protocols::rna::denovo Namespace Reference

Namespaces
	coarse
	movers
	output

Classes
class	RNA_DeNovoPoseInitializer
	Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and jump changes. More...
class	RNA_DeNovoProtocol
	The RNA de novo structure modeling protocol. More...
class	RNA_DeNovoProtocolCreator
class	RNA_FragmentMonteCarlo

Typedefs
typedef utility::pointer::shared_ptr< RNA_DeNovoPoseInitializer >	RNA_DeNovoPoseInitializerOP
typedef utility::pointer::shared_ptr< RNA_DeNovoPoseInitializer const >	RNA_DeNovoPoseInitializerCOP
typedef utility::pointer::shared_ptr< RNA_DeNovoProtocol >	RNA_DeNovoProtocolOP
typedef utility::pointer::shared_ptr< RNA_DeNovoProtocol const >	RNA_DeNovoProtocolCOP
typedef utility::pointer::shared_ptr< RNA_FragmentMonteCarlo >	RNA_FragmentMonteCarloOP
typedef utility::pointer::shared_ptr< RNA_FragmentMonteCarlo const >	RNA_FragmentMonteCarloCOP
typedef numeric::xyzVector< core::Length >	Vector

Functions
static basic::Tracer	TR ("protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer")
static basic::Tracer	TR ("protocols.rna.denovo.RNA_DeNovoProtocol")
std::ostream &	operator<< (std::ostream &os, RNA_DeNovoProtocol const &mover)
void	create_rna_vall_torsions (pose::Pose &pose, utility::io::ozstream &torsions_out, utility::vector1< core::Size > const &exclude_res_list)
void	create_rna_vall_torsions (pose::Pose &pose, std::string const &outfile, utility::vector1< core::Size > const &exclude_res_list)
void	ensure_phosphate_nomenclature_matches_mini (pose::Pose &pose)
void	export_packer_results (utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > pose_list, scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dump)
void	check_base_pair (pose::Pose &pose, FArray1D_int &struct_type)
void	setup_coarse_chainbreak_constraints (pose::Pose &pose, core::Size const &n)
void	print_internal_coords (core::pose::Pose const &pose)
bool	possible_root (core::kinematics::FoldTree const &f, core::Size const &n)
bool	let_rigid_body_jumps_move (core::kinematics::MoveMap &movemap, pose::Pose const &pose, bool const &move_first_rigid_body, bool const &allow_single_rigid_body)
void	translate_virtual_anchor_to_first_rigid_body (pose::Pose &pose)
bool	involved_in_phosphate_torsion (std::string const &atomname)
void	figure_out_base_pair_partner (pose::Pose &pose, std::map< core::Size, core::Size > &partner, bool const strict)
utility::vector1< core::pose::rna::BasePair >	classify_base_pairs_lores (pose::Pose const &pose_input)
void	print_hbonds (pose::Pose &pose)
void	get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)
core::Size	virtualize_bulges (core::pose::Pose &input_pose, utility::vector1< core::Size > const &in_allow_bulge_res_list, core::scoring::ScoreFunctionCOP const &scorefxn, std::string const &tag, bool const allow_pre_virtualize, bool const allow_consecutive_bulges, bool const verbose)
core::scoring::ScoreFunctionOP	get_rna_hires_scorefxn (bool const &include_protein_terms)
utility::vector1< core::Size >	get_moving_res (core::pose::Pose const &pose, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map)
void	delete_non_protein_from_pose (core::pose::Pose &pose)
utility::vector1< core::Size >	get_residues_within_dist_of_RNA (core::pose::Pose const &pose, core::Real const &dist_cutoff)
core::kinematics::FoldTree	get_rnp_docking_fold_tree (pose::Pose const &pose, bool const &with_density)
void	export_packer_results (utility::vector1< std::pair< core::Real, std::string > > &results, utility::vector1< core::pose::PoseOP > pose_list, core::scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dumo=false)
void	check_base_pair (core::pose::Pose &pose, ObjexxFCL::FArray1D_int &struct_type)
bool	is_num_in_list (core::Size const i, utility::vector1< core::Size > const &list)

Typedef Documentation

RNA_DeNovoPoseInitializerCOP

typedef utility::pointer::shared_ptr< RNA_DeNovoPoseInitializer const > protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP

