protocols::rna::denovo::RNA_DeNovoPoseInitializer Class Reference

Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and jump changes. More...

#include <RNA_DeNovoPoseInitializer.hh>

Inheritance diagram for protocols::rna::denovo::RNA_DeNovoPoseInitializer:

Public Member Functions
	RNA_DeNovoPoseInitializer (core::import_pose::RNA_DeNovoParameters const &rna_params_file_info)
	~RNA_DeNovoPoseInitializer () override
void	initialize_for_de_novo_protocol (core::pose::Pose &pose, bool const ignore_secstruct=false)
	"classic" setup, used in denovo protocol. Note: changes pose (virtualizes phosphate). and requires later call of setup_fold_tree_and_jumps_and_variants More...
void	setup_fold_tree_and_jumps_and_variants (core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &rna_jump_mover, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map, core::import_pose::libraries::RNA_ChunkLibrary const &rna_chunk_library, bool const &enumerate=false) const
void	setup_fold_tree_and_jumps_and_variants (core::pose::Pose &pose) const
void	set_root_at_first_rigid_body (bool const setting)
void	set_dock_each_chunk (bool const &setting)
void	set_dock_each_chunk_per_chain (bool const &setting)
void	set_dock_chunks_res (utility::vector1< core::Size > const &dock_chunks_res)
void	set_center_jumps_in_single_stranded (bool const &setting)
void	set_new_fold_tree_initializer (bool const &setting)
bool	new_fold_tree_initializer () const
void	set_model_with_density (bool const &setting)
bool	model_with_density () const
void	set_bps_moves (bool const &setting)
core::import_pose::RNA_DeNovoParameters const &	rna_params () const
void	setup_chainbreak_variants (core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map) const

Private Member Functions
void	initialize_secstruct (core::pose::Pose &pose)
void	override_secstruct (core::pose::Pose &pose)
void	setup_virtual_phosphate_variants (core::pose::Pose &pose) const
void	append_virtual_anchor (core::pose::Pose &pose)
void	setup_jumps (core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &rna_jump_mover, core::import_pose::libraries::RNA_ChunkLibrary const &rna_chunk_library, bool const enumerate=false) const
void	setup_chainbreak_variants (core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map, core::import_pose::RNA_JumpMover const &rna_jump_mover, core::import_pose::libraries::RNA_ChunkLibrary const &rna_chunk_library, bool const &enumerate=false) const
void	setup_fold_tree_through_build_full_model_info (core::pose::Pose &pose, core::import_pose::libraries::RNA_ChunkLibrary const &chunk_library, bool const &enumerate=false) const
core::kinematics::FoldTree	setup_fold_tree_legacy (core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &rna_jump_mover) const
void	setup_block_stack_variants (core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map) const
void	insert_base_pair_jumps (core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &jump_mover, bool &success) const

Private Attributes
core::import_pose::RNA_DeNovoParameters	rna_params_
bool const	assume_non_stem_is_loop
bool	bps_moves_
bool	root_at_first_rigid_body_
bool	dock_each_chunk_
bool	dock_each_chunk_per_chain_
utility::vector1< core::Size >	dock_chunks_res_
bool	center_jumps_in_single_stranded_
bool	new_fold_tree_initializer_
bool	model_with_density_

Detailed Description

Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and jump changes.

Constructor & Destructor Documentation

RNA_DeNovoPoseInitializer()

protocols::rna::denovo::RNA_DeNovoPoseInitializer::RNA_DeNovoPoseInitializer

(

core::import_pose::RNA_DeNovoParameters const &

rna_params_file_info

)

~RNA_DeNovoPoseInitializer()

protocols::rna::denovo::RNA_DeNovoPoseInitializer::~RNA_DeNovoPoseInitializer ( )

overridedefault

Member Function Documentation

append_virtual_anchor()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor ( core::pose::Pose &  pose )

private

References core::import_pose::RNA_DeNovoParameters::add_cutpoint_open(), core::import_pose::RNA_DeNovoParameters::add_obligate_pairing_set(), core::import_pose::RNA_DeNovoParameters::add_rna_pairing(), core::pose::Pose::append_residue_by_jump(), core::pose::full_model_info::append_virtual_residue_to_full_model_info(), core::conformation::ResidueFactory::create_residue(), core::pose::full_model_info::full_model_info_defined(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::import_pose::RNA_DeNovoParameters::rna_pairing_list(), rna_params_, core::pose::rna::BasePair::set_res1(), core::pose::rna::BasePair::set_res2(), core::pose::Pose::size(), protocols::rna::denovo::TR(), core::import_pose::RNA_DeNovoParameters::virtual_anchor_attachment_points(), and core::pose::virtual_type_for_pose().

