The RNA de novo structure modeling protocol. More...

#include <RNA_HelixAssembler.hh>

Public Member Functions
	RNA_HelixAssembler ()
	Construct the protocol object. More...

	~RNA_HelixAssembler ()
	Destroy the protocol object. More...

virtual protocols::moves::MoverOP	clone () const
	Clone this object. More...

void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	apply (core::pose::Pose &pose, std::string const &sequence)
	Apply the loop-rebuild protocol to the input pose. More...

void	random_perturbation (bool const &setting)

void	set_dump (bool const &setting)

void	set_minimize_all (bool const &setting)

void	set_scorefxn (core::scoring::ScoreFunctionOP setting)

void	set_finish_scorefxn (core::scoring::ScoreFunctionOP setting)

void	use_phenix_geo (bool const setting)

void	set_model_and_remove_capping_residues (bool setting)

void	build_helix (core::pose::Pose &pose, std::string const &full_sequence)

core::pose::PoseOP	build_init_pose (std::string const &seq1, std::string const &seq2)

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

void	set_type (std::string const &setting)

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 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
void	initialize_minimizer ()

void	set_Aform_torsions (core::pose::Pose &pose, Size const &n) const

void	build_on_base_pair (core::pose::Pose &pose, Size const &n, char const &seq1, char const &seq2) const

void	minimize_base_step (core::pose::Pose &pose, Size const n, core::scoring::ScoreFunctionOP scorefxn) const

void	put_constraints_on_base_step (core::pose::Pose &pose, Size const &n) const

void	get_rid_of_capping_base_pairs (core::pose::Pose &pose) const

std::string	figure_out_and_remove_dangling_ends (std::string const &full_sequence)

void	build_dangling_ends (core::pose::Pose &pose) const

void	build_dangle_seq1_5prime (core::pose::Pose &pose, std::string const &dangle_seq) const

void	build_dangle_seq2_5prime (core::pose::Pose &pose, std::string const &dangle_seq) const

void	build_dangle_seq1_3prime (core::pose::Pose &pose, std::string const &dangle_seq) const

void	build_dangle_seq2_3prime (core::pose::Pose &pose, std::string const &dangle_seq) const

core::Size	get_cutpoint (core::pose::Pose const &pose) const

void	append_Aform_residue (core::pose::Pose &pose, Size const &n, char const &nt) const

void	prepend_Aform_residue (core::pose::Pose &pose, Size const &n, char const &nt) const

void	perturb_torsion (core::pose::Pose &pose, utility::vector1< core::id::TorsionID > const &id_list) const

void	minimize_append_res (core::pose::Pose &pose, Size const n) const

void	minimize_prepend_res (core::pose::Pose &pose, Size const n) const

void	fill_chain_info (core::pose::Pose &pose, std::string const &full_sequence)

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...

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::RNA_HelixAssembler ( )

Construct the protocol object.

References chemical, FA_RNA, initialize_minimizer(), residue_type_set, and scoring.

Referenced by clone().

protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::~RNA_HelixAssembler ( )

Destroy the protocol object.

Member Function Documentation

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::append_Aform_residue	(	core::pose::Pose &	pose,
		Size const &	n,
		char const &	nt
	)		const

private

References aa_from_oneletter_code(), core::pose::Pose::append_polymer_residue_after_seqpos(), BB, core::chemical::rna::RNA_FittedTorsionInfo::epsilon_aform(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), perturb_torsion(), random_perturbation_, rsd_set_, runtime_assert, set_Aform_torsions(), core::pose::Pose::set_torsion(), torsion_info_, core::pose::Pose::total_residue(), and core::chemical::rna::RNA_FittedTorsionInfo::zeta_aform().

Referenced by build_dangle_seq1_3prime(), build_dangle_seq2_3prime(), and build_on_base_pair().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::apply ( core::pose::Pose & pose )

virtual

Apply the RNA HelixAssembler

Implements protocols::moves::Mover.

References core::pose::Pose::sequence().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::apply	(	core::pose::Pose &	pose,
		std::string const &	sequence
	)

Apply the loop-rebuild protocol to the input pose.

References build_dangling_ends(), build_helix(), figure_out_and_remove_dangling_ends(), fill_chain_info(), and protocols::TR.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq1_3prime	(	core::pose::Pose &	pose,
		std::string const &	dangle_seq
	)		const

private

References append_Aform_residue(), get_cutpoint(), and minimize_append_res().

Referenced by build_dangling_ends().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq1_5prime	(	core::pose::Pose &	pose,
		std::string const &	dangle_seq
	)		const

private

References minimize_prepend_res(), and prepend_Aform_residue().

Referenced by build_dangling_ends().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq2_3prime	(	core::pose::Pose &	pose,
		std::string const &	dangle_seq
	)		const

private

References append_Aform_residue(), minimize_append_res(), nres, and core::pose::Pose::total_residue().

Referenced by build_dangling_ends().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq2_5prime	(	core::pose::Pose &	pose,
		std::string const &	dangle_seq
	)		const

private

References get_cutpoint(), minimize_prepend_res(), and prepend_Aform_residue().

