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protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler Class Reference

#include <StepWiseRNA_AnalyticalLoopCloseSampler.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler:
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Collaboration diagram for protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler:
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Public Member Functions

 StepWiseRNA_AnalyticalLoopCloseSampler (StepWiseRNA_JobParametersCOP &job_parameters_)
 
 ~StepWiseRNA_AnalyticalLoopCloseSampler ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_centroid_screen (bool const setting)
 
void set_base_pairing_only_screen (bool const setting)
 
void set_VDW_atr_rep_screen (bool const setting)
 
void set_silent_file (std::string const &setting)
 
void set_output_filename (std::string const &output_filename)
 
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
void set_fast (bool const &setting)
 
void set_medium_fast (bool const &setting)
 
void set_native_rmsd_screen (bool const &setting)
 
void set_native_screen_rmsd_cutoff (core::Real const &setting)
 
void set_verbose (bool const &setting)
 
void set_o2star_screen (bool const &setting)
 
void set_cluster_rmsd (core::Real const &setting)
 
utility::vector1
< pose_data_struct2 > & 
get_pose_data_list ()
 
core::io::silent::SilentFileDataOPsilent_file_data ()
 
void output_pose_data_list (std::string const final_sampler_output_silent_file) const
 
void set_num_pose_kept (core::Size const &num_pose_kept)
 
void set_base_centroid_screener (StepWiseRNA_BaseCentroidScreenerOP &screener)
 
void set_distinguish_pucker (bool const &setting)
 
void set_finer_sampling_at_chain_closure (bool const &setting)
 
void set_PBP_clustering_at_chain_closure (bool const &setting)
 
void set_user_input_VDW_bin_screener (StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)
 
void set_allow_syn_pyrimidine (bool const &setting)
 
void set_extra_syn_chi_rotamer (bool const &setting)
 
void set_extra_anti_chi_rotamer (bool const &setting)
 
void set_use_phenix_geo (bool const &setting)
 
- 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)
 
Moveroperator= (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
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void initialize_scorefunctions ()
 
void standard_sampling (core::pose::Pose &pose, utility::vector1< pose_data_struct2 > &pose_data_list)
 
void copy_suite_torsion (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const &suite_num)
 
void get_base_atr_rep_score (core::pose::Pose const &pose, core::Real &base_atr_score, core::Real &base_rep_score)
 
bool Full_atom_van_der_Waals_screening_REPLICATE (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)
 
bool Full_atom_van_der_Waals_screening (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)
 
void initialize_o2star_packer_task (core::pose::Pose const &pose)
 
void sample_o2star_hydrogen (core::pose::Pose &pose, core::pose::Pose &pose_with_original_HO2star_torsion)
 
core::Real Pose_selection_by_full_score (utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose &current_pose, std::string const &tag)
 
void Update_pose_data_list (std::string const &tag, utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose const &current_pose, core::Real const &current_score) const
 
void cluster_pose_data_list (utility::vector1< pose_data_struct2 > &pose_data_list)
 
std::string create_tag (std::string const prestring, StepWiseRNA_RotamerGenerator_WrapperOP const &rotamer_generator) const
 
std::string create_torsion_value_string (core::Real const &torsion_value) const
 
std::string create_rotamer_string (core::pose::Pose const &pose) const
 

Private Attributes

StepWiseRNA_JobParametersCOP job_parameters_
 
core::io::silent::SilentFileDataOP sfd_
 
utility::vector1
< pose_data_struct2
pose_data_list_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP atr_rep_screening_scorefxn_
 
core::scoring::ScoreFunctionOP sampling_scorefxn_
 
core::scoring::ScoreFunctionOP o2star_pack_scorefxn_
 
core::scoring::ScoreFunctionOP chainbreak_scorefxn_
 
utility::vector1< core::Sizeworking_rmsd_res_
 
SillyCountStruct count_data_
 
std::string silent_file_
 
std::string output_filename_
 
core::Real const bin_size_
 
core::Real const rep_cutoff_
 
core::Size num_pose_kept_
 
core::Size const multiplier_
 
core::Real cluster_rmsd_
 
bool verbose_
 
bool native_rmsd_screen_
 
core::Real native_screen_rmsd_cutoff_
 
bool o2star_screen_
 
core::pack::task::PackerTaskOP o2star_pack_task_
 
bool fast_
 
bool medium_fast_
 
StepWiseRNA_BaseCentroidScreenerOP base_centroid_screener_
 
bool centroid_screen_
 
bool base_pairing_only_screen_
 
bool VDW_atr_rep_screen_
 
bool distinguish_pucker_
 
core::Real current_score_cutoff_
 
bool finer_sampling_at_chain_closure_
 
bool PBP_clustering_at_chain_closure_
 
bool extra_anti_chi_rotamer_
 
bool extra_syn_chi_rotamer_
 
bool allow_syn_pyrimidine_
 
bool use_phenix_geo_
 
StepWiseRNA_VDW_Bin_ScreenerOP user_input_VDW_bin_screener_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::StepWiseRNA_AnalyticalLoopCloseSampler ( StepWiseRNA_JobParametersCOP job_parameters_)
protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::~StepWiseRNA_AnalyticalLoopCloseSampler ( )