Referenced by initialize_for_de_novo_protocol().

initialize_for_de_novo_protocol()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_for_de_novo_protocol	(	core::pose::Pose &	pose,
		bool const	ignore_secstruct = false
	)

"classic" setup, used in denovo protocol. Note: changes pose (virtualizes phosphate). and requires later call of setup_fold_tree_and_jumps_and_variants

References append_virtual_anchor(), initialize_secstruct(), override_secstruct(), rna_params_, setup_virtual_phosphate_variants(), and core::import_pose::RNA_DeNovoParameters::virtual_anchor_attachment_points().

initialize_secstruct()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct ( core::pose::Pose &  pose )

private

References core::conformation::Residue::aa(), core::chemical::rna::ANTIPARALLEL, assume_non_stem_is_loop, core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), 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::import_pose::RNA_DeNovoParameters::rna_pairing_list(), rna_params_, core::import_pose::RNA_DeNovoParameters::rna_secstruct_legacy(), core::import_pose::RNA_DeNovoParameters::secstruct_defined(), core::pose::rna::secstruct_legacy::set_rna_secstruct_legacy(), core::import_pose::RNA_DeNovoParameters::set_rna_secstruct_legacy(), core::pose::Pose::size(), protocols::rna::denovo::TR(), and core::chemical::rna::WATSON_CRICK.

Referenced by initialize_for_de_novo_protocol().

insert_base_pair_jumps()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps ( core::pose::Pose &  pose, core::import_pose::RNA_JumpMover const &  jump_mover, bool &  success  ) const

private

References core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::import_pose::RNA_JumpMover::atom_level_domain_map(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_RNA(), core::pose::rna::moveable_jump(), new_fold_tree_initializer_, core::pose::Pose::num_jump(), core::pose::Pose::residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by setup_jumps().

model_with_density()

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::model_with_density ( ) const

inline

References model_with_density_.

new_fold_tree_initializer()

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::new_fold_tree_initializer ( ) const

inline

References new_fold_tree_initializer_.

override_secstruct()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::override_secstruct ( core::pose::Pose &  pose )

private

References rna_params_, core::import_pose::RNA_DeNovoParameters::rna_secstruct_legacy(), core::pose::rna::secstruct_legacy::set_rna_secstruct_legacy(), core::import_pose::RNA_DeNovoParameters::set_rna_secstruct_legacy(), core::pose::Pose::size(), and protocols::rna::denovo::TR().

Referenced by initialize_for_de_novo_protocol().

rna_params()

core::import_pose::RNA_DeNovoParameters const& protocols::rna::denovo::RNA_DeNovoPoseInitializer::rna_params ( ) const

inline

References rna_params_.

set_bps_moves()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_bps_moves ( bool const &  setting )

inline

References bps_moves_.

set_center_jumps_in_single_stranded()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_center_jumps_in_single_stranded ( bool const &  setting )

inline

References center_jumps_in_single_stranded_.

set_dock_chunks_res()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_chunks_res ( utility::vector1< core::Size > const &  dock_chunks_res )

inline

References dock_chunks_res_.

set_dock_each_chunk()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_each_chunk ( bool const &  setting )

inline

References dock_each_chunk_.

set_dock_each_chunk_per_chain()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_dock_each_chunk_per_chain ( bool const &  setting )

inline

References dock_each_chunk_per_chain_.

set_model_with_density()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_model_with_density ( bool const &  setting )

inline

References model_with_density_.

set_new_fold_tree_initializer()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_new_fold_tree_initializer ( bool const &  setting )

inline

References new_fold_tree_initializer_.

set_root_at_first_rigid_body()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_root_at_first_rigid_body ( bool const  setting )

inline

References root_at_first_rigid_body_.

setup_block_stack_variants()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_block_stack_variants ( core::pose::Pose &  pose, core::pose::toolbox::AtomLevelDomainMapOP  atom_level_domain_map  ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::BLOCK_STACK_ABOVE, core::import_pose::RNA_DeNovoParameters::block_stack_above_res(), core::chemical::BLOCK_STACK_BELOW, core::import_pose::RNA_DeNovoParameters::block_stack_below_res(), and rna_params_.