RNA_DeNovoPoseInitializerOP

typedef utility::pointer::shared_ptr< RNA_DeNovoPoseInitializer > protocols::rna::denovo::RNA_DeNovoPoseInitializerOP

RNA_DeNovoProtocolCOP

typedef utility::pointer::shared_ptr< RNA_DeNovoProtocol const > protocols::rna::denovo::RNA_DeNovoProtocolCOP

RNA_DeNovoProtocolOP

typedef utility::pointer::shared_ptr< RNA_DeNovoProtocol > protocols::rna::denovo::RNA_DeNovoProtocolOP

RNA_FragmentMonteCarloCOP

typedef utility::pointer::shared_ptr< RNA_FragmentMonteCarlo const > protocols::rna::denovo::RNA_FragmentMonteCarloCOP

RNA_FragmentMonteCarloOP

typedef utility::pointer::shared_ptr< RNA_FragmentMonteCarlo > protocols::rna::denovo::RNA_FragmentMonteCarloOP

Vector

typedef numeric::xyzVector< core::Length > protocols::rna::denovo::Vector

Function Documentation

check_base_pair() [1/2]

void protocols::rna::denovo::check_base_pair	(	core::pose::Pose &	pose,
		ObjexxFCL::FArray1D_int &	struct_type
	)

check_base_pair() [2/2]

void protocols::rna::denovo::check_base_pair	(	pose::Pose &	pose,
		FArray1D_int &	struct_type
	)

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), core::chemical::element::F, core::chemical::element::I, core::conformation::Residue::name1(), core::pose::rna::BasePair::orientation(), core::chemical::rna::possibly_canonical(), core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), core::pose::Pose::residue(), core::scoring::RNA_LORES_WTS, core::scoring::rna::rna_scoring_info_from_pose(), core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list(), core::pose::Pose::size(), core::import_pose::TR(), and core::chemical::rna::WATSON_CRICK.

classify_base_pairs_lores()

utility::vector1< core::pose::rna::BasePair > protocols::rna::denovo::classify_base_pairs_lores

(

pose::Pose const &

pose_input

)

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::RNA_LORES_WTS, core::scoring::rna::rna_scoring_info_from_pose(), core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list(), and core::import_pose::TR().

Referenced by figure_out_base_pair_partner().

create_rna_vall_torsions() [1/2]

void protocols::rna::denovo::create_rna_vall_torsions	(	pose::Pose &	pose,
		std::string const &	outfile,
		utility::vector1< core::Size > const &	exclude_res_list
	)

create_rna_vall_torsions() [2/2]

void protocols::rna::denovo::create_rna_vall_torsions	(	pose::Pose &	pose,
		utility::io::ozstream &	torsions_out,
		utility::vector1< core::Size > const &	exclude_res_list
	)

References core::pose::Pose::append_residue_by_bond(), protocols::idealize::IdealizeMover::apply(), core::id::BB, core::chemical::rna::RNA_Info::c3prime_atom_index(), core::chemical::rna::RNA_Info::c4prime_atom_index(), core::chemical::rna::RNA_Info::c5prime_atom_index(), core::id::CHI, core::chemical::element::F, protocols::idealize::IdealizeMover::fast(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::pose::Pose::fold_tree(), core::pose::rna::get_base_pairing_info(), core::kinematics::Stub::global2local(), core::chemical::element::I, core::kinematics::FoldTree::is_cutpoint(), is_num_in_list(), core::chemical::ResidueTypeBase::name1(), core::chemical::rna::non_main_chain_sugar_atoms, core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rna_base_pair, core::chemical::ResidueType::RNA_info(), core::pose::Pose::size(), core::pose::Pose::torsion(), core::import_pose::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

delete_non_protein_from_pose()

void protocols::rna::denovo::delete_non_protein_from_pose

(

core::pose::Pose &

pose

)

References core::pose::Pose::delete_residue_range_slow(), core::sequence::end, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), protocols::loops::start, and core::pose::Pose::total_residue().

ensure_phosphate_nomenclature_matches_mini()

void protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini

(

pose::Pose &

pose

)

