_in)
 
core::Real weight ()
 
void set_sd (core::Real sd_in)
 
core::Real sd ()
 
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...
 
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
 
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...
 

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

utility::vector1< std::string > src_
 
utility::vector1< std::string > tgt_
 
utility::vector1< std::string > srcE_
 
utility::vector1< std::string > tgtE_
 
utility::vector1< std::string > srcD_
 
utility::vector1< std::string > tgtD_
 
bool bb_
 
bool chi_
 
bool symmetric_sequence_
 
bool distance_pair_
 
core::Real limit_
 
core::Real wt_
 
core::Real sd_
 

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::symmetry::SetupNCSMover::SetupNCSMover ( )

References set_defaults().

protocols::symmetry::SetupNCSMover::SetupNCSMover ( std::string  src,
std::string  tgt 
)

References add_group(), and set_defaults().

protocols::symmetry::SetupNCSMover::SetupNCSMover ( std::string  src,
utility::vector1< std::string >  tgt 
)

References add_group(), and set_defaults().

protocols::symmetry::SetupNCSMover::SetupNCSMover ( utility::vector1< std::string >  src,
utility::vector1< std::string >  tgt 
)

References add_group(), and set_defaults().

protocols::symmetry::SetupNCSMover::~SetupNCSMover ( )
overridedefault

Member Function Documentation

void protocols::symmetry::SetupNCSMover::add_group ( std::string  src,
std::string  tgt 
)
void protocols::symmetry::SetupNCSMover::add_groupD ( std::string  src,
std::string  tgt 
)

References srcD_, and tgtD_.

Referenced by parse_my_tag().

void protocols::symmetry::SetupNCSMover::add_groupE ( std::string  src,
std::string  tgt 
)

References srcE_, and tgtE_.

Referenced by parse_my_tag().

void protocols::symmetry::SetupNCSMover::apply ( core::pose::Pose )
overridevirtual
bool protocols::symmetry::SetupNCSMover::bb ( )
inline

References bb_.

bool protocols::symmetry::SetupNCSMover::chi ( )
inline

References chi_.

moves::MoverOP protocols::symmetry::SetupNCSMover::clone ( ) const
inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. 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.

Reimplemented from protocols::moves::Mover.

bool protocols::symmetry::SetupNCSMover::distance_pair ( )
inline

References distance_pair_.

std::string protocols::symmetry::SetupNCSMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::symmetry::SetupNCSMover::limit ( )
inline

References limit_.

std::string protocols::symmetry::SetupNCSMover::mover_name ( )
static
void protocols::symmetry::SetupNCSMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 add_group(), add_groupD(), add_groupE(), bb_, chi_, distance_pair_, limit_, sd_, symmetric_sequence_, protocols::symmetry::TZ(), and wt_.

void protocols::symmetry::SetupNCSMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Real protocols::symmetry::SetupNCSMover::sd ( )
inline

References sd_.

void protocols::symmetry::SetupNCSMover::set_bb ( bool  bb_in)
inline
void protocols::symmetry::SetupNCSMover::set_chi ( bool  chi_in)
inline

References chi_.

void protocols::symmetry::SetupNCSMover::set_defaults ( )

References bb_, chi_, distance_pair_, limit_, sd_, symmetric_sequence_, and wt_.

Referenced by SetupNCSMover().

void protocols::symmetry::SetupNCSMover::set_limit ( core::Real  limit_in)
inline

References limit_.

void protocols::symmetry::SetupNCSMover::set_sd ( core::Real  sd_in)
inline

References sd_.

void protocols::symmetry::SetupNCSMover::set_symmetric_sequence ( bool  symmetric_sequence_in)
inline

References symmetric_sequence_.

void protocols::symmetry::SetupNCSMover::set_weight ( core::Real  wt_in)
inline

References wt_.

bool protocols::symmetry::SetupNCSMover::symmetric_sequence ( )
inline

References symmetric_sequence_.

core::Real protocols::symmetry::SetupNCSMover::weight ( )
inline

References wt_.

Member Data Documentation

bool protocols::symmetry::SetupNCSMover::bb_
private
bool protocols::symmetry::SetupNCSMover::chi_
private
bool protocols::symmetry::SetupNCSMover::distance_pair_
private
core::Real protocols::symmetry::SetupNCSMover::limit_
private
core::Real protocols::symmetry::SetupNCSMover::sd_
private
utility::vector1< std::string > protocols::symmetry::SetupNCSMover::src_
private

Referenced by add_group(), and apply().

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::srcD_
private

Referenced by add_groupD(), and apply().

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::srcE_
private

Referenced by add_groupE(), and apply().

bool protocols::symmetry::SetupNCSMover::symmetric_sequence_
private
utility::vector1< std::string > protocols::symmetry::SetupNCSMover::tgt_
private

Referenced by add_group(), and apply().

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::tgtD_
private

Referenced by add_groupD(), and apply().

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::tgtE_
private

Referenced by add_groupE(), and apply().

core::Real protocols::symmetry::SetupNCSMover::wt_
private

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