Classes
class	Cluster_Member

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

class	SlicedPoseWorkingParameters

class	StepWiseRNA_Clusterer

class	StepWiseRNA_PoseSelection

class	StepWiseRNA_PoseSetup

class	StepWiseWorkingParametersSetup

Typedefs
typedef utility::pointer::shared_ptr < RNA_AnalyticLoopCloser >	RNA_AnalyticLoopCloserOP

typedef utility::pointer::shared_ptr < StepWiseRNA_Minimizer >	StepWiseRNA_MinimizerOP

typedef utility::pointer::shared_ptr < StepWiseRNA_Minimizer const >	StepWiseRNA_MinimizerCOP

typedef utility::pointer::shared_ptr < StepWiseRNA_PoseSelection >	StepWiseRNA_PoseSelectionOP

typedef utility::pointer::shared_ptr < StepWiseRNA_PoseSelection const >	StepWiseRNA_PoseSelectionCOP

typedef utility::pointer::shared_ptr < StepWiseRNA_PoseSetup >	StepWiseRNA_PoseSetupOP

typedef utility::pointer::shared_ptr < StepWiseRNA_PoseSetup const >	StepWiseRNA_PoseSetupCOP

typedef utility::pointer::shared_ptr < util >	utilOP

typedef utility::pointer::shared_ptr < util const >	utilCOP

Functions
void	apply_chi_cst (core::pose::Pose &pose, core::pose::Pose const &ref_pose)

std::string	get_working_directory ()

utility::vector1< core::Size >	get_fixed_res (core::Size const nres)

bool	is_nonempty_input_silent_file (std::string const &input_silent_file, std::string const &exit_key_string)

utility::vector1< core::Size >	get_input_res (core::Size const nres, std::string const &pose_num)

utility::vector1< std::string >	get_silent_file_tags ()

core::scoring::ScoreFunctionOP	create_scorefxn ()

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP	setup_simple_full_length_rna_working_parameters ()

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP	setup_rna_working_parameters (bool check_for_previously_closed_cutpoint_with_input_pose)

void	setup_copy_DOF_input (StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup)

StepWiseRNA_PoseSetupOP	setup_pose_setup_class (stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &working_parameters, bool const copy_DOF)

bool	get_tag_and_silent_file_for_struct (std::string &swa_silent_file, std::string &out_tag, core::Size const &n, bool const &multiple_shots, std::string const &silent_file)

void	ensure_directory_for_out_silent_file_exists ()

bool	check_can_prepend (utility::vector1< core::Size > const &seq_num_list)

bool	check_can_append (utility::vector1< core::Size > const &seq_num_list)

bool	pair_sort_criterion (std::pair< core::Size, core::Size > pair_one, std::pair< core::Size, core::Size > pair_two)

void	sort_pair_list (utility::vector1< std::pair< core::Size, core::Size > > pair_list)

void	output_pair_size (std::pair< core::Size, core::Size > const &pair_size, std::ostream &outstream)

void	output_pair_size (utility::vector1< std::pair< core::Size, core::Size > > const &pair_size_vector, std::string const &output_string, std::ostream &outstream, core::Size const spacing)

void	output_is_prepend_map (std::string const &tag, std::map< core::Size, bool > const &my_map, core::Size const max_seq_num, std::ostream &outstream, core::Size const tag_spacing)

void	output_bool_list (std::string const &tag, utility::vector1< core::Size > const &size_list, std::ostream &outstream, core::Size const spacing)

void	output_bool_list (std::string const &tag, utility::vector1< bool > const &bool_list, std::ostream &outstream, core::Size const spacing)

void	output_size_list (std::string const &tag, utility::vector1< core::Size > const &size_list, std::ostream &outstream, core::Size const spacing)

void	output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const &pose_name, std::ostream &outstream)

void	output_fold_tree_info (pose::Pose const &pose, std::string pose_name, std::ostream &outstream)

core::Real	full_length_rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< core::Size > const &residue_list, std::string const &full_sequence, bool const verbose, bool const ignore_virtual_atom)

void	print_backbone_torsions (pose::Pose const &pose, core::Size const five_prime_chainbreak)

core::Size	setup_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)

void	remove_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)

core::Size	setup_bulge_jump_point (pose::Pose &pose, core::Size const &moving_base, core::Size const &reference_base, bool const verbose)

void	apply_rotamer (pose::Pose &pose, utility::vector1< Torsion_Info > const &rotamer_list)

bool	is_same_sugar_pucker (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, core::Size const seq_num)

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

void	import_pose_from_silent_file (core::pose::Pose &import_pose, std::string const &silent_file, std::string const &input_tag)

std::string	get_tag_from_pdb_filename (std::string const &pdb_filename)

void	print_WorkingParameters_info (working_parameters::StepWiseWorkingParametersCOP const &const_WP, std::string const &WP_name, std::ostream &outstream, bool const is_simple_full_length_WP)

void	print_WorkingParameters_info (working_parameters::StepWiseWorkingParametersOP const &WP, std::string const &WP_name, std::ostream &outstream, bool const is_simple_full_length_WP)

void	set_nucleotide_to_A_form (pose::Pose &pose, core::Size const seq_num)

std::string	path_basename (std::string const &full_path)

Variables
StepWiseRNA_CountStruct	local_count_data

Typedef Documentation

typedef utility::pointer::shared_ptr< RNA_AnalyticLoopCloser > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloserOP

typedef utility::pointer::shared_ptr< StepWiseRNA_Minimizer const > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_MinimizerCOP

typedef utility::pointer::shared_ptr< StepWiseRNA_Minimizer > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_MinimizerOP

typedef utility::pointer::shared_ptr< StepWiseRNA_PoseSelection const > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelectionCOP

typedef utility::pointer::shared_ptr< StepWiseRNA_PoseSelection > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelectionOP

typedef utility::pointer::shared_ptr< StepWiseRNA_PoseSetup const > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetupCOP

typedef utility::pointer::shared_ptr< StepWiseRNA_PoseSetup > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetupOP

typedef utility::pointer::shared_ptr< util const > protocols::stepwise::legacy::modeler::rna::utilCOP

typedef utility::pointer::shared_ptr< util > protocols::stepwise::legacy::modeler::rna::utilOP

Function Documentation

void protocols::stepwise::legacy::modeler::rna::apply_chi_cst	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose
	)

References core::chemical::ResidueType::atom_index(), core::id::CHI, core::pose::Pose::constraint_set(), core::chemical::ResidueType::is_purine(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::pose::Pose::torsion().

void protocols::stepwise::legacy::modeler::rna::apply_rotamer	(	pose::Pose &	pose,
		utility::vector1< Torsion_Info > const &	rotamer_list
	)

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

bool protocols::stepwise::legacy::modeler::rna::check_can_append ( utility::vector1< core::Size > const & seq_num_list )

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), and protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal().

bool protocols::stepwise::legacy::modeler::rna::check_can_prepend ( utility::vector1< core::Size > const & seq_num_list )

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), and protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal().

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::rna::create_scorefxn ( )

References core::scoring::get_score_function(), core::scoring::rna_sugar_close, and TR().

void protocols::stepwise::legacy::modeler::rna::ensure_directory_for_out_silent_file_exists ( )

References TR().

core::Real protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		utility::vector1< core::Size > const &	residue_list,
		std::string const &	full_sequence,
		bool const	verbose,
		bool const	ignore_virtual_atom
	)

References core::conformation::Residue::has_variant_type(), protocols::mean_field::max(), protocols::stepwise::modeler::output_boolean(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::sequence::parse_out_non_standard_residues(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), protocols::stepwise::modeler::rna::suite_square_deviation(), protocols::TR(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::get_fixed_res ( core::Size const nres )

References TR().

Referenced by setup_rna_working_parameters(), and setup_simple_full_length_rna_working_parameters().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::get_input_res	(	core::Size const	nres,
		std::string const &	pose_num
	)

References core::scoring::missing_res, and TR().

Referenced by setup_rna_working_parameters().

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::get_silent_file_tags ( )

References protocols::stepwise::modeler::rna::output_title_text(), core::pose::rna::tokenize(), and TR().

