#include <VirtualSugarJustInTimeInstantiator.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator:

[legend]

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 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
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< SugarModelingOP >	get_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< SugarModelingOP >	sugar_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

◆ VirtualSugarJustInTimeInstantiator()

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

◆ ~VirtualSugarJustInTimeInstantiator()

protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::~VirtualSugarJustInTimeInstantiator ( )

overridedefault

Member Function Documentation

◆ anchor_sugar_modeling()

SugarModeling const & protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::anchor_sugar_modeling ( )

References sampled_sugar_index(), sugar_modeling_sets_, and working_parameters_.

◆ apply()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References do_the_modeler(), and success_.

◆ do_sugar_sampling()

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

private

Referenced by get_sugar_modeling_set().

◆ do_the_modeler()

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_the_modeler ( core::pose::Pose & pose )

References core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::figure_out_moving_cutpoints_closed(), get_sugar_modeling_set(), core::chemical::ResidueTypeBase::is_RNA(), moving_res_, options_, protocols::stepwise::modeler::rna::output_title_text(), rebuild_bulge_mode_, core::pose::Pose::residue_type(), success(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ get_name()

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.

◆ get_sugar_modeling_set()

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::get_sugar_modeling_set	(	core::pose::Pose &	viewer_pose,
		core::Size const	i
	)

private

References protocols::stepwise::modeler::rna::sugar::convert_sugar_modeling_to_residue_alternative_set(), do_sugar_sampling(), moving_res_, moving_res_legacy_, residue_alternative_sets_, sampled_sugar_index(), setup_sugar_modeling(), core::pose::sort_pose_by_score(), sugar_modeling_sets_, viewer_pose, and working_parameters_.

Referenced by do_the_modeler().

◆ get_sugar_modeling_sets_for_chainbreak()

utility::vector1< SugarModelingOP > protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::get_sugar_modeling_sets_for_chainbreak ( ) const

private

References sugar_modeling_sets_, and working_parameters_.

Referenced by modeler_sugar_at_chain_break(), and prepare_from_prior_sampled_sugar_jobs_for_chain_break().

◆ instantiate_sugar()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugar	(	core::pose::Pose &	pose,
		SugarModeling const &	sugar_modeling,
		core::Size const	sugar_ID
	)		const

private

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

Referenced by instantiate_sugars_at_cutpoint_closed(), and instantiate_sugars_recursively().

◆ instantiate_sugars_at_cutpoint_closed()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_at_cutpoint_closed ( core::pose::Pose & pose ) const

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), instantiate_sugar(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), core::pose::Pose::size(), and sugar_modeling_sets_.

Referenced by prepare_from_prior_sampled_sugar_jobs().

◆ instantiate_sugars_recursively()

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

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

Referenced by prepare_from_prior_sampled_sugar_jobs(), and prepare_from_prior_sampled_sugar_jobs_for_chain_break().

◆ minimize_sugar_sets_legacy()

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

References protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), scorefxn_, sugar_modeling_sets_, and working_parameters_.

Referenced by prepare_from_prior_sampled_sugar_jobs().

◆ modeler_sugar()

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::modeler_sugar ( ) const

References num_sets().

Referenced by prepare_from_prior_sampled_sugar_jobs().

◆ modeler_sugar_at_chain_break()

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::modeler_sugar_at_chain_break ( ) const

References get_sugar_modeling_sets_for_chainbreak().

Referenced by prepare_from_prior_sampled_sugar_jobs_for_chain_break().

◆ num_sets()

core::Size protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::num_sets ( ) const

inline

References sugar_modeling_sets_.

Referenced by instantiate_sugars_recursively(), and modeler_sugar().

◆ prepare_from_prior_sampled_sugar_jobs()

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

References core::pose::Pose::clone(), instantiate_sugars_at_cutpoint_closed(), instantiate_sugars_recursively(), minimize_sugar_sets_legacy(), modeler_sugar(), options_, and sugar_modeling_sets_.

