Rosetta Protocols  2014.16.56682
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler Class Reference

#include <StepWiseRNA_ClassicResidueSampler.hh>

Public Member Functions

 StepWiseRNA_ClassicResidueSampler (StepWiseRNA_JobParametersCOP &job_parameters_)
 
 ~StepWiseRNA_ClassicResidueSampler ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_extra_tag (std::string const setting)
 
void set_silent_file (std::string const &setting)
 
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
void set_pose_list (utility::vector1< PoseOP > &pose_list)
 
utility::vector1< PoseOP > & pose_list ()
 
void set_base_centroid_checker (checker::RNA_BaseCentroidCheckerOP &checker)
 
void set_user_input_VDW_bin_checker (checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)
 
void set_rebuild_bulge_mode (bool const &setting)
 
void set_options (StepWiseRNA_ModelerOptionsCOP options)
 
- Public Member Functions inherited from protocols::moves::MoverForPoseList
 MoverForPoseList ()
 
 ~MoverForPoseList ()
 
virtual void apply (utility::vector1< core::pose::PoseOP > &pose_list)
 
virtual void apply (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Mover & operator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 Strings & info ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void initialize_poses_and_checkers (core::pose::Pose &pose)
 
bool break_early_for_integration_tests ()
 
void output_count_data ()
 
Size get_num_pose_kept ()
 
bool bulge_variant_decision (core::pose::Pose &pose, Real const &delta_atr_score)
 
void apply_bulge_variant (core::pose::Pose &pose) const
 

Private Attributes

StepWiseRNA_JobParametersCOP job_parameters_
 
Size const moving_res_
 
Size const moving_suite_
 
bool const is_prepend_
 
bool const is_internal_
 
Size const actually_moving_res_
 
Size const gap_size_
 
utility::vector1< core::Size >
const 		working_moving_partition_pos_
 
Size const num_nucleotides_
 
bool const is_dinucleotide_
 
bool const close_chain_to_distal_
 
Size const five_prime_chain_break_res_
 
Size const last_append_res_
 
Size const last_prepend_res_
 
Real const atom_atom_overlap_dist_cutoff_
 
std::string extra_tag_
 
bool const build_pose_from_scratch_
 
bool kic_sampling_
 
bool rebuild_bulge_mode_
 
utility::vector1< PoseOP > pose_list_
 
core::scoring::ScoreFunctionOP scorefxn_
 
StepWiseRNA_CountStruct count_data_
 
std::string silent_file_
 
bool native_rmsd_screen_
 
core::Real const bin_size_
 
checker::AtrRepCheckerOP atr_rep_checker_
 
checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker_
 
checker::ChainClosableGeometryCheckerOP chain_closable_geometry_checker_
 
checker::ChainClosureCheckerOP chain_closure_checker_
 
checker::RNA_BaseCentroidCheckerOP base_centroid_checker_
 
pose::PoseOP screening_pose_
 
StepWiseRNA_PoseSelectionOP pose_selection_
 
o2prime::O2PrimePackerOP o2prime_packer_
 
phosphate::MultiPhosphateSamplerOP phosphate_sampler_
 
StepWiseRNA_ModelerOptionsCOP options_
 
rotamer_sampler::RotamerBaseOP rotamer_sampler_
 

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
protocols::filters::Filters_map 		Filters_map
 
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::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::StepWiseRNA_ClassicResidueSampler ( StepWiseRNA_JobParametersCOP &  job_parameters_)

References job_parameters_, length, num_nucleotides_, rebuild_bulge_mode, scoring, protocols::moves::Mover::set_native_pose(), size(), and utility_exit_with_message.

protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::~StepWiseRNA_ClassicResidueSampler ( )

Member Function Documentation

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply ( core::pose::Pose &  pose_to_visualize)
virtual

Implements protocols::moves::MoverForPoseList.

References actually_moving_res_, apply_bulge_variant(), atom_atom_overlap_dist_cutoff_, atr_rep_checker_, base_centroid_checker_, break_early_for_integration_tests(), build_pose_from_scratch_, bulge_variant_decision(), chain_closable_geometry_checker_, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::chain_closable_geometry_count, chain_closure_checker_, protocols::stepwise::sampling::rna::checker::ChainClosureChecker::check_loop_closed(), protocols::stepwise::sampling::rna::checker::ChainClosureChecker::check_screen(), protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::check_that_terminal_res_are_unstacked(), close_chain_to_distal_, protocols::stepwise::sampling::rna::checker::ChainClosureChecker::copy_CCD_torsions(), count_data_, protocols::stepwise::sampling::rna::create_rotamer_string(), protocols::stepwise::sampling::rna::create_tag(), extra_tag_, protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::finalize(), gap_size_, protocols::moves::Mover::get_native_pose(), protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::good_bin_rep_count, initialize_poses_and_checkers(), is_internal_, is_prepend_, protocols::stepwise::sampling::rna::is_residues_in_contact(), job_parameters_, kic_sampling_, last_append_res_, last_prepend_res_, moving_res_, native_rmsd_screen_, num_nucleotides_, o2prime_packer_, options_, output_count_data(), protocols::stepwise::sampling::rna::output_data(), protocols::stepwise::sampling::rna::output_title_text(), phosphate_sampler_, protocols::stepwise::sampling::rna::checker::ChainClosureChecker::pose(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::pose_list(), pose_list_, pose_selection_, protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::pose_selection_by_full_score(), protocols::stepwise::sampling::rna::remove_virtual_rna_residue_variant_type(), protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::residues_contact_screen, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::rmsd_count, protocols::stepwise::sampling::rna::rmsd_over_residue_list(), rotamer_sampler_, screening_pose_, silent_file_, protocols::stepwise::sampling::rna::suite_rmsd(), tag, tag_into_pose(), protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::tot_rotamer_count, protocols::TR, protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::update_base_stub_list_and_check_centroid_interaction(), user_input_VDW_bin_checker_, protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose(), utility_exit_with_message, protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), and working_moving_partition_pos_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply_bulge_variant ( core::pose::Pose &  pose) const
private

References protocols::stepwise::sampling::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::sampling::rna::is_virtual_base(), moving_res_, core::pose::Pose::residue(), and runtime_assert.

Referenced by apply().

bool protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::break_early_for_integration_tests ( )
private

References protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::both_count, count_data_, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::full_score_count, native_rmsd_screen_, options_, and protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::rmsd_count.

Referenced by apply().

bool protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::bulge_variant_decision ( core::pose::Pose &  pose,
Real const &  delta_atr_score 
)
private

References protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::both_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::bulge_at_chain_closure_count, count_data_, protocols::stepwise::sampling::rna::is_virtual_base(), moving_res_, options_, rebuild_bulge_mode_, core::pose::Pose::residue(), runtime_assert, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::tot_rotamer_count, and protocols::TR.

Referenced by apply().

std::string protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

Size protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::get_num_pose_kept ( )
private

References build_pose_from_scratch_, job_parameters_, options_, and protocols::TR.

Referenced by initialize_poses_and_checkers().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers ( core::pose::Pose &  pose)
private

References protocols::stepwise::sampling::rna::add_harmonic_chain_break_constraint(), protocols::stepwise::sampling::rna::add_virtual_O2Prime_hydrogen(), atom_atom_overlap_dist_cutoff_, atr_rep_checker_, base_centroid_checker_, build_pose_from_scratch_, chain_closable_geometry_checker_, chain_closure_checker_, core::pose::Pose::clone(), close_chain_to_distal_, five_prime_chain_break_res_, gap_size_, get_num_pose_kept(), job_parameters_, kic_sampling_, last_append_res_, last_prepend_res_, native_rmsd_screen_, o2prime_packer_, options_, phosphate_sampler_, pose_list_, pose_selection_, protocols::stepwise::sampling::rna::phosphate::remove_terminal_phosphates(), rotamer_sampler_, runtime_assert, scorefxn_, screening_pose_, protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_cluster_rmsd(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_distinguish_pucker(), set_extra_tag(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_num_pose_kept(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_PBP_clustering_at_chain_closure(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_pose_list(), protocols::stepwise::sampling::rna::checker::ChainClosureChecker::set_reinitialize_CCD_torsions(), protocols::rotamer_sampler::rna::setup_rotamer_sampler(), tag_from_pose(), protocols::TR, and working_moving_partition_pos_.

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::output_count_data ( )
private

References atr_rep_checker_, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::base_pairing_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::base_stack_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::bulge_at_chain_closure_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::chain_break_screening_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::chain_closable_geometry_count, close_chain_to_distal_, count_data_, gap_size_, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::good_angle_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::good_distance_count, options_, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::residues_contact_screen, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::rmsd_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::strict_base_pairing_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::tot_rotamer_count, and protocols::TR.

Referenced by apply().

utility::vector1< pose::PoseOP > & protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::pose_list ( )

References pose_list_.

