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protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator Class Reference

#include <VirtualSugarJustInTimeInstantiator.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator:
Inheritance graph
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Public Member Functions

 VirtualSugarJustInTimeInstantiator (working_parameters::StepWiseWorkingParametersCOP &working_parameters_)
 
 ~VirtualSugarJustInTimeInstantiator () 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...
 
bool do_the_modeler (core::pose::Pose &pose)
 
bool modeler_sugar () const
 
bool modeler_sugar_at_chain_break () const
 
void prepare_from_prior_sampled_sugar_jobs (core::pose::Pose const &pose, utility::vector1< core::pose::PoseOP > &starting_pose_data_list, bool const pose_explosion_legacy) const
 
void prepare_from_prior_sampled_sugar_jobs_for_chain_break (core::pose::Pose const &pose, utility::vector1< core::pose::PoseOP > &starting_pose_data_list) const
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_keep_base_fixed (bool const &setting)
 
bool const & success () const
 
void set_options (options::StepWiseModelerOptionsCOP options)
 
core::Size num_sets () const
 
sampler::copy_dofs::ResidueAlternativeSet
const & 
residue_alternative_set (core::Size const n)
 
SugarModeling const & anchor_sugar_modeling ()
 
void instantiate_sugars_at_cutpoint_closed (core::pose::Pose &pose) const
 
- 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 Stringsinfo ()
 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

core::Size sampled_sugar_index (core::Size const i)
 
bool do_sugar_sampling (core::pose::Pose &viewer_pose, SugarModeling &sugar_modeling, std::string const &name)
 
bool setup_sugar_modeling (core::pose::Pose const &pose, core::Size const moving_res, SugarModeling &sugar_modeling)
 
bool get_sugar_modeling_set (core::pose::Pose &viewer_pose, core::Size const i)
 
utility::vector1< SugarModelingOPget_sugar_modeling_sets_for_chainbreak () const
 
void instantiate_sugar (core::pose::Pose &pose, SugarModeling const &sugar_modeling, core::Size const sugar_ID) const
 
void instantiate_sugars_recursively (core::pose::Pose const &pose, utility::vector1< core::pose::PoseOP > &pose_data_list, utility::vector1< SugarModelingOP > const &sugar_modeling_sets, utility::vector1< core::Size > const &sugar_modeling_set_indices) const
 
void minimize_sugar_sets_legacy (core::pose::Pose const &pose, utility::vector1< core::pose::PoseOP > &pose_data_list) const
 

Private Attributes

working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
core::Size const moving_res_
 
bool const rebuild_bulge_mode_
 
utility::vector1< SugarModelingOPsugar_modeling_sets_
 
utility::vector1
< sampler::copy_dofs::ResidueAlternativeSetOP
residue_alternative_sets_
 
bool keep_base_fixed_
 
bool const moving_res_legacy_
 
options::StepWiseModelerOptionsCOP options_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
bool success_
 

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

protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::VirtualSugarJustInTimeInstantiator ( working_parameters::StepWiseWorkingParametersCOP working_parameters_)
protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::~VirtualSugarJustInTimeInstantiator ( )
overridedefault

Member Function Documentation

SugarModeling const & protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::anchor_sugar_modeling ( )
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References do_the_modeler(), and success_.

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling ( core::pose::Pose viewer_pose,
SugarModeling sugar_modeling,
std::string const &  name 
)
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_the_modeler ( core::pose::Pose pose)
std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::get_sugar_modeling_set ( core::pose::Pose viewer_pose,
core::Size const  i 
)
private
utility::vector1< SugarModelingOP > protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::get_sugar_modeling_sets_for_chainbreak ( ) const
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugar ( core::pose::Pose pose,
SugarModeling const &  sugar_modeling,
core::Size const  sugar_ID 
) const
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_at_cutpoint_closed ( core::pose::Pose pose) const
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_recursively ( core::pose::Pose const &  pose,
utility::vector1< core::pose::PoseOP > &  pose_data_list,
utility::vector1< SugarModelingOP > const &  sugar_modeling_sets,
utility::vector1< core::Size > const &  sugar_modeling_set_indices 
) const
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::minimize_sugar_sets_legacy ( core::pose::Pose const &  pose,
utility::vector1< core::pose::PoseOP > &  pose_data_list 
) const
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::modeler_sugar ( ) const
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::modeler_sugar_at_chain_break ( ) const
core::Size protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::num_sets ( ) const
inline
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::prepare_from_prior_sampled_sugar_jobs ( core::pose::Pose const &  pose,
utility::vector1< core::pose::PoseOP > &  starting_pose_data_list,
bool const  pose_explosion_legacy 
) const
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::prepare_from_prior_sampled_sugar_jobs_for_chain_break ( core::pose::Pose const &  pose,
utility::vector1< core::pose::PoseOP > &  starting_pose_data_list 
) const
sampler::copy_dofs::ResidueAlternativeSet const & protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::residue_alternative_set ( core::Size const  n)
Size protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::sampled_sugar_index ( core::Size const  i)
private
void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::set_keep_base_fixed ( bool const &  setting)
inline

References keep_base_fixed_.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::set_options ( options::StepWiseModelerOptionsCOP  options)

References options_.

void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::setup_sugar_modeling ( core::pose::Pose const &  pose,
core::Size const  moving_res,
SugarModeling sugar_modeling 
)
private
bool const& protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::success ( ) const
inline

References success_.

Referenced by do_the_modeler().

Member Data Documentation

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::keep_base_fixed_
private

Referenced by set_keep_base_fixed().

core::Size const protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::moving_res_
private
bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::moving_res_legacy_
private

Referenced by get_sugar_modeling_set().

options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::options_
private
bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::rebuild_bulge_mode_
private

Referenced by do_the_modeler().

utility::vector1< sampler::copy_dofs::ResidueAlternativeSetOP> protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::residue_alternative_sets_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::scorefxn_
private
bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::success_
private

Referenced by apply(), and success().

utility::vector1< SugarModelingOP > protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::sugar_modeling_sets_
private
working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::working_parameters_
private

The documentation for this class was generated from the following files: