#include <RNA_ChunkLibrary.hh>

Inheritance diagram for protocols::rna::RNA_ChunkLibrary:

Collaboration diagram for protocols::rna::RNA_ChunkLibrary:

Public Member Functions
	RNA_ChunkLibrary ()

	RNA_ChunkLibrary (utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, std::map< Size, Size > const &connections_in_big_pose)

	RNA_ChunkLibrary (utility::vector1< std::string > const &pdb_files, utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)

	RNA_ChunkLibrary (utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)

	~RNA_ChunkLibrary ()

void	initialize_rna_chunk_library (utility::vector1< std::string > const &pdb_files, utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)

Size	num_chunk_sets () const

Size	num_chunks (Size const n) const

ChunkSetOP	chunk_set (Size const n) const

void	add_chunk_set (std::string const &silent_file, core::pose::ResMap const &res_map, core::pose::Pose const &big_pose)

void	insert_chunk_into_pose (core::pose::Pose &pose, Size const &chunk_list_index, Size const &chunk_pose_index) const

bool	random_chunk_insertion (core::pose::Pose &pose) const

void	initialize_random_chunks (core::pose::Pose &pose, bool const dump_pdb=false) const

toolbox::AllowInsertOP	allow_insert ()

void	set_allow_insert (toolbox::AllowInsertOP allow_insert)

core::Real const &	chunk_coverage () const

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

bool	check_fold_tree_OK (core::pose::Pose const &pose)

Private Member Functions
void	zero_out_allow_insert (core::pose::ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &scratch_pose, Size const domain_num)

bool	check_fold_tree_OK (core::pose::ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &scratch_pose)

void	figure_out_chunk_coverage ()

void	get_component_sequences (core::pose::Pose const &pose, utility::vector1< std::string > &sequences, utility::vector1< core::Size > &chain_id, utility::vector1< core::Size > &sequence_start) const

void	process_input_file (std::string const &silent_file, utility::vector1< core::pose::PoseOP > &pose_list, bool is_pdb=false) const

void	figure_out_possible_res_maps (utility::vector1< core::pose::ResMap > &res_maps, core::pose::Pose const &scratch_pose, std::string const &sequence_of_big_pose, std::map< Size, Size > const &connections_in_big_pose) const

void	find_res_maps (utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const

void	get_sequence_matches (utility::vector1< utility::vector1< Size > > &matches_to_each_scratch_sequence, utility::vector1< std::string > const &scratch_sequences, std::string const &sequence_of_big_pose) const

void	check_connections (Size const &num_chain, core::pose::ResMap &res_map, utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const

bool	fill_res_map (core::pose::ResMap &res_map, Size const &match_pos, Size const &scratch_start_pos, Size const &scratch_sequence_length) const

void	test_matches (Size const &res1, Size const &res2, core::pose::ResMap &res_map, utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const

bool	check_res_map (core::pose::ResMap const &res_map, core::pose::Pose const &scratch_pose, std::string const &sequence) const

void	check_res_map_recursively (core::pose::ResMap const &res_map_old, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::Size > const &chain_id, core::Size const &num_sequence, core::Size const &num_match, utility::vector1< core::pose::ResMap > &res_maps) const

bool	check_jump_match (core::pose::Pose const &scratch_pose, std::map< core::Size, core::Size > const &connections_in_big_pose, core::pose::ResMap const &res_map, utility::vector1< Size > const &chain_id) const

void	align_to_chunk (core::pose::Pose &pose, ChunkSet const &chunk_set, core::Size const chunk_index) const

Private Attributes
utility::vector1< ChunkSetOP >	chunk_sets_

toolbox::AllowInsertOP	allow_insert_

ObjexxFCL::FArray1D< bool >	covered_by_chunk_

core::Real	chunk_coverage_

bool	coarse_rna_

Detailed Description

Definition at line 108 of file RNA_ChunkLibrary.hh.

Constructor & Destructor Documentation

protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary ( )

Definition at line 185 of file RNA_ChunkLibrary.cc.

protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary	(	utility::vector1< std::string > const &	silent_files,
		core::pose::Pose const &	pose,
		std::map< Size, Size > const &	connections_in_big_pose
	)

Definition at line 196 of file RNA_ChunkLibrary.cc.

References core::sequence::end, core::conformation::Residue::is_coarse(), core::pose::Pose::residue(), and core::pose::Pose::sequence().

protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary	(	utility::vector1< std::string > const &	pdb_files,
		utility::vector1< std::string > const &	silent_files,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	input_res
	)

Definition at line 265 of file RNA_ChunkLibrary.cc.

protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary	(	utility::vector1< std::string > const &	silent_files,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	input_res
	)

Definition at line 252 of file RNA_ChunkLibrary.cc.

protocols::rna::RNA_ChunkLibrary::~RNA_ChunkLibrary ( )

inline

Definition at line 135 of file RNA_ChunkLibrary.hh.

Member Function Documentation

void protocols::rna::RNA_ChunkLibrary::add_chunk_set	(	std::string const &	silent_file,
		core::pose::ResMap const &	res_map,
		core::pose::Pose const &	big_pose
	)

Definition at line 341 of file RNA_ChunkLibrary.cc.

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

void protocols::rna::RNA_ChunkLibrary::align_to_chunk	(	core::pose::Pose &	pose,
		ChunkSet const &	chunk_set,
		core::Size const	chunk_index
	)		const

private

Definition at line 1033 of file RNA_ChunkLibrary.cc.

References core::id::BOGUS_ATOM_ID, protocols::rna::ChunkSet::get_atom_id_map(), core::pose::initialize_atomid_map(), protocols::rna::ChunkSet::mini_pose(), and core::scoring::superimpose_pose().

toolbox::AllowInsertOP protocols::rna::RNA_ChunkLibrary::allow_insert ( )

inline

Definition at line 165 of file RNA_ChunkLibrary.hh.

References allow_insert_.

void protocols::rna::RNA_ChunkLibrary::check_connections	(	Size const &	num_chain,
		core::pose::ResMap &	res_map,
		utility::vector1< Size > const &	chain_id,
		utility::vector1< Size > const &	scratch_sequence_start,
		utility::vector1< std::string > const &	scratch_sequences,
		utility::vector1< utility::vector1< Size > > const &	matches_to_each_scratch_sequence,
		core::pose::Pose const &	scratch_pose,
		std::map< Size, Size > const &	connections_in_big_pose,
		utility::vector1< core::pose::ResMap > &	res_maps
	)		const

private

Definition at line 642 of file RNA_ChunkLibrary.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

bool protocols::rna::RNA_ChunkLibrary::check_fold_tree_OK ( core::pose::Pose const & pose)

Definition at line 433 of file RNA_ChunkLibrary.cc.

References protocols::rna::ChunkSet::check_fold_tree_OK().

bool protocols::rna::RNA_ChunkLibrary::check_fold_tree_OK	(	core::pose::ResMap const &	res_map,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	scratch_pose
	)

private

bool protocols::rna::RNA_ChunkLibrary::check_jump_match	(	core::pose::Pose const &	scratch_pose,
		std::map< core::Size, core::Size > const &	connections_in_big_pose,
		core::pose::ResMap const &	res_map,
		utility::vector1< Size > const &	chain_id
	)		const

private

Definition at line 848 of file RNA_ChunkLibrary.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

bool protocols::rna::RNA_ChunkLibrary::check_res_map	(	core::pose::ResMap const &	res_map,
		core::pose::Pose const &	scratch_pose,
		std::string const &	sequence
	)		const

private

Definition at line 918 of file RNA_ChunkLibrary.cc.

References core::conformation::Residue::name1(), and core::pose::Pose::residue().

void protocols::rna::RNA_ChunkLibrary::check_res_map_recursively	(	core::pose::ResMap const &	res_map_old,
		utility::vector1< std::string > const &	scratch_sequences,
		utility::vector1< utility::vector1< Size > > const &	matches_to_each_scratch_sequence,
		core::pose::Pose const &	scratch_pose,
		std::map< Size, Size > const &	connections_in_big_pose,
		utility::vector1< core::Size > const &	chain_id,
		core::Size const &	num_sequence,
		core::Size const &	num_match,
		utility::vector1< core::pose::ResMap > &	res_maps
	)		const

private

Definition at line 792 of file RNA_ChunkLibrary.cc.

core::Real const& protocols::rna::RNA_ChunkLibrary::chunk_coverage ( ) const

inline

Definition at line 169 of file RNA_ChunkLibrary.hh.

References chunk_coverage_.

ChunkSetOP protocols::rna::RNA_ChunkLibrary::chunk_set ( Size const n) const

inline

Definition at line 149 of file RNA_ChunkLibrary.hh.

References chunk_sets_.

void protocols::rna::RNA_ChunkLibrary::figure_out_chunk_coverage ( )

private

Definition at line 494 of file RNA_ChunkLibrary.cc.

void protocols::rna::RNA_ChunkLibrary::figure_out_possible_res_maps	(	utility::vector1< core::pose::ResMap > &	res_maps,
		core::pose::Pose const &	scratch_pose,
		std::string const &	sequence_of_big_pose,
		std::map< Size, Size > const &	connections_in_big_pose
	)		const

private

Definition at line 552 of file RNA_ChunkLibrary.cc.

bool protocols::rna::RNA_ChunkLibrary::fill_res_map	(	core::pose::ResMap &	res_map,
		Size const &	match_pos,
		Size const &	scratch_start_pos,
		Size const &	scratch_sequence_length
	)		const

private

Definition at line 768 of file RNA_ChunkLibrary.cc.

References protocols::rna::TR().

void protocols::rna::RNA_ChunkLibrary::find_res_maps	(	utility::vector1< Size > const &	chain_id,
		utility::vector1< Size > const &	scratch_sequence_start,
		utility::vector1< std::string > const &	scratch_sequences,
		utility::vector1< utility::vector1< Size > > const &	matches_to_each_scratch_sequence,
		core::pose::Pose const &	scratch_pose,
		std::map< Size, Size > const &	connections_in_big_pose,
		utility::vector1< core::pose::ResMap > &	res_maps
	)		const

private

Definition at line 576 of file RNA_ChunkLibrary.cc.

References core::pose::Pose::sequence(), core::io::serialization::size(), and protocols::rna::TR().

void protocols::rna::RNA_ChunkLibrary::get_component_sequences	(	core::pose::Pose const &	pose,
		utility::vector1< std::string > &	sequences,
		utility::vector1< core::Size > &	chain_id,
		utility::vector1< core::Size > &	sequence_start
	)		const

private

Definition at line 516 of file RNA_ChunkLibrary.cc.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::name1(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::rna::TR().

void protocols::rna::RNA_ChunkLibrary::get_sequence_matches	(	utility::vector1< utility::vector1< Size > > &	matches_to_each_scratch_sequence,
		utility::vector1< std::string > const &	scratch_sequences,
		std::string const &	sequence_of_big_pose
	)		const

private

Definition at line 609 of file RNA_ChunkLibrary.cc.

References protocols::rna::TR().

void protocols::rna::RNA_ChunkLibrary::initialize_random_chunks	(	core::pose::Pose &	pose,
		bool const	dump_pdb = `false`
	)		const

Definition at line 997 of file RNA_ChunkLibrary.cc.

References core::pose::Pose::dump_pdb(), protocols::rna::ChunkSet::insert_chunk_into_pose(), protocols::rna::ChunkSet::num_chunks(), and protocols::rna::RG().

void protocols::rna::RNA_ChunkLibrary::initialize_rna_chunk_library	(	utility::vector1< std::string > const &	pdb_files,
		utility::vector1< std::string > const &	silent_files,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	input_res
	)

Definition at line 276 of file RNA_ChunkLibrary.cc.

References core::conformation::Residue::is_coarse(), core::pose::Pose::residue(), and core::pose::Pose::sequence().

void protocols::rna::RNA_ChunkLibrary::insert_chunk_into_pose	(	core::pose::Pose &	pose,
		Size const &	chunk_list_index,
		Size const &	chunk_pose_index
	)		const

Definition at line 358 of file RNA_ChunkLibrary.cc.

Size protocols::rna::RNA_ChunkLibrary::num_chunk_sets ( ) const

inline

Definition at line 145 of file RNA_ChunkLibrary.hh.

References chunk_sets_.

Size protocols::rna::RNA_ChunkLibrary::num_chunks ( Size const n) const

inline

Definition at line 147 of file RNA_ChunkLibrary.hh.

References chunk_sets_.

void protocols::rna::RNA_ChunkLibrary::process_input_file	(	std::string const &	silent_file,
		utility::vector1< core::pose::PoseOP > &	pose_list,
		bool	is_pdb = `false`
	)		const

private

Definition at line 940 of file RNA_ChunkLibrary.cc.

References core::io::silent::SilentFileData::begin(), core::sequence::end, core::io::silent::SilentFileData::end(), protocols::rna::ensure_phosphate_nomenclature_matches_mini(), protocols::rna::figure_out_reasonable_rna_fold_tree(), core::chemical::ChemicalManager::get_instance(), protocols::rna::make_coarse_pose(), core::import_pose::pose_from_pdb(), core::io::silent::SilentFileData::read_file(), protocols::rna::remove_cutpoints_closed(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::RNA, and protocols::rna::virtualize_5prime_phosphates().

bool protocols::rna::RNA_ChunkLibrary::random_chunk_insertion ( core::pose::Pose & pose) const

Definition at line 369 of file RNA_ChunkLibrary.cc.

References protocols::rna::RG().

void protocols::rna::RNA_ChunkLibrary::set_allow_insert ( toolbox::AllowInsertOP allow_insert)

Definition at line 1053 of file RNA_ChunkLibrary.cc.

void protocols::rna::RNA_ChunkLibrary::superimpose_to_first_chunk ( core::pose::Pose & pose) const

Definition at line 1025 of file RNA_ChunkLibrary.cc.

void protocols::rna::RNA_ChunkLibrary::test_matches	(	Size const &	res1,
		Size const &	res2,
		core::pose::ResMap &	res_map,
		utility::vector1< Size > const &	chain_id,
		utility::vector1< Size > const &	scratch_sequence_start,
		utility::vector1< std::string > const &	scratch_sequences,
		utility::vector1< utility::vector1< Size > > const &	matches_to_each_scratch_sequence,
		core::pose::Pose const &	scratch_pose,
		std::map< Size, Size > const &	connections_in_big_pose,
		utility::vector1< core::pose::ResMap > &	res_maps
	)		const

private

Definition at line 684 of file RNA_ChunkLibrary.cc.

References core::io::serialization::size(), and protocols::rna::TR().

void protocols::rna::RNA_ChunkLibrary::zero_out_allow_insert	(	core::pose::ResMap const &	res_map,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	scratch_pose,
		Size const	domain_num
	)