The RNA de novo structure modeling protocol. More...
#include <RNA_AnalyticLoopCloser.hh>
Public Member Functions | |
| RNA_AnalyticLoopCloser (core::Size const moving_suite, core::Size const chainbreak_suite) | |
| Construct the protocol object. More... | |
| protocols::moves::MoverOP | clone () const override |
| Clone this object. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | apply (core::pose::Pose &pose) override |
| Apply the loop-rebuild protocol to the input pose. More... | |
| void | choose_best_solution_based_on_score_function (core::scoring::ScoreFunctionOP scorefxn) |
| void | choose_least_perturb_solution () |
| void | get_all_solutions (core::pose::Pose &pose, utility::vector1< core::pose::PoseOP > &pose_list) |
| core::Size | nsol () |
| void | fill_solution (core::pose::Pose &pose, core::Size const n) const |
| utility::vector1< core::Real > | get_torsions (core::Size const n) |
| utility::vector1< utility::vector1< core::Real > > | get_torsions_for_all_solutions () |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| 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... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform 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 |
| Inform 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 |
| Generates a new Mover object freshly created with the default ctor. More... | |
| 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... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| 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 | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| 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... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| 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 void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Private Member Functions | |
| bool | close_at_cutpoint (core::pose::Pose &pose) |
| void | figure_out_dof_ids_and_offsets (core::pose::Pose const &pose, utility::vector1< core::Real > const &dt_ang) |
| void | figure_out_offset (core::pose::Pose const &pose, core::id::DOF_ID const &dof_id, core::Real const &original_torsion_value, utility::vector1< core::Real > &offset_save) |
| void | apply_solutions (core::pose::Pose &pose) |
| void | output_chainTORS (utility::vector1< core::Real > const &dt_ang, utility::vector1< core::Real > const &db_ang, utility::vector1< core::Real > const &db_len) const |
| void | fill_chainTORS (core::pose::Pose const &pose, utility::vector1< core::id::NamedAtomID > const &atom_ids, utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &atoms, utility::vector1< core::Real > &dt_ang, utility::vector1< core::Real > &db_ang, utility::vector1< core::Real > &db_len) const |
Private Attributes | |
| core::Size const | moving_suite_ |
| core::Size const | chainbreak_suite_ |
| bool const | verbose_ |
| int | nsol_ |
| core::scoring::ScoreFunctionOP | scorefxn_ |
| utility::vector1< core::id::NamedAtomID > | atom_ids_ |
| utility::vector1< core::Real > | offset_save_ |
| utility::vector1< core::id::DOF_ID > | dof_ids_ |
| utility::vector1< utility::vector1< core::Real > > | t_ang_ |
| utility::vector1< utility::vector1< core::Real > > | b_ang_ |
| utility::vector1< utility::vector1< core::Real > > | b_len_ |
| bool | choose_least_perturb_solution_ |
| bool | choose_best_solution_ |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| 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. 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... | |
Detailed Description
The RNA de novo structure modeling protocol.
Constructor & Destructor Documentation
◆ RNA_AnalyticLoopCloser()
| protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::RNA_AnalyticLoopCloser | ( | core::Size const | moving_suite, |
| core::Size const | chainbreak_suite | ||
| ) |
Construct the protocol object.
Member Function Documentation
◆ apply()
|
overridevirtual |
Apply the loop-rebuild protocol to the input pose.
Apply the RNA Loop Closer – set up for Full Atom Representation.
Implements protocols::moves::Mover.
References close_at_cutpoint().
◆ apply_solutions()
|
private |
References atom_ids_, b_ang_, b_len_, choose_best_solution_, choose_least_perturb_solution_, core::pose::Pose::dump_pdb(), fill_chainTORS(), fill_solution(), nsol_, output_chainTORS(), core::scoring::rg, protocols::hybridization::score, scorefxn_, core::pose::Pose::size(), t_ang_, protocols::TR(), verbose_, and core::pose::Pose::xyz().
Referenced by close_at_cutpoint().
◆ choose_best_solution_based_on_score_function()
| void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_best_solution_based_on_score_function | ( | core::scoring::ScoreFunctionOP | scorefxn | ) |
References choose_best_solution_, choose_least_perturb_solution_, and scorefxn_.
◆ choose_least_perturb_solution()
| void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_least_perturb_solution | ( | ) |
References choose_best_solution_, and choose_least_perturb_solution_.
◆ clone()
|
overridevirtual |
Clone this object.
Reimplemented from protocols::moves::Mover.
◆ close_at_cutpoint()
|
private |
References apply_solutions(), atom_ids_, b_ang_, b_len_, chainbreak_suite_, figure_out_dof_ids_and_offsets(), fill_chainTORS(), moving_suite_, nsol_, protocols::forge::methods::order(), output_chainTORS(), t_ang_, protocols::TR(), verbose_, and core::pose::Pose::xyz().
Referenced by apply().
◆ figure_out_dof_ids_and_offsets()
|
private |
References core::conformation::Residue::atom_index(), core::pose::Pose::atom_tree(), core::chemical::rna::RNA_Info::c3prime_atom_index(), core::chemical::rna::RNA_Info::c4prime_atom_index(), core::chemical::rna::RNA_Info::c5prime_atom_index(), chainbreak_suite_, dof_ids_, figure_out_offset(), moving_suite_, core::chemical::rna::RNA_Info::o3prime_atom_index(), core::chemical::rna::RNA_Info::o5prime_atom_index(), offset_save_, core::chemical::rna::RNA_Info::p_atom_index(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::RNA_info(), and core::kinematics::AtomTree::torsion_angle_dof_id().
Referenced by close_at_cutpoint().
◆ figure_out_offset()
|
private |
References core::id::DOF_ID::BOGUS_DOF_ID(), core::pose::Pose::dof(), dof_ids_, protocols::TR(), and verbose_.
Referenced by figure_out_dof_ids_and_offsets().
◆ fill_chainTORS()
|
private |
References atom_ids_, and core::pose::Pose::xyz().
Referenced by apply_solutions(), and close_at_cutpoint().
◆ fill_solution()
| void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::fill_solution | ( | core::pose::Pose & | pose, |
| core::Size const | n | ||
| ) | const |
References dof_ids_, offset_save_, core::pose::Pose::set_dof(), and t_ang_.
Referenced by apply_solutions(), and get_all_solutions().
◆ get_all_solutions()
| void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_all_solutions | ( | core::pose::Pose & | pose, |
| utility::vector1< core::pose::PoseOP > & | pose_list | ||
| ) |
References core::pose::Pose::dump_pdb(), fill_solution(), nsol_, and verbose_.
◆ get_name()
|
inlineoverridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ get_torsions()
| utility::vector1< Real > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions | ( | core::Size const | n | ) |
References offset_save_, and t_ang_.
Referenced by get_torsions_for_all_solutions().
◆ get_torsions_for_all_solutions()
| utility::vector1< utility::vector1< Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions_for_all_solutions | ( | ) |
References get_torsions(), and t_ang_.
◆ nsol()
|
inline |
References nsol_.
◆ output_chainTORS()
|
private |
References core::chemical::element::F, core::chemical::element::I, and protocols::TR().
Referenced by apply_solutions(), and close_at_cutpoint().
Member Data Documentation
◆ atom_ids_
|
private |
Referenced by apply_solutions(), close_at_cutpoint(), and fill_chainTORS().
◆ b_ang_
|
private |
Referenced by apply_solutions(), and close_at_cutpoint().
◆ b_len_
|
private |
Referenced by apply_solutions(), and close_at_cutpoint().
◆ chainbreak_suite_
|
private |
Referenced by close_at_cutpoint(), and figure_out_dof_ids_and_offsets().
◆ choose_best_solution_
|
private |
◆ choose_least_perturb_solution_
|
private |
◆ dof_ids_
|
private |
Referenced by figure_out_dof_ids_and_offsets(), figure_out_offset(), and fill_solution().
◆ moving_suite_
|
private |
Referenced by close_at_cutpoint(), and figure_out_dof_ids_and_offsets().
◆ nsol_
|
private |
Referenced by apply_solutions(), close_at_cutpoint(), get_all_solutions(), and nsol().
◆ offset_save_
|
private |
Referenced by figure_out_dof_ids_and_offsets(), fill_solution(), and get_torsions().
◆ scorefxn_
|
private |
Referenced by apply_solutions(), and choose_best_solution_based_on_score_function().
◆ t_ang_
|
private |
Referenced by apply_solutions(), close_at_cutpoint(), fill_solution(), get_torsions(), and get_torsions_for_all_solutions().
◆ verbose_
|
private |
Referenced by apply_solutions(), close_at_cutpoint(), figure_out_offset(), and get_all_solutions().
The documentation for this class was generated from the following files:
- src/protocols/stepwise/legacy/modeler/rna/RNA_AnalyticLoopCloser.hh
- src/protocols/stepwise/legacy/modeler/rna/RNA_AnalyticLoopCloser.cc
