core::import_pose::RNA_JumpMover Class Reference

#include <RNA_JumpMover.hh>

Inheritance diagram for core::import_pose::RNA_JumpMover:

Public Member Functions
	RNA_JumpMover (core::import_pose::libraries::RNA_JumpLibraryCOP rna_jump_library, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map)
	~RNA_JumpMover () override
bool	random_jump_change (core::pose::Pose &pose) const
void	add_new_RNA_jump (core::pose::Pose &pose, core::Size const &which_jump, bool &success) const
void	set_chain_connections (utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > const &setting)
core::pose::rna::RNA_BasePairList	rna_pairing_list () const
void	set_rna_pairing_list (core::pose::rna::RNA_BasePairList const &setting)
core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map () const

Private Member Functions
bool	check_forward_backward (core::pose::Pose &pose, Size const jump_pos) const
Size	check_in_chain_connections (Size const &pos1, Size const &pos2) const
void	sample_alternative_chain_connection (core::pose::Pose &pose, Size const &which_jump) const

Private Attributes
core::import_pose::libraries::RNA_JumpLibraryCOP	rna_jump_library_
core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map_
core::pose::rna::RNA_BasePairList	rna_pairing_list_
utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > >	chain_connections_

Constructor & Destructor Documentation

RNA_JumpMover()

core::import_pose::RNA_JumpMover::RNA_JumpMover	(	core::import_pose::libraries::RNA_JumpLibraryCOP	rna_jump_library,
		core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map
	)

~RNA_JumpMover()

core::import_pose::RNA_JumpMover::~RNA_JumpMover ( )

overridedefault

Member Function Documentation

add_new_RNA_jump()

void core::import_pose::RNA_JumpMover::add_new_RNA_jump	(	core::pose::Pose &	pose,
		core::Size const &	which_jump,
		bool &	success
	)		const

References core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION, core::chemical::rna::ANY_BASE_EDGE, core::conformation::Residue::atom_index(), check_forward_backward(), check_in_chain_connections(), core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::chemical::element::I, core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rna_jump_library_, rna_pairing_list_, core::pose::Pose::set_jump(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), and random_jump_change().

atom_level_domain_map()

core::pose::toolbox::AtomLevelDomainMapCOP core::import_pose::RNA_JumpMover::atom_level_domain_map ( ) const

inline

References atom_level_domain_map_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_and_jumps_and_variants(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps().

check_forward_backward()

bool core::import_pose::RNA_JumpMover::check_forward_backward ( core::pose::Pose &  pose, Size const  jump_pos  ) const

private

References core::kinematics::AtomTree::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::pose::Pose::atom_tree(), core::id::AtomID::atomno(), core::kinematics::tree::Atom::get_self_ptr(), core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), and core::id::AtomID::rsd().

Referenced by add_new_RNA_jump().

check_in_chain_connections()

Size core::import_pose::RNA_JumpMover::check_in_chain_connections ( Size const &  pos1, Size const &  pos2  ) const

private

References chain_connections_.

Referenced by add_new_RNA_jump(), and sample_alternative_chain_connection().

random_jump_change()

bool core::import_pose::RNA_JumpMover::random_jump_change

(

core::pose::Pose &

pose

)

const

References add_new_RNA_jump(), core::chemical::ResidueType::atom_index(), atom_level_domain_map_, core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::rna::moveable_jump(), core::pose::Pose::num_jump(), core::pose::Pose::residue_type(), core::scoring::rg, sample_alternative_chain_connection(), and core::kinematics::FoldTree::upstream_jump_residue().

rna_pairing_list()

core::pose::rna::RNA_BasePairList core::import_pose::RNA_JumpMover::rna_pairing_list ( ) const

inline

References rna_pairing_list_.

sample_alternative_chain_connection()

void core::import_pose::RNA_JumpMover::sample_alternative_chain_connection ( core::pose::Pose &  pose, Size const &  which_jump  ) const

private

References chain_connections_, check_in_chain_connections(), core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::rna::fill_in_default_jump_atoms(), core::pose::Pose::fold_tree(), core::chemical::element::I, core::kinematics::FoldTree::jump_point(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::num_jump(), core::scoring::rg, core::pose::Pose::size(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by random_jump_change().

set_chain_connections()

void core::import_pose::RNA_JumpMover::set_chain_connections ( utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > const &  setting )

inline

References chain_connections_.

set_rna_pairing_list()

void core::import_pose::RNA_JumpMover::set_rna_pairing_list ( core::pose::rna::RNA_BasePairList const &  setting )

inline

References rna_pairing_list_.

Member Data Documentation

atom_level_domain_map_

core::pose::toolbox::AtomLevelDomainMapCOP core::import_pose::RNA_JumpMover::atom_level_domain_map_

private

Referenced by atom_level_domain_map(), and random_jump_change().

chain_connections_

utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > core::import_pose::RNA_JumpMover::chain_connections_

private

Referenced by check_in_chain_connections(), sample_alternative_chain_connection(), and set_chain_connections().

rna_jump_library_

core::import_pose::libraries::RNA_JumpLibraryCOP core::import_pose::RNA_JumpMover::rna_jump_library_

private

Referenced by add_new_RNA_jump().

rna_pairing_list_

core::pose::rna::RNA_BasePairList core::import_pose::RNA_JumpMover::rna_pairing_list_

private

Referenced by add_new_RNA_jump(), rna_pairing_list(), and set_rna_pairing_list().

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

• src/core/import_pose/RNA_JumpMover.hh
• src/core/import_pose/RNA_JumpMover.cc