#include <StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD.hh>

Public Member Functions
	StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD (StepWiseRNA_JobParametersCOP &job_parameters_)

	~StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD ()

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=true)

void	prepare_from_prior_sampled_sugar_jobs_for_chain_break (pose::Pose const &pose, utility::vector1< pose::PoseOP > &starting_pose_data_list)

SugarModeling const &	anchor_sugar_modeling ()

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)

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
bool	initialize_parameters (pose::Pose const &pose)

bool	do_consistency_checks ()

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	is_anchor_sugar_virtual (pose::Pose const &pose)

bool	is_current_sugar_virtual (pose::Pose const &pose)

bool	is_five_prime_chain_break_sugar_virtual (pose::Pose const &pose)

bool	is_three_prime_chain_break_sugar_virtual (pose::Pose const &pose)

void	instantiate_sugar (pose::Pose &pose, SugarModeling const &sugar_modeling, Size const sugar_ID)

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_

bool const	is_prepend_

Size const	moving_res_

Size const	five_prime_chain_break_res_

Size const	three_prime_chain_break_res_

Size const	num_nucleotides_

Size const	gap_size_

bool const	rebuild_bulge_mode_

bool	is_anchor_sugar_virt_

bool	is_current_sugar_virt_

bool	is_five_prime_chain_break_sugar_virt_

bool	is_three_prime_chain_break_sugar_virt_

Size	num_virtual_sugar_

SugarModeling	anchor_sugar_modeling_

SugarModeling	current_sugar_modeling_

SugarModeling	five_prime_chain_break_sugar_modeling_

SugarModeling	three_prime_chain_break_sugar_modeling_

bool	keep_base_fixed_

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::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD ( StepWiseRNA_JobParametersCOP & job_parameters_ )

References rebuild_bulge_mode, and size().

protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::~StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD ( )

Member Function Documentation

SugarModeling const & protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::anchor_sugar_modeling ( )

References anchor_sugar_modeling_.

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

virtual

Implements protocols::moves::Mover.

References do_the_sampling(), and success_.

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_consistency_checks ( )

private

References floating_base, gap_size_, is_anchor_sugar_virt_, is_current_sugar_virt_, is_five_prime_chain_break_sugar_virt_, is_three_prime_chain_break_sugar_virt_, job_parameters_, num_nucleotides_, num_virtual_sugar_, options_, runtime_assert, and protocols::TR.

Referenced by initialize_parameters().

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

private

Referenced by do_the_sampling().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_the_sampling ( core::pose::Pose & pose )

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

virtual

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

Implements protocols::moves::Mover.

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::initialize_parameters ( pose::Pose const & pose )

private

References anchor_sugar_modeling_, current_sugar_modeling_, do_consistency_checks(), five_prime_chain_break_sugar_modeling_, is_anchor_sugar_virt_, is_anchor_sugar_virtual(), is_current_sugar_virt_, is_current_sugar_virtual(), is_five_prime_chain_break_sugar_virt_, is_five_prime_chain_break_sugar_virtual(), is_three_prime_chain_break_sugar_virt_, is_three_prime_chain_break_sugar_virtual(), job_parameters_, num_virtual_sugar_, protocols::stepwise::sampling::rna::output_boolean(), three_prime_chain_break_sugar_modeling_, and protocols::TR.

Referenced by do_the_sampling().

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

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 prepare_from_prior_sampled_sugar_jobs(), and prepare_from_prior_sampled_sugar_jobs_for_chain_break().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_anchor_sugar_virtual ( pose::Pose const & pose )

private

References anchor_sugar_modeling_, job_parameters_, and setup_sugar_modeling().

Referenced by initialize_parameters().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_current_sugar_virtual ( pose::Pose const & pose )

private

References current_sugar_modeling_, moving_res_, setup_sugar_modeling(), and virtual_sugar_res.

Referenced by initialize_parameters().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_five_prime_chain_break_sugar_virtual ( pose::Pose const & pose )

private

References five_prime_chain_break_res_, five_prime_chain_break_sugar_modeling_, gap_size_, moving_res_, and setup_sugar_modeling().

Referenced by initialize_parameters().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_three_prime_chain_break_sugar_virtual ( pose::Pose const & pose )

private

References gap_size_, moving_res_, setup_sugar_modeling(), three_prime_chain_break_res_, and three_prime_chain_break_sugar_modeling_.

Referenced by initialize_parameters().

void protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::prepare_from_prior_sampled_sugar_jobs	(	pose::Pose const &	pose,
		utility::vector1< pose::PoseOP > &	starting_pose_data_list,
		bool const	pose_explosion_legacy = `true`
	)

References anchor_sugar_modeling_, core::pose::Pose::clone(), current_sugar_modeling_, five_prime_chain_break_sugar_modeling_, instantiate_sugar(), job_parameters_, protocols::stepwise::sampling::rna::sugar::minimize_all_sampled_floating_bases(), options_, protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, runtime_assert, sampling_sugar(), scorefxn_, tag_into_pose(), three_prime_chain_break_sugar_modeling_, protocols::TR, and utility_exit_with_message.

