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protocols::swa::rna::StepWiseRNA_ResidueSampler Class Reference

#include <StepWiseRNA_ResidueSampler.hh>

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

 StepWiseRNA_ResidueSampler (StepWiseRNA_JobParametersCOP &job_parameters_)
 
 ~StepWiseRNA_ResidueSampler ()
 
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_allow_base_pair_only_centroid_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_integration_test_mode (bool const &setting)
 
void set_verbose (bool const &setting)
 
void set_perform_o2star_pack (bool const &setting)
 
void set_cluster_rmsd (core::Real const &setting)
 
void set_allow_bulge_at_chainbreak (bool 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_parin_favorite_output (bool const &setting)
 
void set_floating_base (bool const &setting)
 
void set_include_syn_chi (bool const &setting)
 
void set_allow_syn_pyrimidine (bool const &setting)
 
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_reinitialize_CCD_torsions (bool const &setting)
 
void set_user_input_VDW_bin_screener (StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)
 
void set_extra_epsilon_rotamer (bool const &setting)
 
void set_extra_beta_rotamer (bool const &setting)
 
void set_extra_anti_chi_rotamer (bool const &setting)
 
void set_extra_syn_chi_rotamer (bool const &setting)
 
void set_sample_both_sugar_base_rotamer (bool const &setting)
 
void set_include_torsion_value_in_tag (bool const &setting)
 
void set_rebuild_bulge_mode (bool const &setting)
 
void set_debug_eplison_south_sugar_mode (bool const &setting)
 
void set_exclude_alpha_beta_gamma_sampling (bool const &setting)
 
void set_combine_long_loop_mode (bool const &setting)
 
void set_do_not_sample_multiple_virtual_sugar (bool const &setting)
 
void set_sample_ONLY_multiple_virtual_sugar (bool const &setting)
 
void set_assert_no_virt_ribose_sampling (bool const &setting)
 
void set_output_pdb (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 Copy_CCD_torsions (core::pose::Pose &pose, core::pose::Pose const &template_pose) const
 
void Copy_CCD_torsions_general (core::pose::Pose &pose, core::pose::Pose const &template_pose, core::Size const five_prime_res, core::Size const three_prime_res) const
 
bool Chain_break_screening (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &constraint_scorefxn)
 
bool Chain_break_screening_general (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, core::Size const five_prime_res)
 
void standard_sampling_WRAPPER (core::pose::Pose &pose, FloatingBaseChainClosureJobParameter const &prev_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &curr_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &five_prime_CB_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &three_prime_CB_sugar_FB_JP)
 
void standard_sampling (core::pose::Pose &pose, utility::vector1< pose_data_struct2 > &pose_data_list, std::string const sugar_tag)
 
void floating_base_sampling (core::pose::Pose &pose, FloatingBaseChainClosureJobParameter const &prev_sugar_FB_JP)
 
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 initialize_o2star_green_packer (core::pose::Pose &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)
 
bool apply_bulge_variant (core::pose::Pose &pose, core::Real const &delta_atr_score)
 
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
 
core::kinematics::Stub get_reference_stub (core::Size const reference_res, core::pose::Pose const &pose) const
 
std::string create_torsion_value_string (core::Real const &torsion_value) const
 
std::string create_rotamer_string (core::pose::Pose const &pose) const
 
bool Is_previous_sugar_virtual (core::pose::Pose const &pose) const
 
bool Is_current_sugar_virtual (core::pose::Pose const &pose) const
 
bool Is_five_prime_chain_break_sugar_virtual (core::pose::Pose const &pose) const
 
bool Is_three_prime_chain_break_sugar_virtual (core::pose::Pose const &pose) const
 
utility::vector1
< pose_data_struct2
previous_floating_base_chain_closure (core::pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, std::string const name)
 

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 chainbreak_scorefxn_
 
core::scoring::ScoreFunctionOP sampling_scorefxn_
 
core::scoring::ScoreFunctionOP o2star_pack_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 perform_o2star_pack_
 
core::pack::task::PackerTaskOP o2star_pack_task_
 
protocols::simple_moves::GreenPackerOP o2star_green_packer_
 
bool const use_green_packer_
 
bool allow_bulge_at_chainbreak_
 
bool fast_
 
bool medium_fast_
 
bool integration_test_mode_
 
bool floating_base_
 
StepWiseRNA_BaseCentroidScreenerOP base_centroid_screener_
 
bool parin_favorite_output_
 
bool centroid_screen_
 
bool allow_base_pair_only_centroid_screen_
 
bool VDW_atr_rep_screen_
 
bool include_syn_chi_
 
bool allow_syn_pyrimidine_
 
bool distinguish_pucker_
 
bool build_pose_from_scratch_
 
core::Real current_score_cutoff_
 
bool finer_sampling_at_chain_closure_
 
bool PBP_clustering_at_chain_closure_
 
bool reinitialize_CCD_torsions_
 
bool extra_epsilon_rotamer_
 
bool extra_beta_rotamer_
 
bool extra_anti_chi_rotamer_
 
bool extra_syn_chi_rotamer_
 
bool sample_both_sugar_base_rotamer_
 
bool include_torsion_value_in_tag_
 
bool rebuild_bulge_mode_
 
bool debug_eplison_south_sugar_mode_
 
bool exclude_alpha_beta_gamma_sampling_
 
bool combine_long_loop_mode_
 
bool do_not_sample_multiple_virtual_sugar_
 
bool sample_ONLY_multiple_virtual_sugar_
 
bool assert_no_virt_ribose_sampling_
 
bool output_pdb_
 
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_ResidueSampler::StepWiseRNA_ResidueSampler ( StepWiseRNA_JobParametersCOP job_parameters_)
protocols::swa::rna::StepWiseRNA_ResidueSampler::~StepWiseRNA_ResidueSampler ( )

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_ResidueSampler::apply ( core::pose::Pose pose_to_visualize)
virtual
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::apply_bulge_variant ( core::pose::Pose pose,
core::Real const &  delta_atr_score 
)
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening ( core::pose::Pose chain_break_screening_pose,
core::scoring::ScoreFunctionOP const &  constraint_scorefxn 
)
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general ( core::pose::Pose chain_break_screening_pose,
core::scoring::ScoreFunctionOP const &  chainbreak_scorefxn,
core::Size const  five_prime_res 
)
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list ( utility::vector1< pose_data_struct2 > &  pose_data_list)
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::Copy_CCD_torsions ( core::pose::Pose pose,
core::pose::Pose const &  template_pose 
) const
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::Copy_CCD_torsions_general ( core::pose::Pose pose,
core::pose::Pose const &  template_pose,
core::Size const  five_prime_res,
core::Size const  three_prime_res 
) const
private
std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::create_rotamer_string ( core::pose::Pose const &  pose) const
private
std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::create_tag ( std::string const  prestring,
StepWiseRNA_RotamerGenerator_WrapperOP const &  rotamer_generator 
) const
private

Referenced by standard_sampling().

std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::create_torsion_value_string ( core::Real const &  torsion_value) const
private

