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Rosetta 3.5
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Rosetta 3.5
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#include <StepWiseRNA_AnalyticalLoopCloseSampler.hh>
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::SilentFileDataOP & | silent_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) | |
| 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 |
| 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 Strings & | info () |
| 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 ¤t_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 ¤t_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 ¤t_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 ¤t_pose, core::Real const ¤t_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 |
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... | |
Definition at line 44 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
| protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::StepWiseRNA_AnalyticalLoopCloseSampler | ( | StepWiseRNA_JobParametersCOP & | job_parameters_) |
Definition at line 102 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References protocols::swa::rna::apply_full_to_sub_mapping(), job_parameters_, protocols::swa::rna::Output_is_prepend_map(), protocols::swa::rna::Output_seq_num_list(), protocols::moves::Mover::set_native_pose(), and working_rmsd_res_.
| protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::~StepWiseRNA_AnalyticalLoopCloseSampler | ( | ) |
Definition at line 143 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
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Apply the minimizer to one pose.
Implements protocols::moves::Mover.
Definition at line 155 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References centroid_screen_, initialize_scorefunctions(), job_parameters_, native_rmsd_screen_, native_screen_rmsd_cutoff_, o2star_screen_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), standard_sampling(), and VDW_atr_rep_screen_.
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Definition at line 576 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References cluster_rmsd_, current_score_cutoff_, distinguish_pucker_, protocols::swa::rna::Get_residue_pucker_state(), protocols::swa::rna::Is_same_ribose_pucker(), job_parameters_, num_pose_kept_, protocols::swa::rna::Output_boolean(), PBP_clustering_at_chain_closure_, protocols::swa::rna::phosphate_base_phosphate_rmsd(), protocols::swa::rna::print_ribose_pucker_state(), protocols::swa::rna::suite_rmsd(), and verbose_.
Referenced by Pose_selection_by_full_score(), and standard_sampling().
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Definition at line 417 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References core::id::BB, core::id::CHI, core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().
Referenced by standard_sampling().
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Definition at line 852 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References core::conformation::Residue::chi(), create_torsion_value_string(), job_parameters_, core::conformation::Residue::mainchain_torsion(), and core::pose::Pose::residue().
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Definition at line 877 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
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Definition at line 835 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
Referenced by create_rotamer_string().
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Definition at line 699 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References atr_rep_screening_scorefxn_, protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, protocols::swa::rna::SillyCountStruct::both_count, count_data_, core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, protocols::swa::rna::SillyCountStruct::good_atr_rotamer_count, protocols::swa::rna::SillyCountStruct::good_bin_rep_count, protocols::swa::rna::SillyCountStruct::good_rep_rotamer_count, protocols::swa::rna::SillyCountStruct::pass_base_centroid_screen, rep_cutoff_, protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::SillyCountStruct::tot_rotamer_count, core::scoring::Energies::total_energies(), VDW_atr_rep_screen_, and verbose_.
Referenced by standard_sampling().
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Definition at line 636 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References atr_rep_screening_scorefxn_, protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, protocols::swa::rna::SillyCountStruct::both_count, protocols::swa::rna::SillyCountStruct::chain_closable_count, count_data_, core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, protocols::swa::rna::SillyCountStruct::good_atr_rotamer_count, protocols::swa::rna::SillyCountStruct::good_bin_rep_count, protocols::swa::rna::SillyCountStruct::good_rep_rotamer_count, protocols::swa::rna::SillyCountStruct::non_clash_ribose, protocols::swa::rna::SillyCountStruct::pass_base_centroid_screen, rep_cutoff_, protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::SillyCountStruct::tot_rotamer_count, core::scoring::Energies::total_energies(), VDW_atr_rep_screen_, and verbose_.
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Definition at line 440 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References core::pose::add_variant_type_to_pose_residue(), atr_rep_screening_scorefxn_, core::pose::Pose::dump_pdb(), core::scoring::fa_atr, core::scoring::fa_rep, job_parameters_, protocols::swa::rna::make_cut_at_moving_suite(), core::kinematics::Jump::set_translation(), and verbose_.