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::apply ( core::pose::Pose pose_to_visualize)
virtual
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list ( utility::vector1< pose_data_struct2 > &  pose_data_list)
private
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::copy_suite_torsion ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
core::Size const &  suite_num 
)
private
std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_rotamer_string ( core::pose::Pose const &  pose) const
private
std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_tag ( std::string const  prestring,
StepWiseRNA_RotamerGenerator_WrapperOP const &  rotamer_generator 
) const
private
std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_torsion_value_string ( core::Real const &  torsion_value) const
private

Referenced by create_rotamer_string().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Full_atom_van_der_Waals_screening ( core::pose::Pose current_pose_screen,
core::Real const &  base_rep_score,
core::Real const &  base_atr_score,
core::Real delta_rep_score,
core::Real delta_atr_score,
core::Size const &  gap_size,
bool const &  Is_internal 
)
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Full_atom_van_der_Waals_screening_REPLICATE ( core::pose::Pose current_pose_screen,
core::Real const &  base_rep_score,
core::Real const &  base_atr_score,
core::Real delta_rep_score,
core::Real delta_atr_score,
core::Size const &  gap_size,
bool const &  Is_internal 
)
private
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_base_atr_rep_score ( core::pose::Pose const &  pose,
core::Real base_atr_score,
core::Real base_rep_score 
)
private
virtual std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_name ( ) const
inlinevirtual

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

Implements protocols::moves::Mover.

utility::vector1< pose_data_struct2 > & protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_pose_data_list ( )

References pose_data_list_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_o2star_packer_task ( core::pose::Pose const &  pose)
private
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_scorefunctions ( )
private
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::output_pose_data_list ( std::string const  final_sampler_output_silent_file) const
Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Pose_selection_by_full_score ( utility::vector1< pose_data_struct2 > &  pose_data_list,
core::pose::Pose current_pose,
std::string const &  tag 
)
private
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::sample_o2star_hydrogen ( core::pose::Pose pose,
core::pose::Pose pose_with_original_HO2star_torsion 
)
private
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_allow_syn_pyrimidine ( bool const &  setting)
inline

References allow_syn_pyrimidine_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_base_centroid_screener ( StepWiseRNA_BaseCentroidScreenerOP screener)
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_base_pairing_only_screen ( bool const  setting)
inline
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_centroid_screen ( bool const  setting)
inline

References centroid_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_cluster_rmsd ( core::Real const &  setting)

References cluster_rmsd_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_distinguish_pucker ( bool const &  setting)
inline

References distinguish_pucker_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_extra_anti_chi_rotamer ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_extra_syn_chi_rotamer ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_fast ( bool const &  setting)

References fast_, and num_pose_kept_.

Referenced by set_num_pose_kept().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_finer_sampling_at_chain_closure ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_medium_fast ( bool const &  setting)

References medium_fast_, and num_pose_kept_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_native_rmsd_screen ( bool const &  setting)

References native_rmsd_screen_.

Referenced by set_num_pose_kept().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_native_screen_rmsd_cutoff ( core::Real const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_num_pose_kept ( core::Size const &  num_pose_kept)
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_o2star_screen ( bool const &  setting)

References o2star_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_output_filename ( std::string const &  output_filename)

References output_filename_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_PBP_clustering_at_chain_closure ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References scorefxn_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_silent_file ( std::string const &  setting)

References silent_file_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_use_phenix_geo ( bool const &  setting)
inline

References use_phenix_geo_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_user_input_VDW_bin_screener ( StepWiseRNA_VDW_Bin_ScreenerOP const &  user_input_VDW_bin_screener)
void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_VDW_atr_rep_screen ( bool const  setting)
inline

References VDW_atr_rep_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_verbose ( bool const &  setting)

References verbose_.

core::io::silent::SilentFileDataOP & protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::silent_file_data ( )

References sfd_.

