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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:
Inheritance graph
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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::Sizedock_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

protocols::rna::denovo::RNA_DeNovoPoseInitializer::RNA_DeNovoPoseInitializer ( core::import_pose::RNA_DeNovoParameters const &  rna_params_file_info)
protocols::rna::denovo::RNA_DeNovoPoseInitializer::~RNA_DeNovoPoseInitializer ( )
overridedefault

Member Function Documentation

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

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct ( core::pose::Pose pose)
private
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
bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::model_with_density ( ) const
inline

References model_with_density_.

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::new_fold_tree_initializer ( ) const
inline
void protocols::rna::denovo::RNA_DeNovoPoseInitializer::override_secstruct ( core::pose::Pose pose)
private
core::import_pose::RNA_DeNovoParameters const& protocols::rna::denovo::RNA_DeNovoPoseInitializer::rna_params ( ) const
inline

References rna_params_.

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

References bps_moves_.

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

References dock_chunks_res_.

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

References dock_each_chunk_.

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

References model_with_density_.

void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_new_fold_tree_initializer ( bool const &  setting)
inline
void protocols::rna::denovo::RNA_DeNovoPoseInitializer::set_root_at_first_rigid_body ( bool const  setting)
inline
void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_block_stack_variants ( core::pose::Pose pose,
core::pose::toolbox::AtomLevelDomainMapOP  atom_level_domain_map 
) const
private
void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants ( core::pose::Pose pose,
core::pose::toolbox::AtomLevelDomainMapOP  atom_level_domain_map 
) const
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
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
void protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants ( core::pose::Pose pose) const
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
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(), core::pack::dunbrack::c, 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::sequence::end, core::kinematics::FoldTree::end(), core::chemical::FA_STANDARD, core::import_pose::figure_out_dock_domain_map(), core::pose::rna::fill_in_default_jump_atoms(), 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::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().

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

Member Data Documentation

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

Referenced by initialize_secstruct().

bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::bps_moves_
private
bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::center_jumps_in_single_stranded_
private
utility::vector1< core::Size > protocols::rna::denovo::RNA_DeNovoPoseInitializer::dock_chunks_res_
private
bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::dock_each_chunk_
private
bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::dock_each_chunk_per_chain_
private
bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::model_with_density_
private
bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::new_fold_tree_initializer_
private
core::import_pose::RNA_DeNovoParameters protocols::rna::denovo::RNA_DeNovoPoseInitializer::rna_params_
private
bool protocols::rna::denovo::RNA_DeNovoPoseInitializer::root_at_first_rigid_body_
private

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