Referenced by standard_sampling().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 57 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
| utility::vector1< pose_data_struct2 > & protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_pose_data_list | ( | ) |
Definition at line 514 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References pose_data_list_.
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Definition at line 780 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References protocols::swa::rna::Contain_seq_num(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::conformation::Residue::is_RNA(), job_parameters_, o2star_pack_task_, core::pose::Pose::residue(), and core::pose::Pose::total_residue().
Referenced by sample_o2star_hydrogen(), and standard_sampling().
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Definition at line 508 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References atr_rep_screening_scorefxn_, chainbreak_scorefxn_, protocols::swa::rna::initialize_common_scorefxns(), o2star_pack_scorefxn_, sampling_scorefxn_, and scorefxn_.
Referenced by apply().
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::output_pose_data_list | ( | std::string const | final_sampler_output_silent_file) | const |
Definition at line 953 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References protocols::moves::Mover::get_native_pose(), job_parameters_, protocols::swa::rna::Output_data(), pose_data_list_, silent_file_data(), and verbose_.
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Definition at line 552 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References cluster_pose_data_list(), multiplier_, num_pose_kept_, protocols::swa::rna::sort_criteria2(), and Update_pose_data_list().
Referenced by standard_sampling().
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Definition at line 816 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::CHI, initialize_o2star_packer_task(), o2star_pack_scorefxn_, o2star_pack_task_, core::pose::Pose::residue(), core::pack::rotamer_trials(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::pose::Pose::total_residue().
Referenced by standard_sampling().
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Definition at line 142 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References allow_syn_pyrimidine_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_base_centroid_screener | ( | StepWiseRNA_BaseCentroidScreenerOP & | screener) |
Definition at line 969 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References base_centroid_screener_.
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Definition at line 67 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References base_pairing_only_screen_.
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Definition at line 62 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References centroid_screen_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_cluster_rmsd | ( | core::Real const & | setting) |
Definition at line 982 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References cluster_rmsd_.
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Definition at line 124 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References distinguish_pucker_.
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Definition at line 152 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References extra_anti_chi_rotamer_.
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Definition at line 147 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References extra_syn_chi_rotamer_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_fast | ( | bool const & | setting) |
Definition at line 898 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References fast_, and num_pose_kept_.
Referenced by set_num_pose_kept().
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Definition at line 129 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References finer_sampling_at_chain_closure_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_medium_fast | ( | bool const & | setting) |
Definition at line 906 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References medium_fast_, and num_pose_kept_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_native_rmsd_screen | ( | bool const & | setting) |
Definition at line 915 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References native_rmsd_screen_.
Referenced by set_num_pose_kept().
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Definition at line 96 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References native_screen_rmsd_cutoff_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_num_pose_kept | ( | core::Size const & | num_pose_kept) |
Definition at line 988 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References fast_, native_rmsd_screen_, num_pose_kept_, set_fast(), and set_native_rmsd_screen().
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_o2star_screen | ( | bool const & | setting) |
Definition at line 928 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References o2star_screen_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_output_filename | ( | std::string const & | output_filename) |
Definition at line 934 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References output_filename_.
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Definition at line 134 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References PBP_clustering_at_chain_closure_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_scorefxn | ( | core::scoring::ScoreFunctionOP const & | scorefxn) |
Definition at line 940 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References scorefxn_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_silent_file | ( | std::string const & | setting) |
Definition at line 892 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References silent_file_.
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Definition at line 157 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
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) |
Definition at line 975 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References user_input_VDW_bin_screener_.
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Definition at line 72 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
References VDW_atr_rep_screen_.
| void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_verbose | ( | bool const & | setting) |
Definition at line 921 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References verbose_.
| core::io::silent::SilentFileDataOP & protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::silent_file_data | ( | ) |
Definition at line 946 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References sfd_.
Referenced by output_pose_data_list(), and standard_sampling().
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Definition at line 184 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
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().