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

References core::pose::Pose::clone(), five_prime_chain_break_sugar_modeling_, instantiate_sugar(), protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, sampling_sugar_at_chain_break(), tag_into_pose(), three_prime_chain_break_sugar_modeling_, and utility_exit_with_message.

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::sampling_sugar ( ) const

References anchor_sugar_modeling_, current_sugar_modeling_, five_prime_chain_break_sugar_modeling_, protocols::stepwise::sampling::rna::sugar::SugarModeling::sample_sugar, and three_prime_chain_break_sugar_modeling_.

Referenced by prepare_from_prior_sampled_sugar_jobs().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::sampling_sugar_at_chain_break ( ) const

References five_prime_chain_break_sugar_modeling_, protocols::stepwise::sampling::rna::sugar::SugarModeling::sample_sugar, and three_prime_chain_break_sugar_modeling_.

Referenced by prepare_from_prior_sampled_sugar_jobs_for_chain_break().

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

inline

void protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::set_options ( StepWiseRNA_ModelerOptionsCOP options )

References options_.

void protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

References scorefxn_.

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::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::legacy::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 is_anchor_sugar_virtual(), is_current_sugar_virtual(), is_five_prime_chain_break_sugar_virtual(), and is_three_prime_chain_break_sugar_virtual().

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

inline

Member Data Documentation

SugarModeling protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::anchor_sugar_modeling_

private

Referenced by anchor_sugar_modeling(), do_the_sampling(), initialize_parameters(), is_anchor_sugar_virtual(), prepare_from_prior_sampled_sugar_jobs(), and sampling_sugar().

SugarModeling protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::current_sugar_modeling_

private

Referenced by do_the_sampling(), initialize_parameters(), is_current_sugar_virtual(), prepare_from_prior_sampled_sugar_jobs(), and sampling_sugar().

Size const protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::five_prime_chain_break_res_

private

Referenced by is_five_prime_chain_break_sugar_virtual().

SugarModeling protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::five_prime_chain_break_sugar_modeling_

private

Referenced by do_the_sampling(), initialize_parameters(), is_five_prime_chain_break_sugar_virtual(), prepare_from_prior_sampled_sugar_jobs(), prepare_from_prior_sampled_sugar_jobs_for_chain_break(), sampling_sugar(), and sampling_sugar_at_chain_break().

Size const protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::gap_size_

private

Referenced by do_consistency_checks(), is_five_prime_chain_break_sugar_virtual(), and is_three_prime_chain_break_sugar_virtual().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_anchor_sugar_virt_

private

Referenced by do_consistency_checks(), do_the_sampling(), and initialize_parameters().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_current_sugar_virt_

private

Referenced by do_consistency_checks(), do_the_sampling(), and initialize_parameters().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_five_prime_chain_break_sugar_virt_

private

Referenced by do_consistency_checks(), do_the_sampling(), and initialize_parameters().

bool const protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_prepend_

private

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::is_three_prime_chain_break_sugar_virt_

private

Referenced by do_consistency_checks(), do_the_sampling(), and initialize_parameters().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::job_parameters_

private

Referenced by do_consistency_checks(), do_sugar_sampling(), initialize_parameters(), is_anchor_sugar_virtual(), prepare_from_prior_sampled_sugar_jobs(), and setup_sugar_modeling().

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::keep_base_fixed_

private

Size const protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::moving_res_

private

Referenced by do_the_sampling(), is_current_sugar_virtual(), is_five_prime_chain_break_sugar_virtual(), and is_three_prime_chain_break_sugar_virtual().

Size const protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::num_nucleotides_

private

Referenced by do_consistency_checks().

Size protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::num_virtual_sugar_

private

Referenced by do_consistency_checks(), and initialize_parameters().

StepWiseRNA_ModelerOptionsCOP protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::options_

private

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

bool const protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::rebuild_bulge_mode_

private

Referenced by do_the_sampling().

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

private

Referenced by do_the_sampling(), and setup_sugar_modeling().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::scorefxn_

private

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

bool protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::success_

private

Referenced by apply().

Size const protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::three_prime_chain_break_res_

private

Referenced by is_three_prime_chain_break_sugar_virtual().

SugarModeling protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::three_prime_chain_break_sugar_modeling_

private

Referenced by do_the_sampling(), initialize_parameters(), is_three_prime_chain_break_sugar_virtual(), prepare_from_prior_sampled_sugar_jobs(), prepare_from_prior_sampled_sugar_jobs_for_chain_break(), sampling_sugar(), and sampling_sugar_at_chain_break().

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

symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/legacy/StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD.hh
symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/legacy/StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation