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

#include <VirtualSugarSampler.hh>

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

 VirtualSugarSampler (working_parameters::StepWiseWorkingParametersCOP &working_parameters, SugarModeling &sugar_modeling)
 
 ~VirtualSugarSampler () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Main Method. More...
 
void apply (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &pose_to_visualize) override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_tag (std::string const &setting)
 
void set_use_phenix_geo (bool const &setting)
 
void set_legacy_mode (bool const &setting)
 
void set_choose_random (bool const &setting)
 
void set_keep_base_fixed (bool const &setting)
 
void set_do_minimize (bool const &setting)
 
void set_do_screens (bool const &setting)
 
void set_integration_test_mode (bool const &setting)
 
void set_virtual_sugar_is_from_prior_step (bool const &setting)
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
- Public Member Functions inherited from protocols::moves::MoverForPoseList
 MoverForPoseList ()
 
 ~MoverForPoseList () override
 
virtual void apply (utility::vector1< core::pose::PoseOP > &pose_list)
 
- 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

void setup_sugar_conformations (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &pose)
 
void minimize_sugar (core::pose::Pose &pose_with_sugar)
 
void get_sugar_setup_scorefxns (core::scoring::ScoreFunctionOP &sugar_scorefxn, core::scoring::ScoreFunctionOP &sugar_scorefxn_without_ch_bond, core::scoring::ScoreFunctionOP &rescaled_sugar_score_fxn_without_ch_bond) const
 
void do_chain_closure_modeler (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)
 
void bulge_chain_closure (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)
 
void bulge_chain_closure_complete (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)
 
void bulge_chain_closure_legacy (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)
 
void bulge_chain_minimize_legacy (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)
 
void reinstantiate_backbone_at_moving_res (core::pose::Pose &pose, core::Size const rebuild_res, core::Size const five_prime_chain_break_res)
 
void initialize_pose_variants_for_chain_closure (utility::vector1< core::pose::PoseOP > &pose_list)
 
void restore_pose_variants_after_chain_closure (utility::vector1< core::pose::PoseOP > &pose_list)
 
bool fast_full_atom_VDW_repulsion_screen (core::pose::Pose const &pose, core::Size const res_1, core::Size const res_2, bool const is_prepend)
 
void setup_VDW_bin_checker (core::pose::Pose const &input_pose)
 
void virtualize_distal_partition (core::pose::Pose &input_pose)
 
void reinstantiate_distal_partition (utility::vector1< core::pose::PoseOP > &final_pose_list)
 
void reinstantiate_distal_partition (core::pose::Pose &current_pose)
 
void reinstate_original_constraints (utility::vector1< core::pose::PoseOP > &pose_list)
 

Private Attributes

working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
SugarModelingsugar_modeling_
 
std::string tag_
 
bool use_phenix_geo_
 
bool keep_base_fixed_
 
bool choose_random_
 
bool do_minimize_
 
bool do_screens_
 
bool integration_test_mode_
 
bool virtual_sugar_is_from_prior_step_
 
bool legacy_mode_
 
bool const do_chain_closure_
 
bool const first_minimize_with_fixed_base_
 
core::Size const max_tries_for_random_sugar_setup_
 
bool sugar_setup_success_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
checker::RNA_VDW_BinCheckerOP VDW_bin_checker_
 
utility::vector1< core::Sizedistal_partition_res_
 
utility::vector1< core::Sizealready_virtualized_res_list_
 
bool moving_phosphate_virtualized_
 
core::pose::PoseOP pose_with_original_terminal_phosphates_
 
core::scoring::constraints::ConstraintSetOP original_constraint_set_
 

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::VirtualSugarSampler::VirtualSugarSampler ( working_parameters::StepWiseWorkingParametersCOP working_parameters,
SugarModeling sugar_modeling 
)
protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::~VirtualSugarSampler ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply ( core::pose::Pose )
overridevirtual
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose pose_to_visualize 
)
overridevirtual
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose viewer_pose 
)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_complete ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose viewer_pose 
)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_legacy ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose viewer_pose 
)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_minimize_legacy ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose viewer_pose 
)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_chain_closure_modeler ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose viewer_pose 
)
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen ( core::pose::Pose const &  pose,
core::Size const  res_1,
core::Size const  res_2,
bool const  is_prepend 
)
private
std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::get_sugar_setup_scorefxns ( core::scoring::ScoreFunctionOP sugar_scorefxn,
core::scoring::ScoreFunctionOP sugar_scorefxn_without_ch_bond,
core::scoring::ScoreFunctionOP rescaled_sugar_score_fxn_without_ch_bond 
) const
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::initialize_pose_variants_for_chain_closure ( utility::vector1< core::pose::PoseOP > &  pose_list)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar ( core::pose::Pose pose_with_sugar)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::reinstantiate_backbone_at_moving_res ( core::pose::Pose pose,
core::Size const  rebuild_res,
core::Size const  five_prime_chain_break_res 
)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::reinstantiate_distal_partition ( utility::vector1< core::pose::PoseOP > &  final_pose_list)
private

References virtual_sugar_is_from_prior_step_.

Referenced by apply().

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::reinstantiate_distal_partition ( core::pose::Pose current_pose)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::reinstate_original_constraints ( utility::vector1< core::pose::PoseOP > &  pose_list)
private

References original_constraint_set_.

Referenced by apply().

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::restore_pose_variants_after_chain_closure ( utility::vector1< core::pose::PoseOP > &  pose_list)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_choose_random ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_do_minimize ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_do_screens ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_integration_test_mode ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_keep_base_fixed ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_legacy_mode ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_tag ( std::string const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_use_phenix_geo ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_virtual_sugar_is_from_prior_step ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_sugar_conformations ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose pose 
)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker ( core::pose::Pose const &  input_pose)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition ( core::pose::Pose input_pose)
private

Member Data Documentation

utility::vector1< core::Size > protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::already_virtualized_res_list_
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::choose_random_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::distal_partition_res_
private
bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_chain_closure_
private

Referenced by apply(), and setup_sugar_conformations().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_minimize_
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_screens_
private
bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::first_minimize_with_fixed_base_
private

Referenced by minimize_sugar().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::integration_test_mode_
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::keep_base_fixed_
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::legacy_mode_
private
core::Size const protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::max_tries_for_random_sugar_setup_
private

Referenced by apply(), and setup_sugar_conformations().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::moving_phosphate_virtualized_
private
core::scoring::constraints::ConstraintSetOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::original_constraint_set_
private
core::pose::PoseOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::pose_with_original_terminal_phosphates_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::scorefxn_
private
SugarModeling& protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::sugar_modeling_
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::sugar_setup_success_
private

Referenced by apply(), and setup_sugar_conformations().

std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::tag_
private

Referenced by apply(), and set_tag().

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::use_phenix_geo_
private
checker::RNA_VDW_BinCheckerOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::VDW_bin_checker_
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtual_sugar_is_from_prior_step_
private
working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::working_parameters_
private

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