core::import_pose::libraries::RNA_ChunkLibrary Class Reference

#include <RNA_ChunkLibrary.hh>

Inheritance diagram for core::import_pose::libraries::RNA_ChunkLibrary:

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, utility::vector1< core::Size > const &allow_insert_res=utility::vector1< core::Size >())
	RNA_ChunkLibrary (utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)
	RNA_ChunkLibrary (core::pose::Pose const &pose)
	~RNA_ChunkLibrary () override
RNA_ChunkLibraryOP	clone () const
	clone the ChunkLibrary More...
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, utility::vector1< core::Size > const &allow_insert_res=utility::vector1< core::Size >())
Size	num_chunk_sets () const
Size	num_chunks (Size const n) const
ChunkSetOP	chunk_set (Size const n) const
utility::vector1< ChunkSetOP >	chunk_sets () 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
core::Size	get_alignment_domain (core::pose::Pose const &pose) const
void	initialize_random_chunks (core::pose::Pose &pose, bool const dump_pdb=false) const
void	insert_random_protein_chunks (core::pose::Pose &pose) const
core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map () const
void	set_atom_level_domain_map (core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map)
core::Real const &	chunk_coverage () const
Size	single_user_input_chunk () const
bool	superimpose_to_single_user_input_chunk (core::pose::Pose &pose) const
bool	check_fold_tree_OK (core::pose::Pose const &pose) const
void	setup_base_pair_step_chunks (core::pose::Pose const &pose, utility::vector1< core::pose::rna::BasePairStep > const &base_pair_steps, BasePairStepLibrary const &base_pair_step_library)
void	update_to_move_rosetta_library_chunks ()

Private Member Functions
void	update_atom_level_domain_map (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_
core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map_
ObjexxFCL::FArray1D< bool >	covered_by_chunk_
core::Real	chunk_coverage_
bool	coarse_rna_
bool	do_rosetta_library_domain_check_

Constructor & Destructor Documentation

RNA_ChunkLibrary() [1/4]

core::import_pose::libraries::RNA_ChunkLibrary::RNA_ChunkLibrary

(

)

RNA_ChunkLibrary() [2/4]

core::import_pose::libraries::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,
		utility::vector1< core::Size > const &	allow_insert_res = utility::vector1< core::Size >()
	)

RNA_ChunkLibrary() [3/4]

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

RNA_ChunkLibrary() [4/4]

core::import_pose::libraries::RNA_ChunkLibrary::RNA_ChunkLibrary

(

core::pose::Pose const &

pose

)

~RNA_ChunkLibrary()

core::import_pose::libraries::RNA_ChunkLibrary::~RNA_ChunkLibrary ( )

overridedefault

Member Function Documentation

add_chunk_set()

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

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

align_to_chunk()

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

private

References core::id::AtomID::BOGUS_ATOM_ID(), core::import_pose::libraries::ChunkSet::get_atom_id_map(), core::pose::initialize_atomid_map(), core::import_pose::libraries::ChunkSet::mini_pose(), core::id::AtomID_Map< T >::set(), and core::scoring::superimpose_pose().

atom_level_domain_map()

core::pose::toolbox::AtomLevelDomainMapOP core::import_pose::libraries::RNA_ChunkLibrary::atom_level_domain_map ( ) const

inline

References atom_level_domain_map_.

check_fold_tree_OK() [1/2]

bool core::import_pose::libraries::RNA_ChunkLibrary::check_fold_tree_OK

(

core::pose::Pose const &

pose

)

const

References core::import_pose::libraries::ChunkSet::check_fold_tree_OK(), core::pose::Pose::fold_tree(), core::import_pose::libraries::ChunkSet::res_map(), and core::import_pose::TR().

check_fold_tree_OK() [2/2]

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

private

check_res_map()

bool core::import_pose::libraries::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(), and core::pose::Pose::residue().

chunk_coverage()

core::Real const& core::import_pose::libraries::RNA_ChunkLibrary::chunk_coverage ( ) const

inline

References chunk_coverage_.

chunk_set()

ChunkSetOP core::import_pose::libraries::RNA_ChunkLibrary::chunk_set ( Size const  n ) const

inline

References chunk_sets_.

chunk_sets()

utility::vector1< ChunkSetOP > core::import_pose::libraries::RNA_ChunkLibrary::chunk_sets ( ) const

inline

References chunk_sets_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

clone()

RNA_ChunkLibraryOP core::import_pose::libraries::RNA_ChunkLibrary::clone

(

)

const

clone the ChunkLibrary

figure_out_chunk_coverage()

void core::import_pose::libraries::RNA_ChunkLibrary::figure_out_chunk_coverage ( )

private

get_alignment_domain()

Size core::import_pose::libraries::RNA_ChunkLibrary::get_alignment_domain

(

core::pose::Pose const &

pose

)

const

References core::import_pose::get_anchor_rsd().