Referenced by set_pose_list(), and protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_base_centroid_checker ( checker::RNA_BaseCentroidCheckerOP &  checker)

References base_centroid_checker_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_extra_tag ( std::string const  setting)
inline

Referenced by initialize_poses_and_checkers().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_options ( StepWiseRNA_ModelerOptionsCOP  options)

References options_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_pose_list ( utility::vector1< PoseOP > &  pose_list)

References pose_list(), and pose_list_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_rebuild_bulge_mode ( bool const &  setting)
inline
void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References scorefxn_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_silent_file ( std::string const &  setting)
inline

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::set_user_input_VDW_bin_checker ( checker::RNA_VDW_BinCheckerOP const &  user_input_VDW_bin_checker)

References user_input_VDW_bin_checker_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling().

Member Data Documentation

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::actually_moving_res_
private

Referenced by apply().

Real const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::atom_atom_overlap_dist_cutoff_
private

Referenced by apply(), and initialize_poses_and_checkers().

checker::AtrRepCheckerOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::atr_rep_checker_
private

Referenced by apply(), initialize_poses_and_checkers(), and output_count_data().

checker::RNA_BaseCentroidCheckerOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::base_centroid_checker_
private

Referenced by apply(), initialize_poses_and_checkers(), and set_base_centroid_checker().

core::Real const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::bin_size_
private
bool const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::build_pose_from_scratch_
private

Referenced by apply(), get_num_pose_kept(), and initialize_poses_and_checkers().

checker::ChainClosableGeometryCheckerOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::chain_closable_geometry_checker_
private

Referenced by apply(), and initialize_poses_and_checkers().

checker::ChainClosureCheckerOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::chain_closure_checker_
private

Referenced by apply(), and initialize_poses_and_checkers().

bool const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::close_chain_to_distal_
private

Referenced by apply(), initialize_poses_and_checkers(), and output_count_data().

StepWiseRNA_CountStruct protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::count_data_
private

Referenced by apply(), break_early_for_integration_tests(), bulge_variant_decision(), and output_count_data().

std::string protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::extra_tag_
private

Referenced by apply().

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::five_prime_chain_break_res_
private

Referenced by initialize_poses_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::gap_size_
private

Referenced by apply(), initialize_poses_and_checkers(), and output_count_data().

bool const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::is_dinucleotide_
private
bool const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::is_internal_
private

Referenced by apply().

bool const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::is_prepend_
private

Referenced by apply().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::job_parameters_
private

Referenced by apply(), get_num_pose_kept(), initialize_poses_and_checkers(), and StepWiseRNA_ClassicResidueSampler().

bool protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::kic_sampling_
private

Referenced by apply(), and initialize_poses_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::last_append_res_
private

Referenced by apply(), and initialize_poses_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::last_prepend_res_
private

Referenced by apply(), and initialize_poses_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::moving_res_
private

Referenced by apply(), apply_bulge_variant(), and bulge_variant_decision().

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::moving_suite_
private
bool protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::native_rmsd_screen_
private

Referenced by apply(), break_early_for_integration_tests(), and initialize_poses_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::num_nucleotides_
private

Referenced by apply(), and StepWiseRNA_ClassicResidueSampler().

o2prime::O2PrimePackerOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::o2prime_packer_
private

Referenced by apply(), and initialize_poses_and_checkers().

StepWiseRNA_ModelerOptionsCOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::options_
private

Referenced by apply(), break_early_for_integration_tests(), bulge_variant_decision(), get_num_pose_kept(), initialize_poses_and_checkers(), output_count_data(), and set_options().

phosphate::MultiPhosphateSamplerOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::phosphate_sampler_
private

Referenced by apply(), and initialize_poses_and_checkers().

utility::vector1< PoseOP > protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::pose_list_
private

Referenced by apply(), initialize_poses_and_checkers(), pose_list(), and set_pose_list().

StepWiseRNA_PoseSelectionOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::pose_selection_
private

Referenced by apply(), and initialize_poses_and_checkers().

bool protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::rebuild_bulge_mode_
private

Referenced by bulge_variant_decision().

rotamer_sampler::RotamerBaseOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::rotamer_sampler_
private

Referenced by apply(), and initialize_poses_and_checkers().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::scorefxn_
private

Referenced by initialize_poses_and_checkers(), and set_scorefxn().

pose::PoseOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::screening_pose_
private

Referenced by apply(), and initialize_poses_and_checkers().

std::string protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::silent_file_
private

Referenced by apply().

checker::RNA_VDW_BinCheckerOP protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::user_input_VDW_bin_checker_
private

Referenced by apply(), and set_user_input_VDW_bin_checker().

utility::vector1< core::Size > const protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::working_moving_partition_pos_
private

Referenced by apply(), and initialize_poses_and_checkers().

The documentation for this class was generated from the following files:
Generated on Mon Apr 21 2014 16:43:59 for Rosetta Protocols by   doxygen 1.8.7