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protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList Class Reference

#include <VirtualSugarSamplerFromStringList.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList:
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Public Member Functions

 VirtualSugarSamplerFromStringList (working_parameters::StepWiseWorkingParametersCOP &working_parameters, utility::vector1< std::string > const &sample_virtual_sugar_string_list)
 
 ~VirtualSugarSamplerFromStringList () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
void set_use_phenix_geo (bool const &setting)
 
void set_legacy_mode (bool const &setting)
 
void set_choose_random (bool const &setting)
 
void set_integration_test_mode (bool const &setting)
 
void set_tag (std::string const &setting)
 
void set_silent_file_out (std::string const &setting)
 
- 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 Member Functions

utility::vector1< SugarModelingsetup_sugar_modeling_list (core::pose::Pose const &pose) const
 
bool empty_sugar_modeling_list (utility::vector1< SugarModeling > const &sugar_modeling_list)
 
bool empty_pose_data_list (utility::vector1< core::pose::PoseOP > const &pose_list, core::Size const n, std::string tag)
 
void output_pose_data_list (utility::vector1< core::pose::PoseOP > &pose_data_list)
 

Private Attributes

working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
utility::vector1< std::string >
const 
sample_virtual_sugar_string_list_
 
std::string silent_file_out_
 
bool use_phenix_geo_
 
bool legacy_mode_
 
bool choose_random_
 
bool integration_test_mode_
 
std::string tag_
 
core::scoring::ScoreFunctionOP scorefxn_
 

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::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::VirtualSugarSamplerFromStringList ( working_parameters::StepWiseWorkingParametersCOP working_parameters,
utility::vector1< std::string > const &  sample_virtual_sugar_string_list 
)
protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::~VirtualSugarSamplerFromStringList ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply(), choose_random_, core::conformation::Conformation::clone(), core::pose::full_model_info::FullModelInfo::clone_info(), core::pose::Pose::conformation(), empty_pose_data_list(), empty_sugar_modeling_list(), integration_test_mode_, legacy_mode_, protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), protocols::stepwise::modeler::rna::sugar::modeler_starting_pose_data_list(), core::pose::full_model_info::nonconst_full_model_info(), output_pose_data_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::sugar::SugarModeling::pose_list, scorefxn_, protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_choose_random(), core::pose::full_model_info::set_full_model_info(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_integration_test_mode(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_legacy_mode(), core::pose::Pose::set_new_conformation(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_scorefxn(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_tag(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_use_phenix_geo(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_virtual_sugar_is_from_prior_step(), setup_sugar_modeling_list(), core::pose::sort_pose_by_score(), core::pose::tag_into_pose(), protocols::TR(), use_phenix_geo_, and working_parameters_.

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::empty_pose_data_list ( utility::vector1< core::pose::PoseOP > const &  pose_list,
core::Size const  n,
std::string  tag 
)
private

References silent_file_out_, and protocols::TR().

Referenced by apply().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::empty_sugar_modeling_list ( utility::vector1< SugarModeling > const &  sugar_modeling_list)
private

References silent_file_out_, and protocols::TR().

Referenced by apply().

std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::output_pose_data_list ( utility::vector1< core::pose::PoseOP > &  pose_data_list)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_choose_random ( bool const &  setting)
inline

References choose_random_.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_integration_test_mode ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_legacy_mode ( bool const &  setting)
inline

References legacy_mode_.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References scorefxn_.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_silent_file_out ( std::string const &  setting)
inline

References silent_file_out_.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_tag ( std::string const &  setting)
inline

References tag_.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_use_phenix_geo ( bool const &  setting)
inline

References use_phenix_geo_.

utility::vector1< SugarModeling > protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list ( core::pose::Pose const &  pose) const
private

Member Data Documentation

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::choose_random_
private

Referenced by apply(), and set_choose_random().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::integration_test_mode_
private

Referenced by apply(), and set_integration_test_mode().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::legacy_mode_
private

Referenced by apply(), and set_legacy_mode().

utility::vector1< std::string > const protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::sample_virtual_sugar_string_list_
private
core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::scorefxn_
private

Referenced by apply(), and set_scorefxn().

std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::silent_file_out_
private
std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::tag_
private

Referenced by output_pose_data_list(), and set_tag().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::use_phenix_geo_
private

Referenced by apply(), and set_use_phenix_geo().

working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::working_parameters_
private

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