Referenced by setup_fold_tree_and_jumps_and_variants().

setup_chainbreak_variants() [1/2]

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants	(	core::pose::Pose &	pose,
		core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map
	)		const

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueTypeBase::base_name(), core::id::BB, core::pose::Pose::conformation(), core::pose::correctly_add_2prime_connection_variants(), core::pose::correctly_add_cutpoint_variants(), core::chemical::CUTPOINT_UPPER, core::import_pose::RNA_DeNovoParameters::cutpoints_cyclize(), core::import_pose::RNA_DeNovoParameters::cutpoints_open(), core::conformation::Conformation::declare_chemical_bond(), core::chemical::FIVE_PRIME_PHOSPHATE, core::chemical::FIVEPRIME_CAP, core::import_pose::RNA_DeNovoParameters::fiveprime_cap(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rna_params_, core::pose::Pose::set_torsion(), core::pose::Pose::size(), core::chemical::THREE_PRIME_PHOSPHATE, core::pose::Pose::torsion(), protocols::rna::denovo::TR(), core::import_pose::RNA_DeNovoParameters::twoprime(), core::chemical::UPPER_TERMINUS_VARIANT, and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by setup_fold_tree_and_jumps_and_variants().

setup_chainbreak_variants() [2/2]

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants ( core::pose::Pose &  pose, core::pose::toolbox::AtomLevelDomainMapOP  atom_level_domain_map, core::import_pose::RNA_JumpMover const &  rna_jump_mover, core::import_pose::libraries::RNA_ChunkLibrary const &  rna_chunk_library, bool const &  enumerate = false  ) const

private

setup_fold_tree_and_jumps_and_variants() [1/2]

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants

(

core::pose::Pose &

pose

)

const

References setup_fold_tree_and_jumps_and_variants().

setup_fold_tree_and_jumps_and_variants() [2/2]

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants	(	core::pose::Pose &	pose,
		core::import_pose::RNA_JumpMover const &	rna_jump_mover,
		core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map,
		core::import_pose::libraries::RNA_ChunkLibrary const &	rna_chunk_library,
		bool const &	enumerate = false
	)		const

References core::import_pose::RNA_JumpMover::atom_level_domain_map(), setup_block_stack_variants(), setup_chainbreak_variants(), and setup_jumps().

Referenced by setup_fold_tree_and_jumps_and_variants().

setup_fold_tree_legacy()

kinematics::FoldTree protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy ( core::pose::Pose &  pose, core::import_pose::RNA_JumpMover const &  rna_jump_mover  ) const

private

References core::import_pose::RNA_JumpMover::atom_level_domain_map(), core::pose::rna::base_pair_moving(), core::pose::rna::base_pair_step_moving(), bps_moves_, core::import_pose::RNA_DeNovoParameters::chain_connections(), core::import_pose::RNA_DeNovoParameters::check_in_pairing_sets(), core::import_pose::RNA_DeNovoParameters::cutpoints_closed(), core::import_pose::RNA_DeNovoParameters::cutpoints_open(), core::import_pose::RNA_BasePairHandler::get_base_pair_steps(), core::pose::rna::secstruct_legacy::get_rna_secstruct_legacy(), core::chemical::element::I, core::conformation::Residue::is_RNA(), protocols::mean_field::max(), protocols::mean_field::min(), model_with_density_, core::conformation::named_atom_id_to_atom_id(), core::import_pose::RNA_DeNovoParameters::obligate_pairing_sets(), core::chemical::rings::q, core::kinematics::FoldTree::random_tree_from_jump_points(), core::pose::Pose::residue(), core::scoring::rg, core::import_pose::RNA_DeNovoParameters::rna_pairing_list(), rna_params_, core::pose::Pose::size(), and core::import_pose::RNA_DeNovoParameters::stem_pairing_sets().

Referenced by setup_jumps().

setup_fold_tree_through_build_full_model_info()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info ( core::pose::Pose &  pose, core::import_pose::libraries::RNA_ChunkLibrary const &  chunk_library, bool const &  enumerate = false  ) const

private

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), core::pose::addVirtualResAsRoot(), core::pose::Pose::append_residue_by_jump(), core::kinematics::FoldTree::begin(), protocols::stepwise::monte_carlo::build_full_model(), center_jumps_in_single_stranded_, core::import_pose::libraries::RNA_ChunkLibrary::chunk_sets(), core::pose::full_model_info::const_full_model_info(), core::pose::copydofs::copy_dofs(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), dock_chunks_res_, core::pose::full_model_info::DOCK_DOMAIN, dock_each_chunk_, dock_each_chunk_per_chain_, core::kinematics::FoldTree::end(), core::sequence::end, core::chemical::FA_STANDARD, core::import_pose::figure_out_dock_domain_map(), core::pose::rna::fill_in_default_jump_atoms(), core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::pose::Pose::insert_residue_by_bond(), core::pose::Pose::insert_residue_by_jump(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::make_pose_from_sequence(), model_with_density_, core::conformation::Residue::name3(), core::pose::full_model_info::nonconst_full_model_info(), core::kinematics::FoldTree::num_jump(), core::pose::rna::remove_bracketed(), core::kinematics::FoldTree::reorder(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue(), rna_params_, core::import_pose::RNA_DeNovoParameters::rna_secstruct_legacy(), core::pose::Pose::sequence(), core::pose::full_model_info::set_full_model_info(), core::pose::full_model_info::FullModelInfo::set_full_model_parameters(), core::pose::full_model_info::FullModelInfo::set_other_pose_list(), core::pose::Pose::size(), protocols::rna::denovo::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by setup_jumps().

setup_jumps()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps ( core::pose::Pose &  pose, core::import_pose::RNA_JumpMover const &  rna_jump_mover, core::import_pose::libraries::RNA_ChunkLibrary const &  rna_chunk_library, bool const  enumerate = false  ) const

private

References core::import_pose::RNA_JumpMover::atom_level_domain_map(), core::pose::rna::fill_in_default_jump_atoms(), core::pose::Pose::fold_tree(), core::import_pose::RNA_DeNovoParameters::fold_tree_from_silent_file(), core::pose::rna::get_rigid_body_jumps(), insert_base_pair_jumps(), core::conformation::Residue::is_RNA(), model_with_density_, core::conformation::named_atom_id_to_atom_id(), new_fold_tree_initializer_, core::kinematics::FoldTree::possible_root(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), rna_params_, root_at_first_rigid_body_, setup_fold_tree_legacy(), setup_fold_tree_through_build_full_model_info(), core::pose::Pose::size(), protocols::rna::denovo::TR(), core::kinematics::FoldTree::upstream_jump_residue(), core::import_pose::RNA_DeNovoParameters::use_fold_tree_from_silent_file(), and core::import_pose::RNA_DeNovoParameters::virtual_anchor_attachment_points().

Referenced by setup_fold_tree_and_jumps_and_variants().

setup_virtual_phosphate_variants()

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_virtual_phosphate_variants ( core::pose::Pose &  pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::import_pose::RNA_DeNovoParameters::cutpoints_open(), core::chemical::FIVEPRIME_CAP, core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rna_params_, core::pose::Pose::size(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by initialize_for_de_novo_protocol().

Member Data Documentation

assume_non_stem_is_loop

bool const protocols::rna::denovo::RNA_DeNovoPoseInitializer::assume_non_stem_is_loop

private

Referenced by initialize_secstruct().

bps_moves_

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::bps_moves_

private

Referenced by set_bps_moves(), and setup_fold_tree_legacy().

center_jumps_in_single_stranded_

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::center_jumps_in_single_stranded_

private

Referenced by set_center_jumps_in_single_stranded(), and setup_fold_tree_through_build_full_model_info().

dock_chunks_res_

utility::vector1< core::Size > protocols::rna::denovo::RNA_DeNovoPoseInitializer::dock_chunks_res_

private

Referenced by set_dock_chunks_res(), and setup_fold_tree_through_build_full_model_info().

dock_each_chunk_

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::dock_each_chunk_

private

Referenced by set_dock_each_chunk(), and setup_fold_tree_through_build_full_model_info().

dock_each_chunk_per_chain_

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::dock_each_chunk_per_chain_

private

Referenced by set_dock_each_chunk_per_chain(), and setup_fold_tree_through_build_full_model_info().

model_with_density_

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::model_with_density_

private

Referenced by model_with_density(), set_model_with_density(), setup_fold_tree_legacy(), setup_fold_tree_through_build_full_model_info(), and setup_jumps().

new_fold_tree_initializer_

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::new_fold_tree_initializer_

private

Referenced by insert_base_pair_jumps(), new_fold_tree_initializer(), set_new_fold_tree_initializer(), and setup_jumps().

rna_params_

core::import_pose::RNA_DeNovoParameters protocols::rna::denovo::RNA_DeNovoPoseInitializer::rna_params_

private

Referenced by append_virtual_anchor(), initialize_for_de_novo_protocol(), initialize_secstruct(), override_secstruct(), rna_params(), setup_block_stack_variants(), setup_chainbreak_variants(), setup_fold_tree_legacy(), setup_fold_tree_through_build_full_model_info(), setup_jumps(), and setup_virtual_phosphate_variants().

root_at_first_rigid_body_

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::root_at_first_rigid_body_

private

Referenced by set_root_at_first_rigid_body(), and setup_jumps().

---

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

• src/protocols/rna/denovo/RNA_DeNovoPoseInitializer.hh
• src/protocols/rna/denovo/RNA_DeNovoPoseInitializer.cc