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Rosetta 3.5
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Rosetta 3.5
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#include <RNA_LoopCloseSampler.hh>
Public Member Functions | |
| RNA_LoopCloseSampler (Size const moving_suite, Size const chainbreak_suite) | |
| ~RNA_LoopCloseSampler () | |
| 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... | |
| utility::vector1 < utility::vector1< Real > > | all_torsion_info () |
| Size | n_construct () |
| void | fill_pose (pose::Pose &pose, Size construct_number) |
| void | clear_all () |
| void | set_bin_size (Size const setting) |
| void | set_epsilon_range (Real const setting) |
| void | set_rep_cutoff (Real const rep_cutoff) |
| void | set_torsion_range (Real const torsion_range) |
| void | set_torsion_increment (Real const torsion_increment) |
| void | set_just_output_score (bool const setting) |
| void | set_sample_only (bool const setting) |
| void | set_sample_native_torsion (bool const setting) |
| void | set_rbs_new_pair (utility::vector1< Real > const &rbs_new_pair) |
| void | set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn) |
 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 | |
| bool | torsion_angles_within_cutoffs (pose::Pose const &pose, Size const moving_suite, Size const chainbreak_suite) |
| void | initialize_rep_scorefxn () |
| Real | initialize_fa_rep (pose::Pose const &pose, utility::vector1< Size > const &moving_suites, scoring::ScoreFunctionOP rep_scorefxn) |
| bool | check_clash (pose::Pose &pose, Real const &fa_rep_score_baseline, Real const &rep_cutoff_, scoring::ScoreFunctionOP rep_scorefxn) |
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 37 of file RNA_LoopCloseSampler.hh.
| protocols::swa::rna::RNA_LoopCloseSampler::RNA_LoopCloseSampler | ( | Size const | moving_suite, |
| Size const | chainbreak_suite | ||
| ) |
Definition at line 72 of file RNA_LoopCloseSampler.cc.
References initialize_rep_scorefxn().
| protocols::swa::rna::RNA_LoopCloseSampler::~RNA_LoopCloseSampler | ( | ) |
Definition at line 91 of file RNA_LoopCloseSampler.cc.
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Definition at line 53 of file RNA_LoopCloseSampler.hh.
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Apply the minimizer to one pose.
Implements protocols::moves::Mover.
Definition at line 96 of file RNA_LoopCloseSampler.cc.
References all_torsion_info_, core::scoring::dna::ALPHA, protocols::swa::rna::RNA_AnalyticLoopCloser::apply(), core::id::BB, core::scoring::dna::BETA, bin_size_, chainbreak_suite_, check_clash(), core::scoring::dna::EPSILON, epsilon_range_, protocols::swa::rna::RNA_AnalyticLoopCloser::fill_solution(), core::scoring::dna::GAMMA, protocols::moves::Mover::get_native_pose(), protocols::swa::rna::Get_residue_pucker_state(), initialize_fa_rep(), moving_suite_, n_construct_, protocols::swa::rna::NORTH, protocols::swa::rna::RNA_AnalyticLoopCloser::nsol(), rep_cutoff_, rep_scorefxn_, sample_native_torsion_, sample_only_, core::pose::Pose::set_torsion(), protocols::swa::rna::SOUTH, core::pose::Pose::torsion(), torsion_angles_within_cutoffs(), torsion_info_, and core::scoring::dna::ZETA.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
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Definition at line 298 of file RNA_LoopCloseSampler.cc.
References core::pose::Pose::energies(), core::scoring::fa_rep, and core::scoring::Energies::total_energies().
Referenced by apply().
| void protocols::swa::rna::RNA_LoopCloseSampler::clear_all | ( | ) |
Definition at line 253 of file RNA_LoopCloseSampler.cc.
References all_torsion_info_, and n_construct_.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
| void protocols::swa::rna::RNA_LoopCloseSampler::fill_pose | ( | pose::Pose & | pose, |
| Size | construct_number | ||
| ) |
Definition at line 228 of file RNA_LoopCloseSampler.cc.
References all_torsion_info_, core::scoring::dna::ALPHA, core::id::BB, core::scoring::dna::BETA, chainbreak_suite_, core::scoring::dna::EPSILON, core::scoring::dna::GAMMA, moving_suite_, core::pose::Pose::set_torsion(), and core::scoring::dna::ZETA.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
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inlinevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 50 of file RNA_LoopCloseSampler.hh.
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Definition at line 269 of file RNA_LoopCloseSampler.cc.
References core::scoring::fa_rep, protocols::swa::rna::make_cut_at_moving_suite(), and sample_only_.
Referenced by apply().
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Definition at line 261 of file RNA_LoopCloseSampler.cc.
References core::scoring::fa_rep, and rep_scorefxn_.
Referenced by RNA_LoopCloseSampler().
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Definition at line 56 of file RNA_LoopCloseSampler.hh.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
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Definition at line 62 of file RNA_LoopCloseSampler.hh.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
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Definition at line 66 of file RNA_LoopCloseSampler.hh.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
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Definition at line 80 of file RNA_LoopCloseSampler.hh.
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Definition at line 91 of file RNA_LoopCloseSampler.hh.
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Definition at line 70 of file RNA_LoopCloseSampler.hh.
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Definition at line 87 of file RNA_LoopCloseSampler.hh.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
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Definition at line 83 of file RNA_LoopCloseSampler.hh.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
| void protocols::swa::rna::RNA_LoopCloseSampler::set_scorefxn | ( | core::scoring::ScoreFunctionOP const & | scorefxn) |
Definition at line 322 of file RNA_LoopCloseSampler.cc.
References scorefxn_.
Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().
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Definition at line 76 of file RNA_LoopCloseSampler.hh.
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Definition at line 73 of file RNA_LoopCloseSampler.hh.
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Definition at line 328 of file RNA_LoopCloseSampler.cc.
References core::scoring::dna::ALPHA, core::id::BB, core::scoring::dna::BETA, core::scoring::dna::EPSILON, core::scoring::dna::GAMMA, protocols::swa::rna::Get_residue_pucker_state(), protocols::swa::rna::NORTH, core::pose::Pose::torsion(), and core::scoring::dna::ZETA.
Referenced by apply().
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Definition at line 130 of file RNA_LoopCloseSampler.hh.
Referenced by apply(), clear_all(), and fill_pose().
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Definition at line 124 of file RNA_LoopCloseSampler.hh.
Referenced by apply().
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Definition at line 121 of file RNA_LoopCloseSampler.hh.
Referenced by apply(), and fill_pose().
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Definition at line 125 of file RNA_LoopCloseSampler.hh.
Referenced by apply().
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Definition at line 126 of file RNA_LoopCloseSampler.hh.
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Definition at line 121 of file RNA_LoopCloseSampler.hh.
Referenced by apply(), and fill_pose().
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Definition at line 124 of file RNA_LoopCloseSampler.hh.
Referenced by apply(), and clear_all().
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Definition at line 127 of file RNA_LoopCloseSampler.hh.
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Definition at line 125 of file RNA_LoopCloseSampler.hh.
Referenced by apply().
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Definition at line 123 of file RNA_LoopCloseSampler.hh.
Referenced by apply(), and initialize_rep_scorefxn().
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Definition at line 126 of file RNA_LoopCloseSampler.hh.
Referenced by apply().
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Definition at line 126 of file RNA_LoopCloseSampler.hh.
Referenced by apply(), and initialize_fa_rep().
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Definition at line 123 of file RNA_LoopCloseSampler.hh.
Referenced by set_scorefxn().
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Definition at line 125 of file RNA_LoopCloseSampler.hh.
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Definition at line 129 of file RNA_LoopCloseSampler.hh.
Referenced by apply().
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Definition at line 125 of file RNA_LoopCloseSampler.hh.
1.8.4