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protocols::simple_moves::CombinePoseMover Class Reference

#include <CombinePoseMover.hh>

Inheritance diagram for protocols::simple_moves::CombinePoseMover:
Inheritance graph
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Public Member Functions

 CombinePoseMover (core::scoring::ScoreFunctionCOP sfxn, core::pose::Pose const &pose_ref)
 
 ~CombinePoseMover () override
 
void apply (core::pose::Pose &pose2) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_default ()
 
void set_max_struct (core::Size const n)
 
void set_max_try (core::Size const n)
 
void set_minfrac_crossover (core::Real const value)
 
void set_maxfrac_crossover (core::Real const value)
 
void set_nonideal (bool const setting)
 
void set_minimize (bool const setting)
 
void set_cartesian (bool const setting)
 
void set_rmsdcut (core::Real const setting)
 
core::Size max_struct () const
 
core::Size max_struct_try () const
 
core::pose::Pose const pose_ref () const
 
std::string pose_tag () const
 
void set_pose_tag (std::string const value)
 
void set_store_silents (bool const value)
 
std::vector
< core::io::silent::SilentStructOP
return_silent () const
 
void clear_combine_history ()
 
void append_combine_history (std::vector< core::Size > const v)
 
std::vector< std::vector
< core::Size > > 
return_combine_history () const
 
- 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...
 

Private Attributes

core::pose::Pose pose_ref_
 
core::Size max_struct_
 
core::Size max_struct_try_
 
core::Real minfrac_crossover_
 
core::Real maxfrac_crossover_
 
bool cartesian_crossover_
 
bool nonideal_
 
bool store_silents_
 
bool do_minimize_
 
std::string pose_tag_
 
core::scoring::ScoreFunctionCOP sfxn_
 
core::scoring::ScoreFunctionCOP sfxn0_
 
core::Real vdwcut_
 
core::Real rmsdcut_
 
std::vector< std::vector
< core::Size > > 
combine_history_
 
std::vector
< core::io::silent::SilentStructOP
sampled_structures_
 

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::simple_moves::CombinePoseMover::CombinePoseMover ( core::scoring::ScoreFunctionCOP  sfxn,
core::pose::Pose const &  pose_ref 
)
protocols::simple_moves::CombinePoseMover::~CombinePoseMover ( )
overridedefault

Member Function Documentation

void protocols::simple_moves::CombinePoseMover::append_combine_history ( std::vector< core::Size > const  v)
inline

References combine_history_.

void protocols::simple_moves::CombinePoseMover::apply ( core::pose::Pose )
overridevirtual
void protocols::simple_moves::CombinePoseMover::clear_combine_history ( )
inline

References combine_history_.

std::string protocols::simple_moves::CombinePoseMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

core::Size protocols::simple_moves::CombinePoseMover::max_struct ( ) const
inline

References max_struct_.

core::Size protocols::simple_moves::CombinePoseMover::max_struct_try ( ) const
inline

References max_struct_try_.

core::pose::Pose const protocols::simple_moves::CombinePoseMover::pose_ref ( ) const
inline

References pose_ref_.

std::string protocols::simple_moves::CombinePoseMover::pose_tag ( ) const
inline

References pose_tag_.

std::vector< std::vector< core::Size > > protocols::simple_moves::CombinePoseMover::return_combine_history ( ) const
inline

References combine_history_.

std::vector< core::io::silent::SilentStructOP > protocols::simple_moves::CombinePoseMover::return_silent ( ) const
inline
void protocols::simple_moves::CombinePoseMover::set_cartesian ( bool const  setting)
inline
void protocols::simple_moves::CombinePoseMover::set_default ( )
void protocols::simple_moves::CombinePoseMover::set_max_struct ( core::Size const  n)
inline
void protocols::simple_moves::CombinePoseMover::set_max_try ( core::Size const  n)
inline
void protocols::simple_moves::CombinePoseMover::set_maxfrac_crossover ( core::Real const  value)
inline
void protocols::simple_moves::CombinePoseMover::set_minfrac_crossover ( core::Real const  value)
inline
void protocols::simple_moves::CombinePoseMover::set_minimize ( bool const  setting)
inline

References do_minimize_.

void protocols::simple_moves::CombinePoseMover::set_nonideal ( bool const  setting)
inline
void protocols::simple_moves::CombinePoseMover::set_pose_tag ( std::string const  value)
inline

References pose_tag_.

void protocols::simple_moves::CombinePoseMover::set_rmsdcut ( core::Real const  setting)
inline
void protocols::simple_moves::CombinePoseMover::set_store_silents ( bool const  value)
inline

Member Data Documentation

bool protocols::simple_moves::CombinePoseMover::cartesian_crossover_
private

Referenced by set_cartesian().

std::vector< std::vector< core::Size > > protocols::simple_moves::CombinePoseMover::combine_history_
private
bool protocols::simple_moves::CombinePoseMover::do_minimize_
private

Referenced by set_minimize().

core::Size protocols::simple_moves::CombinePoseMover::max_struct_
private

Referenced by max_struct(), and set_max_struct().

core::Size protocols::simple_moves::CombinePoseMover::max_struct_try_
private

Referenced by max_struct_try(), and set_max_try().

core::Real protocols::simple_moves::CombinePoseMover::maxfrac_crossover_
private

Referenced by set_maxfrac_crossover().

core::Real protocols::simple_moves::CombinePoseMover::minfrac_crossover_
private

Referenced by set_minfrac_crossover().

bool protocols::simple_moves::CombinePoseMover::nonideal_
private

Referenced by set_nonideal().

core::pose::Pose protocols::simple_moves::CombinePoseMover::pose_ref_
private

Referenced by pose_ref().

std::string protocols::simple_moves::CombinePoseMover::pose_tag_
private

Referenced by pose_tag(), and set_pose_tag().

core::Real protocols::simple_moves::CombinePoseMover::rmsdcut_
private

Referenced by set_rmsdcut().

std::vector< core::io::silent::SilentStructOP > protocols::simple_moves::CombinePoseMover::sampled_structures_
private

Referenced by return_silent().

core::scoring::ScoreFunctionCOP protocols::simple_moves::CombinePoseMover::sfxn0_
private
core::scoring::ScoreFunctionCOP protocols::simple_moves::CombinePoseMover::sfxn_
private
bool protocols::simple_moves::CombinePoseMover::store_silents_
private

Referenced by set_store_silents().

core::Real protocols::simple_moves::CombinePoseMover::vdwcut_
private

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