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Rosetta 3.5
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Rosetta 3.5
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#include <StepWiseRNA_Minimizer.hh>
Public Member Functions | |
| StepWiseRNA_Minimizer (utility::vector1< pose_data_struct2 > const &pose_data_list, StepWiseRNA_JobParametersCOP &job_parameters) | |
| ~StepWiseRNA_Minimizer () | |
| 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_silent_file (std::string const &silent_file) |
| void | set_move_map_list (utility::vector1< core::kinematics::MoveMap > const &move_map_list) |
| void | set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn) |
| core::io::silent::SilentFileDataOP & | silent_file_data () |
| void | set_base_centroid_screener (StepWiseRNA_BaseCentroidScreenerOP &screener) |
| void | set_native_edensity_score_cutoff (core::Real const &setting) |
| void | set_verbose (bool const setting) |
| void | set_centroid_screen (bool const setting) |
| void | set_perform_o2star_pack (bool const setting) |
| void | set_output_before_o2star_pack (bool const setting) |
| void | set_rm_virt_phosphate (bool const setting) |
| void | set_perform_minimize (bool const setting) |
| void | set_num_pose_minimize (Size const setting) |
| void | set_minimize_and_score_sugar (bool const setting) |
| void | set_native_rmsd_screen (bool const setting) |
| void | set_native_screen_rmsd_cutoff (core::Real const setting) |
| void | set_user_input_VDW_bin_screener (StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener) |
| void | set_rename_tag (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 | |
| utility::vector1 < core::kinematics::MoveMap > | Get_default_movemap (core::pose::Pose const &pose) const |
| void | Figure_out_moving_residues (core::kinematics::MoveMap &mm, core::pose::Pose const &pose) const |
| bool | pass_all_pose_screens (core::pose::Pose &pose, std::string const in_tag, core::io::silent::SilentFileData &silent_file_data) const |
| void | Freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const nres) const |
| void | output_empty_minimizer_silent_file () const |
| void | output_pose_data_wrapper (std::string &tag, char tag_first_char, core::pose::Pose &pose, core::io::silent::SilentFileData &silent_file_data, std::string const out_silent_file) const |
| core::Size | figure_out_actual_five_prime_chain_break_res (core::pose::Pose const &pose) const |
| bool | native_edensity_score_screener (core::pose::Pose &pose, core::pose::Pose &native_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... | |
| protocols::swa::rna::StepWiseRNA_Minimizer::StepWiseRNA_Minimizer | ( | utility::vector1< pose_data_struct2 > const & | pose_data_list, |
| StepWiseRNA_JobParametersCOP & | job_parameters | ||
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References job_parameters_, and protocols::moves::Mover::set_native_pose().
| protocols::swa::rna::StepWiseRNA_Minimizer::~StepWiseRNA_Minimizer | ( | ) |
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Apply the minimizer to one pose.
Implements protocols::moves::Mover.
References centroid_screen_, protocols::swa::rna::Contain_seq_num(), figure_out_actual_five_prime_chain_break_res(), Freeze_sugar_torsions(), Get_default_movemap(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), job_parameters_, minimize_and_score_sugar_, protocols::swa::rna::minimizer_sort_criteria(), move_map_list_, native_edensity_score_cutoff_, native_screen_, native_screen_rmsd_cutoff_, core::optimization::MinimizerOptions::nblist_auto_update(), num_pose_minimize_, protocols::swa::rna::o2star_minimize(), output_before_o2star_pack_, protocols::swa::rna::Output_boolean(), output_empty_minimizer_silent_file(), protocols::swa::rna::Output_movemap(), output_pose_data_wrapper(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), pass_all_pose_screens(), perform_electron_density_screen_, perform_minimize_, perform_o2star_pack_, pose_data_list_, protocols::swa::rna::pose_data_struct2::pose_OP, core::pose::remove_variant_type_from_pose_residue(), protocols::swa::rna::Remove_virtual_O2Star_hydrogen(), rename_tag_, rm_virt_phosphate_, protocols::noesy_assign::round(), protocols::swa::rna::pose_data_struct2::score, scorefxn_, silent_file_, silent_file_data(), protocols::swa::rna::pose_data_struct2::tag, core::pose::Pose::total_residue(), user_input_VDW_bin_screener_, and verbose_.
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References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::BB, core::id::CHI, core::pose::Pose::conformation(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Conformation::get_torsion_angle_atom_ids(), job_parameters_, core::kinematics::FoldTree::num_jump(), core::scoring::rna::NUM_RNA_CHI_TORSIONS(), core::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS(), protocols::swa::rna::Output_boolean(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().
Referenced by Get_default_movemap().
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References core::id::BB, core::id::CHI, and core::kinematics::MoveMap::set().
Referenced by apply().
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References Figure_out_moving_residues().
Referenced by apply().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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References core::scoring::elec_dens_atomwise, native_edensity_score_cutoff_, and core::pose::Pose::total_residue().
Referenced by pass_all_pose_screens().
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References protocols::swa::rna::file_exists(), and silent_file_.
Referenced by apply().
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References protocols::moves::Mover::get_native_pose(), job_parameters_, and protocols::swa::rna::Output_data().
Referenced by apply(), and pass_all_pose_screens().
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References base_centroid_screener_, centroid_screen_, protocols::swa::rna::Check_chain_closable(), protocols::swa::rna::check_for_messed_up_structure(), core::scoring::dna::DELTA, protocols::moves::Mover::get_native_pose(), core::conformation::Residue::has_variant_type(), job_parameters_, protocols::loops::loop_rmsd(), core::conformation::Residue::mainchain_torsion(), native_edensity_score_screener(), native_screen_, native_screen_rmsd_cutoff_, output_pose_data_wrapper(), perform_electron_density_screen_, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::swa::rna::rmsd_over_residue_list(), silent_file_, protocols::swa::rna::suite_rmsd(), core::pose::Pose::total_residue(), user_input_VDW_bin_screener_, and verbose_.
Referenced by apply().
| void protocols::swa::rna::StepWiseRNA_Minimizer::set_base_centroid_screener | ( | StepWiseRNA_BaseCentroidScreenerOP & | screener) |
References base_centroid_screener_.
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References centroid_screen_.
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References minimize_and_score_sugar_.
| void protocols::swa::rna::StepWiseRNA_Minimizer::set_move_map_list | ( | utility::vector1< core::kinematics::MoveMap > const & | move_map_list) |
References move_map_list_.
| void protocols::swa::rna::StepWiseRNA_Minimizer::set_native_edensity_score_cutoff | ( | core::Real const & | setting) |
References native_edensity_score_cutoff_, and perform_electron_density_screen_.
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References native_screen_.
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References native_screen_rmsd_cutoff_.
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References num_pose_minimize_.
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References output_before_o2star_pack_.
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References perform_minimize_.
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References perform_o2star_pack_.
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References rename_tag_.
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References rm_virt_phosphate_.
| void protocols::swa::rna::StepWiseRNA_Minimizer::set_scorefxn | ( | core::scoring::ScoreFunctionOP const & | scorefxn) |
References scorefxn_.
| void protocols::swa::rna::StepWiseRNA_Minimizer::set_silent_file | ( | std::string const & | silent_file) |
References silent_file_.
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References user_input_VDW_bin_screener_.
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References verbose_.
| core::io::silent::SilentFileDataOP & protocols::swa::rna::StepWiseRNA_Minimizer::silent_file_data | ( | ) |
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Referenced by pass_all_pose_screens(), and set_base_centroid_screener().
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Referenced by apply(), pass_all_pose_screens(), and set_centroid_screen().
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Referenced by apply(), and set_minimize_and_score_sugar().
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Referenced by apply(), and set_move_map_list().
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Referenced by apply(), native_edensity_score_screener(), and set_native_edensity_score_cutoff().
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Referenced by apply(), pass_all_pose_screens(), and set_native_rmsd_screen().
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Referenced by apply(), pass_all_pose_screens(), and set_native_screen_rmsd_cutoff().
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Referenced by apply(), and set_num_pose_minimize().
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Referenced by apply(), and set_output_before_o2star_pack().
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Referenced by apply(), pass_all_pose_screens(), and set_native_edensity_score_cutoff().
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Referenced by apply(), and set_perform_minimize().
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Referenced by apply(), and set_perform_o2star_pack().
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Referenced by apply().
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Referenced by apply(), and set_rename_tag().
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Referenced by apply(), and set_rm_virt_phosphate().
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Referenced by apply(), and set_scorefxn().
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Referenced by silent_file_data().
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Referenced by apply(), output_empty_minimizer_silent_file(), pass_all_pose_screens(), and set_silent_file().
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Referenced by apply(), pass_all_pose_screens(), and set_user_input_VDW_bin_screener().
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Referenced by apply(), pass_all_pose_screens(), and set_verbose().
1.8.4