Referenced by output_pose_data_list(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling ( core::pose::Pose pose,
utility::vector1< pose_data_struct2 > &  pose_data_list 
)
private

References core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::Add_virtual_O2Star_hydrogen(), allow_syn_pyrimidine_, protocols::swa::rna::ANTI, protocols::rna::RNA_IdealCoord::apply(), protocols::swa::rna::RNA_LoopCloseSampler::apply(), base_centroid_screener_, protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, core::id::BB, protocols::swa::rna::BOTH, protocols::swa::rna::SillyCountStruct::both_count, protocols::swa::rna::SillyCountStruct::bulge_at_chain_closure_count, centroid_screen_, protocols::swa::rna::SillyCountStruct::chain_break_screening_count, protocols::swa::rna::SillyCountStruct::chain_closable_count, core::id::CHI, protocols::swa::rna::RNA_LoopCloseSampler::clear_all(), cluster_pose_data_list(), copy_suite_torsion(), count_data_, distinguish_pucker_, extra_anti_chi_rotamer_, extra_syn_chi_rotamer_, protocols::swa::rna::RNA_LoopCloseSampler::fill_pose(), finer_sampling_at_chain_closure_, Full_atom_van_der_Waals_screening(), get_base_atr_rep_score(), protocols::moves::Mover::get_native_pose(), protocols::swa::rna::SillyCountStruct::good_angle_count, protocols::swa::rna::SillyCountStruct::good_atr_rotamer_count, protocols::swa::rna::SillyCountStruct::good_bin_rep_count, protocols::swa::rna::SillyCountStruct::good_distance_count, protocols::swa::rna::SillyCountStruct::good_rep_rotamer_count, initialize_o2star_packer_task(), core::scoring::rna::is_purine(), job_parameters_, protocols::swa::rna::RNA_LoopCloseSampler::n_construct(), native_rmsd_screen_, native_screen_rmsd_cutoff_, protocols::swa::rna::NORTH, num_pose_kept_, o2star_screen_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_data(), protocols::swa::rna::Output_title_text(), pose_data_list_, Pose_selection_by_full_score(), core::pose::Pose::residue(), protocols::swa::rna::SillyCountStruct::rmsd_count, protocols::swa::rna::rmsd_over_residue_list(), sample_o2star_hydrogen(), scorefxn_, protocols::swa::rna::RNA_LoopCloseSampler::set_bin_size(), protocols::swa::rna::RNA_LoopCloseSampler::set_epsilon_range(), protocols::swa::rna::RNA_LoopCloseSampler::set_sample_native_torsion(), protocols::swa::rna::RNA_LoopCloseSampler::set_sample_only(), protocols::swa::rna::RNA_LoopCloseSampler::set_scorefxn(), silent_file_, silent_file_data(), protocols::swa::rna::sort_criteria2(), protocols::swa::rna::SOUTH, protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::suite_rmsd(), protocols::swa::rna::SillyCountStruct::tot_rotamer_count, use_phenix_geo_, user_input_VDW_bin_screener_, and verbose_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Update_pose_data_list ( std::string const &  tag,
utility::vector1< pose_data_struct2 > &  pose_data_list,
core::pose::Pose const &  current_pose,
core::Real const &  current_score 
) const
private

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::allow_syn_pyrimidine_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::atr_rep_screening_scorefxn_
private
StepWiseRNA_BaseCentroidScreenerOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::base_centroid_screener_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::base_pairing_only_screen_
private
core::Real const protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::bin_size_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::centroid_screen_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::chainbreak_scorefxn_
private
core::Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_rmsd_
private
SillyCountStruct protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::count_data_
private
core::Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::current_score_cutoff_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::distinguish_pucker_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::extra_anti_chi_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::extra_syn_chi_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::fast_
private

Referenced by set_fast(), and set_num_pose_kept().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::finer_sampling_at_chain_closure_
private
StepWiseRNA_JobParametersCOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::job_parameters_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::medium_fast_
private

Referenced by set_medium_fast().

core::Size const protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::multiplier_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::native_rmsd_screen_
private
core::Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::native_screen_rmsd_cutoff_
private
core::Size protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::num_pose_kept_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::o2star_pack_scorefxn_
private
core::pack::task::PackerTaskOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::o2star_pack_task_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::o2star_screen_
private
std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::output_filename_
private

Referenced by set_output_filename().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::PBP_clustering_at_chain_closure_
private
utility::vector1< pose_data_struct2 > protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::pose_data_list_
private
core::Real const protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::rep_cutoff_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::sampling_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::scorefxn_
private
core::io::silent::SilentFileDataOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::sfd_
private

Referenced by silent_file_data().

std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::silent_file_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::use_phenix_geo_
private
StepWiseRNA_VDW_Bin_ScreenerOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::user_input_VDW_bin_screener_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::VDW_atr_rep_screen_
private
bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::verbose_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::working_rmsd_res_
private

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