Referenced by build_dangling_ends().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangling_ends ( core::pose::Pose & pose ) const

private

References build_dangle_seq1_3prime(), build_dangle_seq1_5prime(), build_dangle_seq2_3prime(), build_dangle_seq2_5prime(), dangle_seq1_3prime_, dangle_seq1_5prime_, dangle_seq2_3prime_, and dangle_seq2_5prime_.

Referenced by apply().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_helix	(	core::pose::Pose &	pose,
		std::string const &	full_sequence
	)

References build_init_pose(), build_on_base_pair(), capping_residues_, dump_, core::pose::Pose::dump_pdb(), finish_scorefxn_, get_rid_of_capping_base_pairs(), minimize_base_step(), model_and_remove_capping_residues_, put_constraints_on_base_step(), scorefxn_, and protocols::TR.

Referenced by apply().

pose::PoseOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_init_pose	(	std::string const &	seq1,
		std::string const &	seq2
	)

References core::io::pdb::build_pose_from_pdb_as_is(), chi1_torsion_atom(), core::pose::Pose::fold_tree(), basic::database::full_name(), get_sequence_len(), make_pose_from_sequence(), core::pose::Pose::n_residue(), core::kinematics::FoldTree::new_jump(), path, core::pose::Pose::residue(), rsd_set_, core::pose::Pose::sequence(), set_Aform_torsions(), core::pose::Pose::set_jump(), and core::kinematics::FoldTree::set_jump_atoms().

Referenced by build_helix().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_on_base_pair	(	core::pose::Pose &	pose,
		Size const &	n,
		char const &	seq1,
		char const &	seq2
	)		const

private

References append_Aform_residue(), prepend_Aform_residue(), and set_full_model_info().

Referenced by build_helix().

protocols::moves::MoverOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::clone ( ) const

virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_HelixAssembler().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::figure_out_and_remove_dangling_ends ( std::string const & full_sequence )

private

References dangle_seq1_3prime_, dangle_seq1_5prime_, dangle_seq2_3prime_, dangle_seq2_5prime_, protocols::stepwise::modeler::rna::helix::is_blank_seq(), and runtime_assert.

Referenced by apply().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::fill_chain_info	(	core::pose::Pose &	pose,
		std::string const &	full_sequence
	)

private

References protocols::stepwise::modeler::rna::helix::is_blank_seq(), nres, and core::pose::Pose::pdb_info().

Referenced by apply().

Size protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::get_cutpoint ( core::pose::Pose const & pose ) const

private

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by build_dangle_seq1_3prime(), build_dangle_seq2_5prime(), and get_rid_of_capping_base_pairs().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::get_rid_of_capping_base_pairs ( core::pose::Pose & pose ) const

private

References core::chemical::rna::chi1_torsion_atom(), core::pose::Pose::delete_polymer_residue(), core::pose::Pose::fold_tree(), get_cutpoint(), core::kinematics::FoldTree::new_jump(), nres, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), runtime_assert, core::kinematics::FoldTree::set_jump_atoms(), and core::pose::Pose::total_residue().

Referenced by build_helix().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::initialize_minimizer ( )

private

References minimizer_, minimizer_options_, and core::optimization::MinimizerOptions::nblist_auto_update().

Referenced by RNA_HelixAssembler().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_append_res	(	core::pose::Pose &	pose,
		Size const	n
	)		const

private

References finish_scorefxn_, minimize_all_, minimizer_, minimizer_options_, core::optimization::AtomTreeMinimizer::run(), runtime_assert, scorefxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by build_dangle_seq1_3prime(), and build_dangle_seq2_3prime().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_base_step	(	core::pose::Pose &	pose,
		Size const	n,
		core::scoring::ScoreFunctionOP	scorefxn
	)		const

private

References atom_pair_constraint, cst_weight, minimize_all_, minimize_jump_, minimizer_, minimizer_options_, core::optimization::AtomTreeMinimizer::run(), and core::kinematics::MoveMap::set_bb().

Referenced by build_helix().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_prepend_res	(	core::pose::Pose &	pose,
		Size const	n
	)		const

private

References finish_scorefxn_, minimize_all_, minimizer_, minimizer_options_, core::optimization::AtomTreeMinimizer::run(), runtime_assert, scorefxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), and core::pose::Pose::total_residue().

Referenced by build_dangle_seq1_5prime(), and build_dangle_seq2_5prime().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::perturb_torsion	(	core::pose::Pose &	pose,
		utility::vector1< core::id::TorsionID > const &	id_list
	)		const

private

References numeric::random::RandomGenerator::gaussian(), perturb_amplitude_, core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().

Referenced by append_Aform_residue(), and prepend_Aform_residue().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::prepend_Aform_residue	(	core::pose::Pose &	pose,
		Size const &	n,
		char const &	nt
	)		const

private

References aa_from_oneletter_code(), core::chemical::rna::RNA_FittedTorsionInfo::alpha_aform(), BB, core::chemical::rna::RNA_FittedTorsionInfo::beta_aform(), core::pose::Pose::fold_tree(), core::chemical::rna::RNA_FittedTorsionInfo::gamma_aform(), core::kinematics::FoldTree::is_cutpoint(), perturb_torsion(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), random_perturbation_, rsd_set_, runtime_assert, set_Aform_torsions(), core::pose::Pose::set_torsion(), and torsion_info_.

Referenced by build_dangle_seq1_5prime(), build_dangle_seq2_5prime(), and build_on_base_pair().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::put_constraints_on_base_step	(	core::pose::Pose &	pose,
		Size const &	n
	)		const

private

References core::pose::Pose::constraint_set(), pairings, and protocols::farna::setup_base_pair_constraints().

Referenced by build_helix().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::random_perturbation ( bool const & setting )

inline

References random_perturbation_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_Aform_torsions	(	core::pose::Pose &	pose,
		Size const &	n
	)		const

private

References core::chemical::rna::RNA_FittedTorsionInfo::alpha_aform(), apply_pucker(), BB, core::chemical::rna::RNA_FittedTorsionInfo::beta_aform(), core::chemical::rna::RNA_FittedTorsionInfo::delta_north(), core::chemical::rna::RNA_FittedTorsionInfo::epsilon_aform(), core::chemical::rna::RNA_FittedTorsionInfo::gamma_aform(), NORTH, core::pose::Pose::set_torsion(), torsion_info_, use_phenix_geo_, and core::chemical::rna::RNA_FittedTorsionInfo::zeta_aform().

Referenced by append_Aform_residue(), build_init_pose(), and prepend_Aform_residue().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_dump ( bool const & setting )

inline

References dump_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_finish_scorefxn ( core::scoring::ScoreFunctionOP setting )

References finish_scorefxn_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_minimize_all ( bool const & setting )

inline

References minimize_all_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_model_and_remove_capping_residues ( bool setting )

inline

References model_and_remove_capping_residues_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_scorefxn ( core::scoring::ScoreFunctionOP setting )

References scorefxn_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::use_phenix_geo ( bool const setting )

References core::chemical::FA_RNA, core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), rsd_set_, and use_phenix_geo_.

Member Data Documentation

std::string const protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::capping_residues_

private

Referenced by build_helix().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq1_3prime_

private

Referenced by build_dangling_ends(), and figure_out_and_remove_dangling_ends().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq1_5prime_

private

Referenced by build_dangling_ends(), and figure_out_and_remove_dangling_ends().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq2_3prime_

private

Referenced by build_dangling_ends(), and figure_out_and_remove_dangling_ends().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq2_5prime_

private

Referenced by build_dangling_ends(), and figure_out_and_remove_dangling_ends().

bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dump_

private

Referenced by build_helix(), and set_dump().

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::finish_scorefxn_

private

Referenced by build_helix(), minimize_append_res(), minimize_prepend_res(), and set_finish_scorefxn().

bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_all_

private

Referenced by minimize_append_res(), minimize_base_step(), minimize_prepend_res(), and set_minimize_all().

bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_jump_

private

Referenced by minimize_base_step().

core::optimization::AtomTreeMinimizerOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimizer_

private

Referenced by initialize_minimizer(), minimize_append_res(), minimize_base_step(), and minimize_prepend_res().

core::optimization::MinimizerOptionsOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimizer_options_

private

Referenced by initialize_minimizer(), minimize_append_res(), minimize_base_step(), and minimize_prepend_res().

bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::model_and_remove_capping_residues_

private

Referenced by build_helix(), and set_model_and_remove_capping_residues().

core::Real protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::perturb_amplitude_

private

Referenced by perturb_torsion().

bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::random_perturbation_

private

Referenced by append_Aform_residue(), prepend_Aform_residue(), and random_perturbation().

core::chemical::ResidueTypeSetCAP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::rsd_set_

private

Referenced by append_Aform_residue(), build_init_pose(), prepend_Aform_residue(), and use_phenix_geo().

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::scorefxn_

private

Referenced by build_helix(), minimize_append_res(), minimize_prepend_res(), and set_scorefxn().

core::chemical::rna::RNA_FittedTorsionInfo const protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::torsion_info_

private

Referenced by append_Aform_residue(), prepend_Aform_residue(), and set_Aform_torsions().

bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::use_phenix_geo_

private

Referenced by set_Aform_torsions(), and use_phenix_geo().

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

src/protocols/stepwise/modeler/rna/helix/RNA_HelixAssembler.hh
src/protocols/stepwise/modeler/rna/helix/RNA_HelixAssembler.cc

Private Attributes
bool	dump_

bool	random_perturbation_

bool	minimize_all_

bool	minimize_jump_

bool	use_phenix_geo_

core::chemical::ResidueTypeSetCAP	rsd_set_

core::chemical::rna::RNA_FittedTorsionInfo const	torsion_info_

core::Real	perturb_amplitude_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	finish_scorefxn_

bool	model_and_remove_capping_residues_

std::string const	capping_residues_

core::optimization::AtomTreeMinimizerOP	minimizer_

core::optimization::MinimizerOptionsOP	minimizer_options_

std::string	dangle_seq1_5prime_

std::string	dangle_seq1_3prime_

std::string	dangle_seq2_5prime_

std::string	dangle_seq2_3prime_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation