#include <VirtualSugarSamplerFromStringList.hh>
Public Member Functions | |
| VirtualSugarSamplerFromStringList (working_parameters::StepWiseWorkingParametersCOP &working_parameters, utility::vector1< std::string > const &sample_virtual_sugar_string_list) | |
| ~VirtualSugarSamplerFromStringList () override | |
| void | apply (core::pose::Pose &pose_to_visualize) override |
| Main Method. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn) |
| void | set_use_phenix_geo (bool const &setting) |
| void | set_legacy_mode (bool const &setting) |
| void | set_choose_random (bool const &setting) |
| void | set_integration_test_mode (bool const &setting) |
| void | set_tag (std::string const &setting) |
| void | set_silent_file_out (std::string const &setting) |
 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 MoverOP | clone () const |
| Return a clone of the Mover object. 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 | |
| utility::vector1< SugarModeling > | setup_sugar_modeling_list (core::pose::Pose const &pose) const |
| bool | empty_sugar_modeling_list (utility::vector1< SugarModeling > const &sugar_modeling_list) |
| bool | empty_pose_data_list (utility::vector1< core::pose::PoseOP > const &pose_list, core::Size const n, std::string tag) |
| void | output_pose_data_list (utility::vector1< core::pose::PoseOP > &pose_data_list) |
Private Attributes | |
| working_parameters::StepWiseWorkingParametersCOP | working_parameters_ |
| utility::vector1< std::string > const | sample_virtual_sugar_string_list_ |
| std::string | silent_file_out_ |
| bool | use_phenix_geo_ |
| bool | legacy_mode_ |
| bool | choose_random_ |
| bool | integration_test_mode_ |
| std::string | tag_ |
| core::scoring::ScoreFunctionOP | scorefxn_ |
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... | |
Constructor & Destructor Documentation
◆ VirtualSugarSamplerFromStringList()
| protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::VirtualSugarSamplerFromStringList | ( | working_parameters::StepWiseWorkingParametersCOP & | working_parameters, |
| utility::vector1< std::string > const & | sample_virtual_sugar_string_list | ||
| ) |
◆ ~VirtualSugarSamplerFromStringList()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply(), choose_random_, core::conformation::Conformation::clone(), core::pose::full_model_info::FullModelInfo::clone_info(), core::pose::Pose::conformation(), empty_pose_data_list(), empty_sugar_modeling_list(), integration_test_mode_, legacy_mode_, protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), protocols::stepwise::modeler::rna::sugar::modeler_starting_pose_data_list(), core::pose::full_model_info::nonconst_full_model_info(), output_pose_data_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::sugar::SugarModeling::pose_list, scorefxn_, protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_choose_random(), core::pose::full_model_info::set_full_model_info(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_integration_test_mode(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_legacy_mode(), core::pose::Pose::set_new_conformation(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_scorefxn(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_tag(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_use_phenix_geo(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_virtual_sugar_is_from_prior_step(), setup_sugar_modeling_list(), core::pose::sort_pose_by_score(), core::pose::tag_into_pose(), protocols::TR(), use_phenix_geo_, and working_parameters_.
◆ empty_pose_data_list()
|
private |
References silent_file_out_, and protocols::TR().
Referenced by apply().
◆ empty_sugar_modeling_list()
|
private |
References silent_file_out_, and protocols::TR().
Referenced by apply().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ output_pose_data_list()
|
private |
References protocols::stepwise::modeler::rna::output_data(), silent_file_out_, tag_, core::pose::tag_from_pose(), and working_parameters_.
Referenced by apply().
◆ set_choose_random()
|
inline |
References choose_random_.
◆ set_integration_test_mode()
|
inline |
References integration_test_mode_.
◆ set_legacy_mode()
|
inline |
References legacy_mode_.
◆ set_scorefxn()
| void protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::set_scorefxn | ( | core::scoring::ScoreFunctionOP const & | scorefxn | ) |
References scorefxn_.
◆ set_silent_file_out()
|
inline |
References silent_file_out_.
◆ set_tag()
|
inline |
References tag_.
◆ set_use_phenix_geo()
|
inline |
References use_phenix_geo_.
◆ setup_sugar_modeling_list()
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private |
References protocols::stepwise::modeler::rna::check_is_working_res(), protocols::stepwise::modeler::rna::check_validity_and_get_working_res(), core::conformation::Residue::has_variant_type(), protocols::stepwise::modeler::output_boolean(), core::pose::rna::remove_bracketed(), core::pose::Pose::residue(), sample_virtual_sugar_string_list_, core::pose::Pose::size(), protocols::stepwise::modeler::rna::string_to_int(), protocols::stepwise::modeler::rna::tokenize(), protocols::TR(), core::chemical::VIRTUAL_RIBOSE, core::chemical::VIRTUAL_RNA_RESIDUE, and working_parameters_.
Referenced by apply().
Member Data Documentation
◆ choose_random_
|
private |
Referenced by apply(), and set_choose_random().
◆ integration_test_mode_
|
private |
Referenced by apply(), and set_integration_test_mode().
◆ legacy_mode_
|
private |
Referenced by apply(), and set_legacy_mode().
◆ sample_virtual_sugar_string_list_
|
private |
Referenced by setup_sugar_modeling_list().
◆ scorefxn_
|
private |
Referenced by apply(), and set_scorefxn().
◆ silent_file_out_
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private |
Referenced by empty_pose_data_list(), empty_sugar_modeling_list(), output_pose_data_list(), and set_silent_file_out().
◆ tag_
|
private |
Referenced by output_pose_data_list(), and set_tag().
◆ use_phenix_geo_
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private |
Referenced by apply(), and set_use_phenix_geo().
◆ working_parameters_
|
private |
Referenced by apply(), output_pose_data_list(), and setup_sugar_modeling_list().
The documentation for this class was generated from the following files:
- src/protocols/stepwise/modeler/rna/sugar/VirtualSugarSamplerFromStringList.hh
- src/protocols/stepwise/modeler/rna/sugar/VirtualSugarSamplerFromStringList.cc