◆ prepare_from_prior_sampled_sugar_jobs_for_chain_break()

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

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

◆ residue_alternative_set()

sampler::copy_dofs::ResidueAlternativeSet const & protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::residue_alternative_set ( core::Size const n )

References residue_alternative_sets_.

◆ sampled_sugar_index()

Size protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::sampled_sugar_index ( core::Size const i )

private

References sugar_modeling_sets_.

Referenced by anchor_sugar_modeling(), and get_sugar_modeling_set().

◆ set_keep_base_fixed()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::set_keep_base_fixed ( bool const & setting )

inline

References keep_base_fixed_.

◆ set_options()

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

References options_.

◆ set_scorefxn()

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

References scorefxn_.

◆ setup_sugar_modeling()

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

private

References protocols::stepwise::modeler::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::modeler::rna::sugar::SugarModeling::bulge_suite, protocols::stepwise::modeler::rna::sugar::get_reference_res_for_virtual_sugar_based_on_fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), protocols::stepwise::modeler::rna::sugar::is_sugar_virtual(), protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res, options_, protocols::stepwise::modeler::rna::sugar::SugarModeling::reference_res, core::pose::Pose::residue_type(), protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state(), protocols::TR(), and working_parameters_.

Referenced by get_sugar_modeling_set().

◆ success()

bool const& protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::success ( ) const

inline

References success_.

Referenced by do_the_modeler().

Member Data Documentation

◆ keep_base_fixed_

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

private

Referenced by set_keep_base_fixed().

◆ moving_res_

core::Size const protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::moving_res_

private

Referenced by do_the_modeler(), and get_sugar_modeling_set().

◆ moving_res_legacy_

bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::moving_res_legacy_

private

Referenced by get_sugar_modeling_set().

◆ options_

options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::options_

private

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

◆ rebuild_bulge_mode_

bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::rebuild_bulge_mode_

private

Referenced by do_the_modeler().

◆ residue_alternative_sets_

utility::vector1< sampler::copy_dofs::ResidueAlternativeSetOP> protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::residue_alternative_sets_

private

Referenced by get_sugar_modeling_set(), and residue_alternative_set().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::scorefxn_

private

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

◆ success_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::success_

private

Referenced by apply(), and success().

◆ sugar_modeling_sets_

utility::vector1< SugarModelingOP > protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::sugar_modeling_sets_

private

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

◆ working_parameters_

working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::working_parameters_

private

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

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

src/protocols/stepwise/modeler/rna/sugar/VirtualSugarJustInTimeInstantiator.hh
src/protocols/stepwise/modeler/rna/sugar/VirtualSugarJustInTimeInstantiator.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ VirtualSugarJustInTimeInstantiator()

◆ ~VirtualSugarJustInTimeInstantiator()

Member Function Documentation

◆ anchor_sugar_modeling()

◆ apply()

◆ do_sugar_sampling()

◆ do_the_modeler()

◆ get_name()

◆ get_sugar_modeling_set()

◆ get_sugar_modeling_sets_for_chainbreak()

◆ instantiate_sugar()

◆ instantiate_sugars_at_cutpoint_closed()

◆ instantiate_sugars_recursively()

◆ minimize_sugar_sets_legacy()

◆ modeler_sugar()

◆ modeler_sugar_at_chain_break()

◆ num_sets()

◆ prepare_from_prior_sampled_sugar_jobs()

◆ prepare_from_prior_sampled_sugar_jobs_for_chain_break()

◆ residue_alternative_set()

◆ sampled_sugar_index()

◆ set_keep_base_fixed()

◆ set_options()

◆ set_scorefxn()

◆ setup_sugar_modeling()

◆ success()

Member Data Documentation

◆ keep_base_fixed_

◆ moving_res_

◆ moving_res_legacy_

◆ options_

◆ rebuild_bulge_mode_

◆ residue_alternative_sets_

◆ scorefxn_

◆ success_

◆ sugar_modeling_sets_

◆ working_parameters_