get_indices_of_moving_chunks()

utility::vector1< Size > core::import_pose::libraries::RNA_ChunkLibrary::get_indices_of_moving_chunks

(

)

const

initialize_random_chunks()

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

References core::io::pdb::dump_pdb(), core::pose::Pose::dump_pdb(), core::import_pose::libraries::ChunkSet::insert_chunk_into_pose(), core::import_pose::libraries::ChunkSet::num_chunks(), core::scoring::rg, and core::import_pose::libraries::ChunkSet::user_input().

initialize_rna_chunk_library()

void core::import_pose::libraries::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,
		utility::vector1< core::Size > const &	allow_insert_res = utility::vector1< core::Size >()
	)

References core::pose::Pose::annotated_sequence(), core::chemical::ResidueType::is_coarse(), core::chemical::ResidueTypeBase::is_RNA(), core::sequence::parse_out_non_standard_residues(), core::import_pose::process_input_file(), core::pose::Pose::residue_type(), core::pose::Pose::sequence(), and core::pose::Pose::total_residue().

insert_chunk_into_pose()

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

insert_random_protein_chunks()

void core::import_pose::libraries::RNA_ChunkLibrary::insert_random_protein_chunks

(

core::pose::Pose &

pose

)

const

References core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), core::import_pose::libraries::ChunkSet::num_chunks(), core::scoring::rg, and core::import_pose::libraries::ChunkSet::user_input().

num_chunk_sets()

Size core::import_pose::libraries::RNA_ChunkLibrary::num_chunk_sets ( ) const

inline

References chunk_sets_.

num_chunks()

Size core::import_pose::libraries::RNA_ChunkLibrary::num_chunks

(

Size const

n

)

const

num_moving_chunks()

Size core::import_pose::libraries::RNA_ChunkLibrary::num_moving_chunks

(

)

const

random_chunk_insertion()

bool core::import_pose::libraries::RNA_ChunkLibrary::random_chunk_insertion

(

core::pose::Pose &

pose

)

const

References core::import_pose::libraries::ChunkSet::insert_chunk_into_pose(), core::import_pose::libraries::ChunkSet::num_chunks(), and core::scoring::rg.

set_atom_level_domain_map()

void core::import_pose::libraries::RNA_ChunkLibrary::set_atom_level_domain_map

(

core::pose::toolbox::AtomLevelDomainMapOP

atom_level_domain_map

)

setup_base_pair_step_chunks()

void core::import_pose::libraries::RNA_ChunkLibrary::setup_base_pair_step_chunks	(	core::pose::Pose const &	pose,
		utility::vector1< core::pose::rna::BasePairStep > const &	base_pair_steps,
		BasePairStepLibrary const &	base_pair_step_library
	)

References core::pose::rna::base_pair_step_moving(), core::import_pose::libraries::check_base_pair_step_availability(), core::import_pose::libraries::BasePairStepLibrary::mini_pose_list(), core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN, core::import_pose::libraries::BasePairStepLibrary::scratch_pose(), and core::pose::Pose::sequence().

single_user_input_chunk()

Size core::import_pose::libraries::RNA_ChunkLibrary::single_user_input_chunk

(

)

const

References core::import_pose::libraries::ChunkSet::num_chunks(), and core::import_pose::libraries::ChunkSet::user_input().

superimpose_to_single_user_input_chunk()

bool core::import_pose::libraries::RNA_ChunkLibrary::superimpose_to_single_user_input_chunk

(

core::pose::Pose &

pose

)

const

update_atom_level_domain_map()

void core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map ( 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::id::AtomID::atomno(), core::pose::Pose::fold_tree(), core::conformation::Residue::has(), core::import_pose::involved_in_phosphate_torsion(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN, and core::import_pose::TR().

update_to_move_rosetta_library_chunks()

void core::import_pose::libraries::RNA_ChunkLibrary::update_to_move_rosetta_library_chunks

(

)

References core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN.

Member Data Documentation

atom_level_domain_map_

core::pose::toolbox::AtomLevelDomainMapOP core::import_pose::libraries::RNA_ChunkLibrary::atom_level_domain_map_

private

Referenced by atom_level_domain_map().

chunk_coverage_

core::Real core::import_pose::libraries::RNA_ChunkLibrary::chunk_coverage_

private

Referenced by chunk_coverage().

chunk_sets_

utility::vector1< ChunkSetOP > core::import_pose::libraries::RNA_ChunkLibrary::chunk_sets_

private

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

coarse_rna_

bool core::import_pose::libraries::RNA_ChunkLibrary::coarse_rna_

private

covered_by_chunk_

ObjexxFCL::FArray1D<bool> core::import_pose::libraries::RNA_ChunkLibrary::covered_by_chunk_

private

do_rosetta_library_domain_check_

bool core::import_pose::libraries::RNA_ChunkLibrary::do_rosetta_library_domain_check_

private

---

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

• src/core/import_pose/libraries/RNA_ChunkLibrary.hh
• src/core/import_pose/libraries/RNA_ChunkLibrary.cc