Referenced by setup_copy_DOF_input(), and setup_rna_working_parameters().

bool protocols::stepwise::legacy::modeler::rna::get_tag_and_silent_file_for_struct	(	std::string &	swa_silent_file,
		std::string &	out_tag,
		core::Size const &	n,
		bool const &	multiple_shots,
		std::string const &	silent_file
	)

References core::io::silent::initialize_tag_is_done(), and TR().

std::string protocols::stepwise::legacy::modeler::rna::get_tag_from_pdb_filename ( std::string const & pdb_filename )

References protocols::denovo_design::movers::pdb_filename().

std::string protocols::stepwise::legacy::modeler::rna::get_working_directory ( )

References GetCurrentDir.

void protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file	(	core::pose::Pose &	import_pose,
		std::string const &	silent_file,
		std::string const &	input_tag
	)

References core::io::silent::SilentFileData::begin(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::sequence::end, core::io::silent::SilentFileData::end(), core::chemical::FA_STANDARD, and core::io::silent::SilentFileData::read_file().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose().

bool protocols::stepwise::legacy::modeler::rna::is_nonempty_input_silent_file	(	std::string const &	input_silent_file,
		std::string const &	exit_key_string
	)

References TR().

bool protocols::stepwise::legacy::modeler::rna::is_same_sugar_pucker	(	core::pose::Pose const &	current_pose,
		core::pose::Pose const &	cluster_center_pose,
		core::Size const	seq_num
	)

References core::pose::rna::get_residue_pucker_state().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster().

void protocols::stepwise::legacy::modeler::rna::output_bool_list	(	std::string const &	tag,
		utility::vector1< core::Size > const &	size_list,
		std::ostream &	outstream,
		core::Size const	spacing
	)

References output_bool_list().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend(), and protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_additional_cutpoint_closed().

void protocols::stepwise::legacy::modeler::rna::output_bool_list	(	std::string const &	tag,
		utility::vector1< bool > const &	bool_list,
		std::ostream &	outstream,
		core::Size const	spacing
	)

References protocols::stepwise::modeler::output_boolean().

Referenced by output_bool_list(), and print_WorkingParameters_info().

void protocols::stepwise::legacy::modeler::rna::output_fold_tree_info	(	kinematics::FoldTree const &	fold_tree,
		std::string const &	pose_name,
		std::ostream &	outstream
	)

References core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::downstream_atom(), core::kinematics::FoldTree::jump_point(), core::kinematics::FoldTree::num_cutpoint(), and core::kinematics::FoldTree::upstream_atom().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree(), and protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree().

void protocols::stepwise::legacy::modeler::rna::output_fold_tree_info	(	pose::Pose const &	pose,
		std::string	pose_name,
		std::ostream &	outstream
	)

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

Referenced by print_WorkingParameters_info(), and setup_bulge_jump_point().

void protocols::stepwise::legacy::modeler::rna::output_is_prepend_map	(	std::string const &	tag,
		std::map< core::Size, bool > const &	my_map,
		core::Size const	max_seq_num,
		std::ostream &	outstream,
		core::Size const	tag_spacing
	)

Referenced by print_WorkingParameters_info(), and protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup().

void protocols::stepwise::legacy::modeler::rna::output_pair_size	(	std::pair< core::Size, core::Size > const &	pair_size,
		std::ostream &	outstream
	)

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list(), and protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup().

void protocols::stepwise::legacy::modeler::rna::output_pair_size	(	utility::vector1< std::pair< core::Size, core::Size > > const &	pair_size_vector,
		std::string const &	output_string,
		std::ostream &	outstream,
		core::Size const	spacing
	)

References core::sequence::left.

void protocols::stepwise::legacy::modeler::rna::output_size_list	(	std::string const &	tag,
		utility::vector1< core::Size > const &	size_list,
		std::ostream &	outstream,
		core::Size const	spacing
	)

References core::chemical::element::I.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_additional_cutpoint_closed().

bool protocols::stepwise::legacy::modeler::rna::pair_sort_criterion	(	std::pair< core::Size, core::Size >	pair_one,
		std::pair< core::Size, core::Size >	pair_two
	)

Referenced by sort_pair_list().

std::string protocols::stepwise::legacy::modeler::rna::path_basename ( std::string const & full_path )

void protocols::stepwise::legacy::modeler::rna::print_backbone_torsions	(	pose::Pose const &	pose,
		core::Size const	five_prime_chainbreak
	)

References core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants().

void protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info	(	working_parameters::StepWiseWorkingParametersCOP const &	const_WP,
		std::string const &	WP_name,
		std::ostream &	outstream,
		bool const	is_simple_full_length_WP
	)

References print_WorkingParameters_info().

