protocols::farna::RNA_ChunkLibrary Class Reference

#include <RNA_ChunkLibrary.hh>

Public Member Functions
	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)
	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
utility::vector1< Size >	get_indices_of_moving_chunks () const
Size	num_moving_chunks () 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)
void	setup_base_pair_step_chunks (core::pose::Pose const &pose, utility::vector1< BasePairStep > base_pair_steps)

Private Member Functions
void	update_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 ()
bool	check_res_map (core::pose::ResMap const &res_map, core::pose::Pose const &scratch_pose, std::string const &sequence) 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_
BasePairStepLibraryOP	base_pair_step_library_

Constructor & Destructor Documentation

protocols::farna::RNA_ChunkLibrary::RNA_ChunkLibrary

(

)

protocols::farna::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
	)

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

protocols::farna::RNA_ChunkLibrary::~RNA_ChunkLibrary

(

)

Member Function Documentation

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

References protocols::farna::process_input_file(), and core::pose::Pose::sequence().

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

private

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

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

inline

References allow_insert_.

Referenced by protocols::farna::RNA_DeNovoProtocol::initialize_movers().

bool protocols::farna::RNA_ChunkLibrary::check_fold_tree_OK

(

core::pose::Pose const &

pose

)

References protocols::farna::ChunkSet::check_fold_tree_OK(), and utility_exit_with_message.

Referenced by protocols::farna::RNA_DeNovoProtocol::do_random_moves().

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

private

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

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

inline

References chunk_coverage_.

Referenced by protocols::farna::RNA_DeNovoProtocol::initialize_movers().

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

inline

References chunk_sets_.

void protocols::farna::RNA_ChunkLibrary::figure_out_chunk_coverage ( )

private

utility::vector1< Size > protocols::farna::RNA_ChunkLibrary::get_indices_of_moving_chunks

(

)

const

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

References core::pose::Pose::dump_pdb(), protocols::farna::ChunkSet::insert_chunk_into_pose(), protocols::farna::ChunkSet::num_chunks(), protocols::farna::RG, and numeric::random::RandomGenerator::uniform().

Referenced by protocols::farna::RNA_DeNovoProtocol::apply(), and protocols::farna::RNA_DeNovoProtocol::do_random_moves().

void protocols::farna::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
	)

References core::conformation::Residue::is_coarse(), protocols::farna::process_input_file(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and utility_exit_with_message.

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

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

inline

References chunk_sets_.

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

inline

References chunk_sets_.

Size protocols::farna::RNA_ChunkLibrary::num_moving_chunks

(

)

const

Referenced by protocols::farna::RNA_DeNovoProtocol::setup_monte_carlo_cycles().

bool protocols::farna::RNA_ChunkLibrary::random_chunk_insertion

(

core::pose::Pose &

pose

)

const

References protocols::farna::ChunkSet::insert_chunk_into_pose(), protocols::farna::ChunkSet::num_chunks(), numeric::random::RandomGenerator::random_element(), protocols::farna::RG, runtime_assert, and numeric::random::RandomGenerator::uniform().

Referenced by protocols::farna::RNA_DeNovoProtocol::random_chunk_trial().

void protocols::farna::RNA_ChunkLibrary::set_allow_insert

(

toolbox::AllowInsertOP

allow_insert

)

Referenced by protocols::farna::RNA_DeNovoProtocol::initialize_movers().

void protocols::farna::RNA_ChunkLibrary::setup_base_pair_step_chunks	(	core::pose::Pose const &	pose,
		utility::vector1< BasePairStep >	base_pair_steps
	)

References protocols::farna::BasePairStep::i(), protocols::farna::BasePairStep::i_next(), protocols::farna::BasePairStepLibrary::initialize(), protocols::farna::BasePairStep::j(), protocols::farna::BasePairStep::j_next(), named_atom_id_to_atom_id(), q, runtime_assert, core::pose::Pose::sequence(), and utility_exit_with_message.

Referenced by protocols::farna::RNA_DeNovoProtocol::initialize_movers().

void protocols::farna::RNA_ChunkLibrary::superimpose_to_first_chunk

(

core::pose::Pose &

pose

)

const

References runtime_assert.

Referenced by protocols::farna::RNA_DeNovoProtocol::align_and_output_to_silent_file().

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

private

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::pose::Pose::fold_tree(), core::conformation::Residue::has(), protocols::farna::involved_in_phosphate_torsion(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Member Data Documentation

toolbox::AllowInsertOP protocols::farna::RNA_ChunkLibrary::allow_insert_

private

Referenced by allow_insert().

BasePairStepLibraryOP protocols::farna::RNA_ChunkLibrary::base_pair_step_library_

private

core::Real protocols::farna::RNA_ChunkLibrary::chunk_coverage_

private

Referenced by chunk_coverage().

utility::vector1< ChunkSetOP > protocols::farna::RNA_ChunkLibrary::chunk_sets_

private

Referenced by chunk_set(), num_chunk_sets(), and num_chunks().

bool protocols::farna::RNA_ChunkLibrary::coarse_rna_

private

ObjexxFCL::FArray1D<bool> protocols::farna::RNA_ChunkLibrary::covered_by_chunk_

private

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

• src/protocols/farna/RNA_ChunkLibrary.hh
• src/protocols/farna/RNA_ChunkLibrary.cc