protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator Class Reference

#include <StepWiseRNA_VirtualSugarJustInTimeInstantiator.hh>

Public Member Functions
	StepWiseRNA_VirtualSugarJustInTimeInstantiator (StepWiseRNA_JobParametersCOP &job_parameters_)
	~StepWiseRNA_VirtualSugarJustInTimeInstantiator ()
virtual void	apply (pose::Pose &pose_to_visualize)
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
bool	do_the_sampling (core::pose::Pose &pose)
bool	sampling_sugar () const
bool	sampling_sugar_at_chain_break () const
void	prepare_from_prior_sampled_sugar_jobs (pose::Pose const &pose, utility::vector1< pose::PoseOP > &starting_pose_data_list, bool const pose_explosion_legacy) const
void	prepare_from_prior_sampled_sugar_jobs_for_chain_break (pose::Pose const &pose, utility::vector1< pose::PoseOP > &starting_pose_data_list) const
void	set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
void	set_keep_base_fixed (bool const &setting)
bool const &	success () const
void	set_options (StepWiseRNA_ModelerOptionsCOP options)
Size	num_sets () const
rotamer_sampler::copy_dofs::ResidueAlternativeSet const &	residue_alternative_set (Size const n)
SugarModeling const &	anchor_sugar_modeling ()
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
	Return a clone of the Mover object. More...
virtual void	parse_my_tag (TagCOP tag, basic::datacache::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
	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...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

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

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_
Size const	moving_res_
bool const	rebuild_bulge_mode_
utility::vector1< SugarModelingOP >	sugar_modeling_sets_
utility::vector1 < rotamer_sampler::copy_dofs::ResidueAlternativeSetOP >	residue_alternative_sets_
bool	keep_base_fixed_
bool const	moving_res_legacy_
bool const	include_current_
StepWiseRNA_ModelerOptionsCOP	options_
core::scoring::ScoreFunctionOP	scorefxn_
std::map< Size, Size >	reference_res_for_each_virtual_sugar_
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 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. 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::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::StepWiseRNA_VirtualSugarJustInTimeInstantiator

(

StepWiseRNA_JobParametersCOP &

job_parameters_

)

References rebuild_bulge_mode.

protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::~StepWiseRNA_VirtualSugarJustInTimeInstantiator

(

)

Member Function Documentation

SugarModeling const & protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::anchor_sugar_modeling

(

)

References job_parameters_, sampled_sugar_index(), and sugar_modeling_sets_.

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::apply ( pose::Pose &  pose_to_visualize )

virtual

Implements protocols::moves::Mover.

References do_the_sampling(), and success_.

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling ( pose::Pose &  viewer_pose, SugarModeling &  sugar_modeling, std::string const  name  )

private

References protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply(), job_parameters_, options_, protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, scorefxn_, protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_choose_random(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_do_minimize(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_integration_test_mode(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_keep_base_fixed(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_legacy_mode(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_scorefxn(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_tag(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_use_phenix_geo(), and protocols::TR.

Referenced by get_sugar_modeling_set().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_the_sampling

(

core::pose::Pose &

pose

)

References protocols::stepwise::sampling::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::figure_out_moving_cutpoints_closed(), protocols::stepwise::sampling::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree(), get_sugar_modeling_set(), job_parameters_, utility::tools::make_vector1(), moving_res_, protocols::stepwise::sampling::rna::output_title_text(), rebuild_bulge_mode_, reference_res_for_each_virtual_sugar_, success(), and protocols::TR.

Referenced by apply().

std::string protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::get_sugar_modeling_set ( pose::Pose &  viewer_pose, Size const  i  )

private

References core::pose::Pose::clone(), protocols::stepwise::sampling::rna::sugar::convert_sugar_modeling_to_residue_alternative_set(), do_sugar_sampling(), job_parameters_, moving_res_, moving_res_legacy_, residue_alternative_sets_, sampled_sugar_index(), setup_sugar_modeling(), sort_pose_by_score(), and sugar_modeling_sets_.

Referenced by do_the_sampling().

utility::vector1< SugarModelingOP > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::get_sugar_modeling_sets_for_chainbreak ( ) const

private

References job_parameters_, and sugar_modeling_sets_.

Referenced by prepare_from_prior_sampled_sugar_jobs_for_chain_break(), and sampling_sugar_at_chain_break().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::instantiate_sugar ( pose::Pose &  pose, SugarModeling const &  sugar_modeling, Size const  sugar_ID  ) const

private

References protocols::stepwise::sampling::rna::sugar::copy_bulge_res_and_sugar_torsion(), protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, tag_from_pose(), and tag_into_pose().

Referenced by instantiate_sugars_recursively(), and prepare_from_prior_sampled_sugar_jobs().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::instantiate_sugars_recursively ( pose::Pose const &  pose, utility::vector1< pose::PoseOP > &  pose_data_list, utility::vector1< SugarModelingOP > const &  sugar_modeling_sets, utility::vector1< Size > const &  sugar_modeling_set_indices  ) const

private

References core::pose::Pose::clone(), instantiate_sugar(), num_sets(), q, runtime_assert, and tag_into_pose().