Referenced by create_rotamer_string().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling ( core::pose::Pose pose,
FloatingBaseChainClosureJobParameter const &  prev_sugar_FB_JP 
)
private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::swa::rna::Add_harmonic_chainbreak_constraint(), core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::Add_virtual_O2Star_hydrogen(), allow_base_pair_only_centroid_screen_, protocols::swa::rna::Analyze_base_bin_map(), protocols::swa::rna::Base_centroid_screening(), protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, protocols::swa::rna::SillyCountStruct::both_count, build_pose_from_scratch_, centroid_bin_size, centroid_screen_, Chain_break_screening(), protocols::swa::rna::SillyCountStruct::chain_break_screening_count, Chain_break_screening_general(), protocols::swa::rna::SillyCountStruct::chain_closable_count, chainbreak_scorefxn_, protocols::swa::rna::Check_chain_closable(), protocols::swa::rna::Check_chain_closable_floating_base(), protocols::swa::rna::check_floating_base_chain_closable(), cluster_pose_data_list(), combine_long_loop_mode_, protocols::swa::rna::Contain_seq_num(), protocols::swa::rna::convert_euler_to_coordinate_matrix(), protocols::swa::rna::copy_all_o2star_torsions(), protocols::swa::rna::copy_bulge_res_and_ribose_torsion(), Copy_CCD_torsions(), Copy_CCD_torsions_general(), count_data_, core::kinematics::distance(), euler_angle_bin_size, euler_z_bin_size, extra_anti_chi_rotamer_, extra_syn_chi_rotamer_, fast_, Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), get_base_atr_rep_score(), protocols::swa::rna::get_max_centroid_to_atom_distance(), protocols::moves::Mover::get_native_pose(), get_reference_stub(), core::scoring::rna::get_rna_base_centroid(), core::scoring::rna::get_rna_base_coordinate_system(), 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, core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::has_variant_type(), integration_test_mode_, job_parameters_, core::kinematics::Stub::M, medium_fast_, protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res, native_rmsd_screen_, native_screen_rmsd_cutoff_, protocols::swa::rna::SillyCountStruct::non_clash_ribose, num_pose_kept_, O3I_C5I_PLUS_ONE_MAX_DIST, O3I_C5IPLUS2_MAX_DIST, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_data(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::SillyCountStruct::pass_base_centroid_screen, protocols::swa::rna::FloatingBaseChainClosureJobParameter::PDL, perform_o2star_pack_, pose_data_list_, Pose_selection_by_full_score(), protocols::swa::rna::print_atom_info(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::swa::rna::SillyCountStruct::rmsd_count, protocols::swa::rna::rmsd_over_residue_list(), sample_o2star_hydrogen(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::sample_sugar, protocols::swa::rna::set_base_coordinate_frame(), protocols::swa::rna::setup_chain_break_jump_point(), protocols::swa::rna::setup_residue_at_origin_list(), silent_file_, silent_file_data(), protocols::swa::rna::sort_criteria(), protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::suite_rmsd(), protocols::swa::rna::SillyCountStruct::tot_rotamer_count, core::pose::Pose::total_residue(), use_green_packer_, user_input_VDW_bin_screener_, core::kinematics::Stub::v, and verbose_.

Referenced by apply().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::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_ResidueSampler::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_ResidueSampler::get_base_atr_rep_score ( core::pose::Pose const &  pose,
core::Real base_atr_score,
core::Real base_rep_score 
)
private
std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

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

References pose_data_list_.

core::kinematics::Stub protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub ( core::Size const  reference_res,
core::pose::Pose const &  pose 
) const
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_green_packer ( core::pose::Pose pose)
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_packer_task ( core::pose::Pose const &  pose)
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_scorefunctions ( )
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_current_sugar_virtual ( core::pose::Pose const &  pose) const
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_five_prime_chain_break_sugar_virtual ( core::pose::Pose const &  pose) const
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_previous_sugar_virtual ( core::pose::Pose const &  pose) const
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_three_prime_chain_break_sugar_virtual ( core::pose::Pose const &  pose) const
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::output_pose_data_list ( std::string const  final_sampler_output_silent_file) const
Real protocols::swa::rna::StepWiseRNA_ResidueSampler::Pose_selection_by_full_score ( utility::vector1< pose_data_struct2 > &  pose_data_list,
core::pose::Pose current_pose,
std::string const &  tag 
)
private
utility::vector1< pose_data_struct2 > protocols::swa::rna::StepWiseRNA_ResidueSampler::previous_floating_base_chain_closure ( core::pose::Pose viewer_pose,
FloatingBaseChainClosureJobParameter const &  FB_job_params,
std::string const  name 
)
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::sample_o2star_hydrogen ( core::pose::Pose pose,
core::pose::Pose pose_with_original_HO2star_torsion 
)
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_allow_base_pair_only_centroid_screen ( bool const  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_allow_bulge_at_chainbreak ( bool const &  setting)
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_allow_syn_pyrimidine ( bool const &  setting)
inline

References allow_syn_pyrimidine_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_assert_no_virt_ribose_sampling ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_base_centroid_screener ( StepWiseRNA_BaseCentroidScreenerOP screener)
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_centroid_screen ( bool const  setting)
inline

References centroid_screen_.

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

References cluster_rmsd_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_combine_long_loop_mode ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_debug_eplison_south_sugar_mode ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_distinguish_pucker ( bool const &  setting)
inline

References distinguish_pucker_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_do_not_sample_multiple_virtual_sugar ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_exclude_alpha_beta_gamma_sampling ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_anti_chi_rotamer ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_beta_rotamer ( bool const &  setting)
inline

References extra_beta_rotamer_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_epsilon_rotamer ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_syn_chi_rotamer ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_fast ( bool const &  setting)

References fast_, and num_pose_kept_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_finer_sampling_at_chain_closure ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_floating_base ( bool const &  setting)
inline

References floating_base_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_include_syn_chi ( bool const &  setting)
inline

References include_syn_chi_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_include_torsion_value_in_tag ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_integration_test_mode ( bool const &  setting)
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_medium_fast ( bool const &  setting)

References medium_fast_, and num_pose_kept_.

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

References native_rmsd_screen_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_native_screen_rmsd_cutoff ( core::Real const &  setting)
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_num_pose_kept ( core::Size const &  num_pose_kept)

References num_pose_kept_.

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

References output_filename_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_output_pdb ( bool const  setting)
inline

References output_pdb_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_parin_favorite_output ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_PBP_clustering_at_chain_closure ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_perform_o2star_pack ( bool const &  setting)

References perform_o2star_pack_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_rebuild_bulge_mode ( bool const &  setting)
inline

References rebuild_bulge_mode_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_reinitialize_CCD_torsions ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_sample_both_sugar_base_rotamer ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_sample_ONLY_multiple_virtual_sugar ( bool const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References scorefxn_.

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

References silent_file_.

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

References VDW_atr_rep_screen_.

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

References verbose_.

core::io::silent::SilentFileDataOP & protocols::swa::rna::StepWiseRNA_ResidueSampler::silent_file_data ( )
void protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling ( core::pose::Pose pose,
utility::vector1< pose_data_struct2 > &  pose_data_list,
std::string const  sugar_tag 
)
private

References protocols::swa::rna::Add_harmonic_chainbreak_constraint(), core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::Add_virtual_O2Star_hydrogen(), protocols::swa::rna::align_poses(), allow_base_pair_only_centroid_screen_, allow_bulge_at_chainbreak_, allow_syn_pyrimidine_, apply_bulge_variant(), protocols::swa::rna::apply_rotamer(), base_centroid_screener_, protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, protocols::swa::rna::SillyCountStruct::both_count, build_pose_from_scratch_, protocols::swa::rna::SillyCountStruct::bulge_at_chain_closure_count, centroid_screen_, Chain_break_screening(), protocols::swa::rna::SillyCountStruct::chain_break_screening_count, protocols::swa::rna::SillyCountStruct::chain_closable_count, chainbreak_scorefxn_, protocols::swa::rna::Check_chain_closable(), protocols::swa::rna::Check_chain_closable_floating_base(), cluster_pose_data_list(), combine_long_loop_mode_, protocols::swa::rna::copy_all_o2star_torsions(), Copy_CCD_torsions(), count_data_, create_rotamer_string(), create_tag(), debug_eplison_south_sugar_mode_, exclude_alpha_beta_gamma_sampling_, extra_anti_chi_rotamer_, extra_beta_rotamer_, extra_epsilon_rotamer_, extra_syn_chi_rotamer_, fast_, 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, include_syn_chi_, include_torsion_value_in_tag_, initialize_o2star_green_packer(), initialize_o2star_packer_task(), integration_test_mode_, protocols::swa::rna::Is_residues_in_contact(), job_parameters_, medium_fast_, native_rmsd_screen_, native_screen_rmsd_cutoff_, num_pose_kept_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_data(), protocols::swa::rna::Output_title_text(), perform_o2star_pack_, Pose_selection_by_full_score(), protocols::swa::rna::remove_virtual_rna_residue_variant_type(), protocols::swa::rna::SillyCountStruct::residues_contact_screen, protocols::swa::rna::SillyCountStruct::rmsd_count, protocols::swa::rna::rmsd_over_residue_list(), sample_both_sugar_base_rotamer_, sample_o2star_hydrogen(), silent_file_, silent_file_data(), protocols::swa::rna::sort_criteria(), protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::suite_rmsd(), protocols::swa::rna::SillyCountStruct::tot_rotamer_count, use_green_packer_, user_input_VDW_bin_screener_, and verbose_.

Referenced by standard_sampling_WRAPPER().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling_WRAPPER ( core::pose::Pose pose,
FloatingBaseChainClosureJobParameter const &  prev_sugar_FB_JP,
FloatingBaseChainClosureJobParameter const &  curr_sugar_FB_JP,
FloatingBaseChainClosureJobParameter const &  five_prime_CB_sugar_FB_JP,
FloatingBaseChainClosureJobParameter const &  three_prime_CB_sugar_FB_JP 
)
private
void protocols::swa::rna::StepWiseRNA_ResidueSampler::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_ResidueSampler::allow_base_pair_only_centroid_screen_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::allow_bulge_at_chainbreak_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::allow_syn_pyrimidine_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::assert_no_virt_ribose_sampling_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_ResidueSampler::atr_rep_screening_scorefxn_
private
StepWiseRNA_BaseCentroidScreenerOP protocols::swa::rna::StepWiseRNA_ResidueSampler::base_centroid_screener_
private
core::Real const protocols::swa::rna::StepWiseRNA_ResidueSampler::bin_size_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::build_pose_from_scratch_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::centroid_screen_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_ResidueSampler::chainbreak_scorefxn_
private
core::Real protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_rmsd_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::combine_long_loop_mode_
private
SillyCountStruct protocols::swa::rna::StepWiseRNA_ResidueSampler::count_data_
private
core::Real protocols::swa::rna::StepWiseRNA_ResidueSampler::current_score_cutoff_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::debug_eplison_south_sugar_mode_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::distinguish_pucker_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::do_not_sample_multiple_virtual_sugar_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::exclude_alpha_beta_gamma_sampling_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::extra_anti_chi_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::extra_beta_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::extra_epsilon_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::extra_syn_chi_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::fast_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::finer_sampling_at_chain_closure_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_
private

Referenced by apply(), and set_floating_base().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::include_syn_chi_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::include_torsion_value_in_tag_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::integration_test_mode_
private
StepWiseRNA_JobParametersCOP protocols::swa::rna::StepWiseRNA_ResidueSampler::job_parameters_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::medium_fast_
private
core::Size const protocols::swa::rna::StepWiseRNA_ResidueSampler::multiplier_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::native_rmsd_screen_
private
core::Real protocols::swa::rna::StepWiseRNA_ResidueSampler::native_screen_rmsd_cutoff_
private
core::Size protocols::swa::rna::StepWiseRNA_ResidueSampler::num_pose_kept_
private
protocols::simple_moves::GreenPackerOP protocols::swa::rna::StepWiseRNA_ResidueSampler::o2star_green_packer_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_ResidueSampler::o2star_pack_scorefxn_
private
core::pack::task::PackerTaskOP protocols::swa::rna::StepWiseRNA_ResidueSampler::o2star_pack_task_
private
std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::output_filename_
private

Referenced by set_output_filename().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::output_pdb_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::parin_favorite_output_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::PBP_clustering_at_chain_closure_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::perform_o2star_pack_
private
utility::vector1< pose_data_struct2 > protocols::swa::rna::StepWiseRNA_ResidueSampler::pose_data_list_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::rebuild_bulge_mode_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::reinitialize_CCD_torsions_
private
core::Real const protocols::swa::rna::StepWiseRNA_ResidueSampler::rep_cutoff_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::sample_both_sugar_base_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_ResidueSampler::sample_ONLY_multiple_virtual_sugar_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_ResidueSampler::sampling_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_ResidueSampler::scorefxn_
private
core::io::silent::SilentFileDataOP protocols::swa::rna::StepWiseRNA_ResidueSampler::sfd_
private

Referenced by silent_file_data().

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

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