References core::conformation::Residue::atom_index(), core::pose::rna::get_op2_op1_sign(), core::chemical::ResidueType::has(), core::conformation::Residue::is_RNA(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), core::import_pose::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

export_packer_results() [1/2]

void protocols::rna::denovo::export_packer_results	(	utility::vector1< std::pair< core::Real, std::string > > &	results,
		utility::vector1< core::pose::PoseOP >	pose_list,
		core::scoring::ScoreFunctionOP &	scorefxn,
		std::string const &	outfile,
		bool const	dumo = false
	)

References core::pose::Pose::dump_pdb(), core::chemical::element::F, core::conformation::membrane::out, and core::io::silent::SilentFileData::write_silent_struct().

export_packer_results() [2/2]

void protocols::rna::denovo::export_packer_results	(	utility::vector1< std::pair< Real, std::string > > &	results,
		utility::vector1< pose::PoseOP >	pose_list,
		scoring::ScoreFunctionOP &	scorefxn,
		std::string const &	outfile,
		bool const	dump
	)

References core::pose::Pose::dump_pdb(), core::chemical::element::F, core::conformation::membrane::out, and core::io::silent::SilentFileData::write_silent_struct().

figure_out_base_pair_partner()

void protocols::rna::denovo::figure_out_base_pair_partner	(	pose::Pose &	pose,
		std::map< core::Size, core::Size > &	partner,
		bool const	strict
	)

References core::conformation::Residue::aa(), core::id::CHI, classify_base_pairs_lores(), core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), core::chemical::rna::get_watson_crick_base_pair_atoms(), core::pose::rna::BasePair::orientation(), core::chemical::rna::possibly_canonical(), core::chemical::rna::possibly_canonical_strict(), core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), core::pose::Pose::residue(), core::pose::Pose::torsion(), core::conformation::Residue::type(), core::chemical::rna::WATSON_CRICK, and core::conformation::Residue::xyz().

get_default_allowed_bulge_res()

void protocols::rna::denovo::get_default_allowed_bulge_res	(	utility::vector1< core::Size > &	allow_bulge_res_list,
		core::pose::Pose const &	pose,
		bool const	verbose
	)

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::import_pose::TR().

Referenced by virtualize_bulges().

get_moving_res()

utility::vector1< core::Size > protocols::rna::denovo::get_moving_res	(	core::pose::Pose const &	pose,
		core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map
	)

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

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::reroot_pose_before_align_and_return_moving_res(), and protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_monte_carlo_cycles().

get_residues_within_dist_of_RNA()

utility::vector1< core::Size > protocols::rna::denovo::get_residues_within_dist_of_RNA	(	core::pose::Pose const &	pose,
		core::Real const &	dist_cutoff
	)

References core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name3(), protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::rna::denovo::movers::RNA_Minimizer::apply(), and protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing().

get_rna_hires_scorefxn()

core::scoring::ScoreFunctionOP protocols::rna::denovo::get_rna_hires_scorefxn

(

bool const &

include_protein_terms

)

References core::scoring::ScoreFunctionFactory::create_score_function(), and core::scoring::get_score_function().

Referenced by protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_scorefxn(), and protocols::rna::denovo::RNA_DeNovoProtocol::initialize_scorefxn().

get_rnp_docking_fold_tree()

core::kinematics::FoldTree protocols::rna::denovo::get_rnp_docking_fold_tree	(	pose::Pose const &	pose,
		bool const &	with_density
	)

References core::kinematics::FoldTree::add_edge(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::total_residue().

Referenced by protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rnp_fold_tree().

involved_in_phosphate_torsion()

bool protocols::rna::denovo::involved_in_phosphate_torsion

(

std::string const &

atomname

)

References core::chemical::rna::atoms_involved_in_phosphate_torsion.

is_num_in_list()

bool protocols::rna::denovo::is_num_in_list ( core::Size const  i, utility::vector1< core::Size > const &  list  )

inline

Referenced by create_rna_vall_torsions().

let_rigid_body_jumps_move()

bool protocols::rna::denovo::let_rigid_body_jumps_move	(	core::kinematics::MoveMap &	movemap,
		pose::Pose const &	pose,
		bool const &	move_first_rigid_body,
		bool const &	allow_single_rigid_body
	)

References core::pose::rna::get_rigid_body_jumps(), core::kinematics::MoveMap::set_jump(), and protocols::loops::start.

Referenced by protocols::rna::denovo::movers::RNP_HighResMover::initialize(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), and protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rigid_body_mover().

operator<<()

std::ostream & protocols::rna::denovo::operator<<	(	std::ostream &	os,
		RNA_DeNovoProtocol const &	mover
	)

References protocols::rna::denovo::RNA_DeNovoProtocol::show().

possible_root()

bool protocols::rna::denovo::possible_root	(	core::kinematics::FoldTree const &	f,
		core::Size const &	n
	)

References core::kinematics::FoldTree::possible_root().

print_hbonds()

void protocols::rna::denovo::print_hbonds

(

pose::Pose &

pose

)

References core::chemical::ResidueType::atom_name(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbond, core::chemical::ResidueTypeBase::name1(), core::pose::Pose::residue_type(), and core::import_pose::TR().

print_internal_coords()

void protocols::rna::denovo::print_internal_coords

(

core::pose::Pose const &

pose

)

References protocols::comparative_modeling::features::A, core::kinematics::AtomTree::atom(), core::chemical::ResidueType::atom_name(), core::pose::Pose::atom_tree(), core::id::D, core::kinematics::AtomTree::dof(), core::chemical::element::F, core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueType::natoms(), core::id::PHI, core::pose::Pose::residue_type(), core::pose::Pose::size(), core::id::THETA, and core::import_pose::TR().

setup_coarse_chainbreak_constraints()

void protocols::rna::denovo::setup_coarse_chainbreak_constraints	(	pose::Pose &	pose,
		core::Size const &	n
	)

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::scoring::coarse_chainbreak_constraint, core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), and core::import_pose::TR().

TR() [1/2]

static basic::Tracer protocols::rna::denovo::TR ( "protocols.rna.denovo.RNA_DeNovoProtocol"  )

static

TR() [2/2]

static basic::Tracer protocols::rna::denovo::TR ( "protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer"  )

static

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::rna::denovo::movers::RNA_HelixMover::apply(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::rna::denovo::movers::RNA_Relaxer::apply(), protocols::rna::denovo::movers::RNP_HighResMover::apply(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_after_jump_change(), protocols::rna::denovo::RNA_DeNovoProtocol::calc_rmsds(), protocols::rna::denovo::RNA_FragmentMonteCarlo::check_for_loop_modeling_case(), protocols::rna::denovo::RNA_FragmentMonteCarlo::check_score_filter(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::close_at_all_cutpoints(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::close_the_loop(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_pivot_res_and_scratch_res(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::finalize(), protocols::rna::denovo::movers::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::rna::denovo::coarse::CoarseRNA_Fragments::find_source_positions(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::initialize(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo(), protocols::rna::denovo::movers::RNA_Minimizer::o2prime_trials(), protocols::rna::denovo::RNA_DeNovoProtocol::output_silent_struct(), protocols::rna::denovo::RNA_DeNovoProtocol::output_to_silent_file(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::override_secstruct(), protocols::rna::denovo::movers::RNA_Minimizer::packing_trials(), protocols::rna::denovo::coarse::CoarseRNA_Fragments::pick_random_fragment(), protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps(), protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_monte_carlo_cycles(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rigid_body_mover(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::rna::denovo::RNA_FragmentMonteCarlo::update_pose_constraints(), and protocols::rna::denovo::RNA_FragmentMonteCarlo::update_rna_denovo_master_mover().

translate_virtual_anchor_to_first_rigid_body()

void protocols::rna::denovo::translate_virtual_anchor_to_first_rigid_body

(

pose::Pose &

pose

)

References core::import_pose::get_anchor_rsd(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves().

virtualize_bulges()

core::Size protocols::rna::denovo::virtualize_bulges	(	core::pose::Pose &	input_pose,
		utility::vector1< core::Size > const &	in_allow_bulge_res_list,
		core::scoring::ScoreFunctionCOP const &	scorefxn,
		std::string const &	tag,
		bool const	allow_pre_virtualize,
		bool const	allow_consecutive_bulges,
		bool const	verbose
	)

References core::pose::rna::apply_virtual_rna_residue_variant_type(), get_default_allowed_bulge_res(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::scoring::rna_bulge, core::pose::Pose::size(), core::import_pose::TR(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::apply().