Referenced by prepare_from_prior_sampled_sugar_jobs(), and prepare_from_prior_sampled_sugar_jobs_for_chain_break().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::minimize_sugar_sets_legacy ( pose::Pose const &  pose, utility::vector1< pose::PoseOP > &  pose_data_list  ) const

private

References job_parameters_, protocols::stepwise::sampling::rna::sugar::minimize_all_sampled_floating_bases(), scorefxn_, and sugar_modeling_sets_.

Referenced by prepare_from_prior_sampled_sugar_jobs().

Size protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::num_sets ( ) const

inline

Referenced by instantiate_sugars_recursively(), and sampling_sugar().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::prepare_from_prior_sampled_sugar_jobs	(	pose::Pose const &	pose,
		utility::vector1< pose::PoseOP > &	starting_pose_data_list,
		bool const	pose_explosion_legacy
	)		const

References core::pose::Pose::clone(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), instantiate_sugar(), instantiate_sugars_recursively(), core::kinematics::FoldTree::is_cutpoint(), minimize_sugar_sets_legacy(), options_, core::pose::Pose::residue(), runtime_assert, sampling_sugar(), sugar_modeling_sets_, and core::pose::Pose::total_residue().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::prepare_from_prior_sampled_sugar_jobs_for_chain_break	(	pose::Pose const &	pose,
		utility::vector1< pose::PoseOP > &	starting_pose_data_list
	)		const

References core::pose::Pose::dump_pdb(), get_sugar_modeling_sets_for_chainbreak(), instantiate_sugars_recursively(), runtime_assert, and sampling_sugar_at_chain_break().

rotamer_sampler::copy_dofs::ResidueAlternativeSet const & protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::residue_alternative_set

(

Size const

n

)

References residue_alternative_sets_, and runtime_assert.

Size protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::sampled_sugar_index ( Size const  i )

private

References sugar_modeling_sets_.

Referenced by anchor_sugar_modeling(), and get_sugar_modeling_set().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::sampling_sugar

(

)

const

References num_sets().

Referenced by prepare_from_prior_sampled_sugar_jobs().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::sampling_sugar_at_chain_break

(

)

const

References get_sugar_modeling_sets_for_chainbreak(), and size().

Referenced by prepare_from_prior_sampled_sugar_jobs_for_chain_break().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::set_keep_base_fixed ( bool const &  setting )

inline

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::set_options

(

StepWiseRNA_ModelerOptionsCOP

options

)

References options_.

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::set_scorefxn

(

core::scoring::ScoreFunctionOP const &

scorefxn

)

References scorefxn_.

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::setup_sugar_modeling ( pose::Pose const &  pose, Size const  moving_res, SugarModeling &  sugar_modeling  )

private

References protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_suite, core::chemical::ResidueType::has_variant_type(), protocols::stepwise::sampling::rna::sugar::is_sugar_virtual(), job_parameters_, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res_base_state, protocols::stepwise::sampling::rna::sugar::SugarModeling::reference_res, reference_res_for_each_virtual_sugar_, core::pose::Pose::residue_type(), SYN, and protocols::TR.

Referenced by get_sugar_modeling_set().

bool const& protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::success ( ) const

inline

Referenced by do_the_sampling().

Member Data Documentation

bool const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::include_current_

private

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::job_parameters_

private

Referenced by anchor_sugar_modeling(), do_sugar_sampling(), do_the_sampling(), get_sugar_modeling_set(), get_sugar_modeling_sets_for_chainbreak(), minimize_sugar_sets_legacy(), and setup_sugar_modeling().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::keep_base_fixed_

private

Size const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::moving_res_

private

Referenced by do_the_sampling(), and get_sugar_modeling_set().

bool const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::moving_res_legacy_

private

Referenced by get_sugar_modeling_set().

StepWiseRNA_ModelerOptionsCOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::options_

private

Referenced by do_sugar_sampling(), prepare_from_prior_sampled_sugar_jobs(), and set_options().

bool const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::rebuild_bulge_mode_

private

Referenced by do_the_sampling().

std::map< Size, Size > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::reference_res_for_each_virtual_sugar_

private

Referenced by do_the_sampling(), and setup_sugar_modeling().

utility::vector1< rotamer_sampler::copy_dofs::ResidueAlternativeSetOP> protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::residue_alternative_sets_

private

Referenced by get_sugar_modeling_set(), and residue_alternative_set().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::scorefxn_

private

Referenced by do_sugar_sampling(), minimize_sugar_sets_legacy(), and set_scorefxn().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::success_

private

Referenced by apply().

utility::vector1< SugarModelingOP > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::sugar_modeling_sets_

private

Referenced by anchor_sugar_modeling(), get_sugar_modeling_set(), get_sugar_modeling_sets_for_chainbreak(), minimize_sugar_sets_legacy(), prepare_from_prior_sampled_sugar_jobs(), and sampled_sugar_index().

---

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/StepWiseRNA_VirtualSugarJustInTimeInstantiator.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/StepWiseRNA_VirtualSugarJustInTimeInstantiator.cc