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Definition at line 522 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.
References current_score_cutoff_, protocols::moves::Mover::get_native_pose(), protocols::swa::rna::pose_data_struct2::pose_OP, core::scoring::rms_at_corresponding_heavy_atoms(), protocols::swa::rna::pose_data_struct2::score, core::pose::setPoseExtraScores(), protocols::swa::rna::pose_data_struct2::tag, and verbose_.
Referenced by Pose_selection_by_full_score().
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Definition at line 269 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_allow_syn_pyrimidine(), and standard_sampling().
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Definition at line 234 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), get_base_atr_rep_score(), and initialize_scorefunctions().
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Definition at line 258 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_base_centroid_screener(), and standard_sampling().
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Definition at line 261 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_base_pairing_only_screen().
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Definition at line 244 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
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Definition at line 260 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by apply(), set_centroid_screen(), and standard_sampling().
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Definition at line 237 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by initialize_scorefunctions().
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Definition at line 248 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by cluster_pose_data_list(), and set_cluster_rmsd().
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Definition at line 241 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), and standard_sampling().
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Definition at line 264 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by cluster_pose_data_list(), and Update_pose_data_list().
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Definition at line 263 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by cluster_pose_data_list(), set_distinguish_pucker(), and standard_sampling().
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Definition at line 267 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_extra_anti_chi_rotamer(), and standard_sampling().
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Definition at line 268 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_extra_syn_chi_rotamer(), and standard_sampling().
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Definition at line 255 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_fast(), and set_num_pose_kept().
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Definition at line 265 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_finer_sampling_at_chain_closure(), and standard_sampling().
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Definition at line 228 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by apply(), cluster_pose_data_list(), create_rotamer_string(), get_base_atr_rep_score(), initialize_o2star_packer_task(), output_pose_data_list(), standard_sampling(), and StepWiseRNA_AnalyticalLoopCloseSampler().
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Definition at line 256 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_medium_fast().
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Definition at line 247 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by Pose_selection_by_full_score().
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Definition at line 250 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by apply(), set_native_rmsd_screen(), set_num_pose_kept(), and standard_sampling().
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Definition at line 251 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by apply(), set_native_screen_rmsd_cutoff(), and standard_sampling().
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Definition at line 246 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by cluster_pose_data_list(), Pose_selection_by_full_score(), set_fast(), set_medium_fast(), set_num_pose_kept(), and standard_sampling().
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Definition at line 236 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by initialize_scorefunctions(), and sample_o2star_hydrogen().
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Definition at line 254 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by initialize_o2star_packer_task(), and sample_o2star_hydrogen().
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Definition at line 253 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by apply(), set_o2star_screen(), and standard_sampling().
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Definition at line 243 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_output_filename().
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Definition at line 266 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by cluster_pose_data_list(), and set_PBP_clustering_at_chain_closure().
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Definition at line 231 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by get_pose_data_list(), output_pose_data_list(), and standard_sampling().
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Definition at line 245 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by Full_atom_van_der_Waals_screening(), and Full_atom_van_der_Waals_screening_REPLICATE().
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Definition at line 235 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by initialize_scorefunctions().
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Definition at line 233 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by initialize_scorefunctions(), set_scorefxn(), and standard_sampling().
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Definition at line 230 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by silent_file_data().
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Definition at line 242 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_silent_file(), and standard_sampling().
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Definition at line 270 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_use_phenix_geo(), and standard_sampling().
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Definition at line 272 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by set_user_input_VDW_bin_screener(), and standard_sampling().
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Definition at line 262 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by apply(), Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), and set_VDW_atr_rep_screen().
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Definition at line 249 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by cluster_pose_data_list(), Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), get_base_atr_rep_score(), output_pose_data_list(), set_verbose(), standard_sampling(), and Update_pose_data_list().
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Definition at line 239 of file StepWiseRNA_AnalyticalLoopCloseSampler.hh.
Referenced by StepWiseRNA_AnalyticalLoopCloseSampler().
1.8.4