Referenced by setup_simple_full_length_rna_working_parameters(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants().

void protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info	(	working_parameters::StepWiseWorkingParametersOP const &	WP,
		std::string const &	WP_name,
		std::ostream &	outstream,
		bool const	is_simple_full_length_WP
	)

References output_bool_list(), protocols::stepwise::modeler::output_boolean(), output_fold_tree_info(), output_is_prepend_map(), protocols::stepwise::modeler::rna::output_seq_num_list(), and protocols::stepwise::modeler::rna::output_title_text().

Referenced by print_WorkingParameters_info().

void protocols::stepwise::legacy::modeler::rna::remove_chain_break_jump_point	(	core::pose::Pose &	pose,
		core::Size const	moving_res,
		core::Size const	reference_res
	)

References core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::jump_nr().

void protocols::stepwise::legacy::modeler::rna::set_nucleotide_to_A_form	(	pose::Pose &	pose,
		core::Size const	seq_num
	)

References core::id::BB, core::chemical::rna::CHI, and core::pose::Pose::set_torsion().

core::Size protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point	(	pose::Pose &	pose,
		core::Size const &	moving_base,
		core::Size const &	reference_base,
		bool const	verbose
	)

References core::pose::Pose::fold_tree(), output_fold_tree_info(), core::pose::Pose::residue(), and protocols::TR().

Referenced by setup_chain_break_jump_point().

core::Size protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point	(	core::pose::Pose &	pose,
		core::Size const	moving_res,
		core::Size const	reference_res
	)

References setup_bulge_jump_point().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::additional_setup_for_floating_base(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars().

void protocols::stepwise::legacy::modeler::rna::setup_copy_DOF_input ( StepWiseRNA_PoseSetupOP & stepwise_rna_pose_setup )

References get_silent_file_tags(), and TR().

Referenced by setup_pose_setup_class().

StepWiseRNA_PoseSetupOP protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class	(	stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &	working_parameters,
		bool const	copy_DOF
	)

References core::chemical::FA_STANDARD, core::pose::rna::make_phosphate_nomenclature_matches_mini(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), setup_copy_DOF_input(), and TR().

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::setup_rna_working_parameters ( bool check_for_previously_closed_cutpoint_with_input_pose )

References get_fixed_res(), get_input_res(), get_silent_file_tags(), core::sequence::read_fasta_file_and_concatenate(), core::pose::rna::remove_bracketed(), and TR().

void protocols::stepwise::legacy::modeler::rna::setup_simple_fold_tree ( core::pose::Pose & pose )

References core::pose::Pose::fold_tree(), protocols::star::simple_fold_tree(), core::kinematics::FoldTree::simple_tree(), and core::pose::Pose::size().

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters ( )

Oct 28, 2011:This function is an alternative way to setup the working_parameters//////////////////////////////////////////////////// The original working_parameters was designed primarily for use during the SWA building step///////////////////////////////////////// However since then, many other other SWA and FARFAR class make use of it especially the full pose length version//////////////// Hence the original working_parameters setup has become clumbersome for most usage (containing many options and independencies)////// The new job_parameter setup function is a work in progress and will be updated as needed./////////////////////////////////////// For example right now (Oct 28, 2011), it only contains parameters needed by output_data()///////////////////////////////////////

References core::pose::rna::apply_virtual_rna_residue_variant_type(), core::chemical::FA_STANDARD, core::pose::full_model_info::full_to_sub(), get_fixed_res(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), print_WorkingParameters_info(), core::sequence::read_fasta_file_and_concatenate(), core::pose::rna::remove_bracketed(), core::pose::rna::string_to_int(), core::pose::rna::tokenize(), and TR().

void protocols::stepwise::legacy::modeler::rna::sort_pair_list ( utility::vector1< std::pair< core::Size, core::Size > > pair_list )

References pair_sort_criterion().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list().

Variable Documentation

protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct protocols::stepwise::legacy::modeler::rna::local_count_data

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation