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

#include <RNA_HelixAssembler.hh>

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

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

void	apply (core::pose::Pose &pose)
	Apply the loop-rebuild protocol to the input pose. More...

virtual std::string	get_name () const

void	apply (core::pose::Pose &pose, std::string const &full_sequence_in)
	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)

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

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, std::string const &seq1, std::string 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	add_capping_base_pairs_to_full_sequence ()

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

void	figure_out_and_remove_dangling_ends ()

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, std::string const &nt) const

void	prepend_Aform_residue (core::pose::Pose &pose, Size const &n, std::string 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	get_sequence (core::Size const n)

void	remove_first_base_pair (std::string &full_sequence, std::map< Size, std::string > &non_standard_residues, std::string &sequence_helix1, std::string &sequence_helix2) const

void	remove_last_base_pair (std::string &full_sequence, std::map< Size, std::string > &non_standard_residues, std::string &sequence_helix1, std::string &sequence_helix2) const

core::conformation::ResidueOP	get_residue (std::string const &nt) const

Private Attributes
bool	dump_

bool	random_perturbation_

bool	minimize_all_

bool	minimize_jump_

bool	use_phenix_geo_

core::chemical::ResidueTypeSetCOP	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_

std::string	full_sequence_

std::map< core::Size, std::string >	non_standard_residues_

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

◆ RNA_HelixAssembler()

core::import_pose::RNA_HelixAssembler::RNA_HelixAssembler ( )

Construct the protocol object.

References initialize_minimizer().

◆ ~RNA_HelixAssembler()

core::import_pose::RNA_HelixAssembler::~RNA_HelixAssembler ( )

virtualdefault

Destroy the protocol object.

Member Function Documentation

◆ add_capping_base_pairs_to_full_sequence()

void core::import_pose::RNA_HelixAssembler::add_capping_base_pairs_to_full_sequence ( )

private

References capping_residues_, full_sequence_, protocols::features::L, non_standard_residues_, and core::import_pose::TR().

Referenced by build_helix().

◆ append_Aform_residue()

void core::import_pose::RNA_HelixAssembler::append_Aform_residue	(	core::pose::Pose &	pose,
		Size const &	n,
		std::string const &	nt
	)		const

private

References core::pose::Pose::append_polymer_residue_after_seqpos(), core::id::BB, core::id::CHI, core::chemical::rna::RNA_FittedTorsionInfo::epsilon_aform(), core::pose::Pose::fold_tree(), get_residue(), core::kinematics::FoldTree::is_cutpoint(), perturb_torsion(), random_perturbation_, set_Aform_torsions(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), torsion_info_, core::pose::full_model_info::update_full_model_info_from_pose(), and core::chemical::rna::RNA_FittedTorsionInfo::zeta_aform().

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

◆ apply() [1/2]

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

Apply the loop-rebuild protocol to the input pose.

Apply the RNA HelixAssembler

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

Referenced by core::import_pose::dump_stems().

◆ apply() [2/2]

void core::import_pose::RNA_HelixAssembler::apply	(	core::pose::Pose &	pose,
		std::string const &	full_sequence_in
	)

Apply the loop-rebuild protocol to the input pose.

References build_dangling_ends(), build_helix(), figure_out_and_remove_dangling_ends(), fill_chain_info(), full_sequence_, non_standard_residues_, core::sequence::parse_out_non_standard_residues(), and core::import_pose::TR().

◆ build_dangle_seq1_3prime()

void core::import_pose::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().

◆ build_dangle_seq1_5prime()

void core::import_pose::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().

◆ build_dangle_seq2_3prime()

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

private

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

Referenced by build_dangling_ends().

◆ build_dangle_seq2_5prime()

void core::import_pose::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().

◆ build_dangling_ends()

void core::import_pose::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().

◆ build_helix()

void core::import_pose::RNA_HelixAssembler::build_helix ( core::pose::Pose & pose )

References add_capping_base_pairs_to_full_sequence(), build_init_pose(), build_on_base_pair(), dump_, core::pose::Pose::dump_pdb(), finish_scorefxn_, full_sequence_, get_rid_of_capping_base_pairs(), get_sequence(), minimize_base_step(), model_and_remove_capping_residues_, put_constraints_on_base_step(), scorefxn_, and core::import_pose::TR().

Referenced by apply().

◆ build_init_pose()

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

References core::io::pdb::build_pose_from_pdb_as_is(), core::chemical::rna::chi1_torsion_atom(), core::pose::Pose::fold_tree(), core::pose::get_sequence_len(), core::pose::Pose::jump(), core::pose::make_pose_from_sequence(), core::kinematics::FoldTree::new_jump(), protocols::hybridization::path, core::pose::Pose::residue_type(), rsd_set_, set_Aform_torsions(), and core::kinematics::FoldTree::set_jump_atoms().

Referenced by build_helix(), and protocols::recces::pose_setup_turner().

◆ build_on_base_pair()

void core::import_pose::RNA_HelixAssembler::build_on_base_pair	(	core::pose::Pose &	pose,
		Size const &	n,
		std::string const &	seq1,
		std::string const &	seq2
	)		const

private

References append_Aform_residue(), prepend_Aform_residue(), and core::pose::full_model_info::update_full_model_info_from_pose().

Referenced by build_helix().

◆ figure_out_and_remove_dangling_ends()

void core::import_pose::RNA_HelixAssembler::figure_out_and_remove_dangling_ends ( )

private

References dangle_seq1_3prime_, dangle_seq1_5prime_, dangle_seq2_3prime_, dangle_seq2_5prime_, full_sequence_, get_sequence(), core::import_pose::is_blank_seq(), non_standard_residues_, remove_first_base_pair(), and remove_last_base_pair().

Referenced by apply().

◆ fill_chain_info()

void core::import_pose::RNA_HelixAssembler::fill_chain_info ( core::pose::Pose & pose )

private

References core::pose::Pose::pdb_info(), core::pose::full_model_info::set_full_model_info(), and core::pose::Pose::size().

Referenced by apply().

◆ get_cutpoint()

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

private

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

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

◆ get_name()

std::string core::import_pose::RNA_HelixAssembler::get_name ( ) const

virtual

◆ get_residue()

core::conformation::ResidueOP core::import_pose::RNA_HelixAssembler::get_residue ( std::string const & nt ) const

private

References core::conformation::ResidueFactory::create_residue(), core::pose::residue_types_from_sequence(), and rsd_set_.

Referenced by append_Aform_residue(), and prepend_Aform_residue().

◆ get_rid_of_capping_base_pairs()

void core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs ( core::pose::Pose & pose )

private

References core::chemical::rna::chi1_torsion_atom(), core::pose::Pose::delete_polymer_residue(), core::pose::Pose::fold_tree(), full_sequence_, get_cutpoint(), core::kinematics::FoldTree::new_jump(), non_standard_residues_, remove_first_base_pair(), remove_last_base_pair(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::size(), and core::pose::full_model_info::update_full_model_info_from_pose().

Referenced by build_helix().

◆ get_sequence()

std::string core::import_pose::RNA_HelixAssembler::get_sequence ( core::Size const n )

private

References full_sequence_, and non_standard_residues_.

Referenced by build_helix(), and figure_out_and_remove_dangling_ends().

◆ initialize_minimizer()

void core::import_pose::RNA_HelixAssembler::initialize_minimizer ( )

private

References minimizer_, and minimizer_options_.

Referenced by RNA_HelixAssembler().

◆ minimize_append_res()

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

private

References finish_scorefxn_, minimize_all_, minimizer_, minimizer_options_, 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().

◆ minimize_base_step()

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

private

References core::scoring::base_pair_constraint, minimize_all_, minimize_jump_, minimizer_, minimizer_options_, scorefxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), and core::import_pose::TR().

Referenced by build_helix().

◆ minimize_prepend_res()

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

private

References finish_scorefxn_, minimize_all_, minimizer_, minimizer_options_, scorefxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), and core::pose::Pose::size().

Referenced by build_dangle_seq1_5prime(), and build_dangle_seq2_5prime().

◆ perturb_torsion()

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

private

References perturb_amplitude_, core::scoring::rg, core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().

Referenced by append_Aform_residue(), and prepend_Aform_residue().

◆ prepend_Aform_residue()

void core::import_pose::RNA_HelixAssembler::prepend_Aform_residue	(	core::pose::Pose &	pose,
		Size const &	n,
		std::string const &	nt
	)		const

private

References core::chemical::rna::RNA_FittedTorsionInfo::alpha_aform(), core::id::BB, core::chemical::rna::RNA_FittedTorsionInfo::beta_aform(), core::id::CHI, core::pose::Pose::fold_tree(), core::chemical::rna::RNA_FittedTorsionInfo::gamma_aform(), get_residue(), core::kinematics::FoldTree::is_cutpoint(), perturb_torsion(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), random_perturbation_, set_Aform_torsions(), core::pose::Pose::set_torsion(), torsion_info_, and core::pose::full_model_info::update_full_model_info_from_pose().

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

◆ put_constraints_on_base_step()

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

private

References core::pose::Pose::constraint_set(), and core::pose::rna::setup_base_pair_constraints().

Referenced by build_helix().

◆ random_perturbation()

void core::import_pose::RNA_HelixAssembler::random_perturbation ( bool const & setting )

inline

References random_perturbation_.

◆ remove_first_base_pair()

void core::import_pose::RNA_HelixAssembler::remove_first_base_pair	(	std::string &	full_sequence,
		std::map< Size, std::string > &	non_standard_residues,
		std::string &	sequence_helix1,
		std::string &	sequence_helix2
	)		const

private

References full_sequence_, and protocols::features::L.

Referenced by figure_out_and_remove_dangling_ends(), and get_rid_of_capping_base_pairs().

◆ remove_last_base_pair()

void core::import_pose::RNA_HelixAssembler::remove_last_base_pair	(	std::string &	full_sequence,
		std::map< Size, std::string > &	non_standard_residues,
		std::string &	sequence_helix1,
		std::string &	sequence_helix2
	)		const