#include <ChunkSet.hh>

Inheritance diagram for core::import_pose::libraries::ChunkSet:

Public Member Functions
	ChunkSet (utility::vector1< core::pose::PoseOP > const &pose_list, core::pose::ResMap const &res_map)

	ChunkSet (utility::vector1< core::pose::MiniPoseOP > const &mini_pose_list, core::pose::Pose const &example_pose, core::pose::ResMap const &res_map)

	~ChunkSet () override

void	insert_chunk_into_pose (core::pose::Pose &pose, Size const &chunk_pose_index, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, bool do_rosetta_library_domain_check=true) const

void	insert_protein_chunk_into_pose (core::pose::Pose &pose, Size const &chunk_pose_index, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, bool do_rosetta_library_domain_check=true) const

Size	num_chunks () const

std::map< core::id::AtomID, core::id::AtomID >	get_atom_id_map (core::pose::Pose &pose, core::pose::toolbox::AtomID_Mapper const &atom_id_mapper_to_target_vanilla_pose) const

core::pose::MiniPoseOP const	mini_pose (Size const idx) const

bool	check_fold_tree_OK (core::pose::Pose const &pose) const

void	set_user_input (bool const &setting)

bool	user_input () const

core::pose::ResMap const &	res_map () const

Private Member Functions
void	setup_atom_id_mask_and_mapper (core::pose::Pose const &pose)

void	setup_atom_id_mask (core::pose::Pose const &pose)

std::map< core::id::AtomID, core::Size >	get_atom_id_domain_map_for_rosetta_library_chunk (std::map< core::id::AtomID, core::id::AtomID > atom_id_map, core::pose::Pose const &pose, core::pose::toolbox::AtomLevelDomainMap const &atom_level_domain_map, bool do_rosetta_library_domain_check=true) const

void	filter_atom_id_map_with_mask (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map) const

void	setup_atom_id_mapper_to_vanilla_chunk_pose (core::pose::Pose const &pose)

void	filter_poses_have_same_sequence_and_variants ()

Private Attributes
utility::vector1 < core::pose::MiniPoseOP >	mini_pose_list_

core::pose::ResMap	res_map_

std::map< core::id::AtomID, bool >	atom_id_mask_

bool	user_input_

core::pose::toolbox::AtomID_MapperCOP	atom_id_mapper_to_vanilla_chunk_pose_

Constructor & Destructor Documentation

core::import_pose::libraries::ChunkSet::ChunkSet	(	utility::vector1< core::pose::PoseOP > const &	pose_list,
		core::pose::ResMap const &	res_map
	)

core::import_pose::libraries::ChunkSet::ChunkSet	(	utility::vector1< core::pose::MiniPoseOP > const &	mini_pose_list,
		core::pose::Pose const &	example_pose,
		core::pose::ResMap const &	res_map
	)

core::import_pose::libraries::ChunkSet::~ChunkSet ( )

overridedefault

Member Function Documentation

bool core::import_pose::libraries::ChunkSet::check_fold_tree_OK ( core::pose::Pose const & pose ) const

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), mini_pose_list_, core::pose::Pose::num_jump(), res_map_, core::pose::Pose::size(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::check_fold_tree_OK().

void core::import_pose::libraries::ChunkSet::filter_atom_id_map_with_mask ( std::map< core::id::AtomID, core::id::AtomID > & atom_id_map ) const

private

References atom_id_mask_.

Referenced by get_atom_id_map().

void core::import_pose::libraries::ChunkSet::filter_poses_have_same_sequence_and_variants ( )

private

References mini_pose_list_, core::pose::parse_sequence(), core::import_pose::libraries::remove_terminus_variant_types_for_rna(), core::pose::MiniPose::sequence(), core::import_pose::TR(), and core::pose::MiniPose::variant_types().

std::map< core::id::AtomID, core::Size > core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk	(	std::map< core::id::AtomID, core::id::AtomID >	atom_id_map,
		core::pose::Pose const &	pose,
		core::pose::toolbox::AtomLevelDomainMap const &	atom_level_domain_map,
		bool	do_rosetta_library_domain_check = `true`
	)		const

private

References core::pose::Pose::annotated_sequence(), core::conformation::atom_id_to_named_atom_id(), core::pose::toolbox::AtomLevelDomainMap::get_domain(), mini_pose_list_, core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN, core::pose::toolbox::AtomLevelDomainMap::show(), core::id::to_string(), core::import_pose::TR(), and user_input().

Referenced by insert_chunk_into_pose(), and insert_protein_chunk_into_pose().

std::map< core::id::AtomID, core::id::AtomID > core::import_pose::libraries::ChunkSet::get_atom_id_map	(	core::pose::Pose &	pose,
		core::pose::toolbox::AtomID_Mapper const &	atom_id_mapper_to_target_vanilla_pose
	)		const

References atom_id_mapper_to_vanilla_chunk_pose_, core::pose::toolbox::AtomID_Mapper::calculate_atom_id_map(), filter_atom_id_map_with_mask(), mini_pose_list_, and res_map_.

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::align_to_chunk(), insert_chunk_into_pose(), and insert_protein_chunk_into_pose().

void core::import_pose::libraries::ChunkSet::insert_chunk_into_pose	(	core::pose::Pose &	pose,
		Size const &	chunk_pose_index,
		core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map,
		bool	do_rosetta_library_domain_check = `true`
	)		const

References core::pose::copydofs::copy_dofs(), get_atom_id_domain_map_for_rosetta_library_chunk(), get_atom_id_map(), mini_pose_list_, and user_input().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::initialize_random_chunks(), and core::import_pose::libraries::RNA_ChunkLibrary::random_chunk_insertion().

void core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose	(	core::pose::Pose &	pose,
		Size const &	chunk_pose_index,
		core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map,
		bool	do_rosetta_library_domain_check = `true`
	)		const

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::pack::dunbrack::c, protocols::stepwise::modeler::protein::contains_protein(), core::pose::copydofs::copy_dofs(), core::pose::Pose::fold_tree(), get_atom_id_domain_map_for_rosetta_library_chunk(), get_atom_id_map(), core::chemical::is_canonical_L_aa_or_gly(), core::pose::Pose::jump(), mini_pose_list_, core::kinematics::FoldTree::num_jump(), core::pose::MiniPose::sequence(), core::pose::Pose::set_jump(), and user_input().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::insert_random_protein_chunks().

core::pose::MiniPoseOP const core::import_pose::libraries::ChunkSet::mini_pose ( Size const idx ) const

References mini_pose_list_.

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::align_to_chunk().

Size core::import_pose::libraries::ChunkSet::num_chunks ( ) const

inline

References mini_pose_list_.

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::initialize_random_chunks(), core::import_pose::libraries::RNA_ChunkLibrary::insert_random_protein_chunks(), core::import_pose::libraries::RNA_ChunkLibrary::random_chunk_insertion(), and core::import_pose::libraries::RNA_ChunkLibrary::single_user_input_chunk().

core::pose::ResMap const& core::import_pose::libraries::ChunkSet::res_map ( ) const

inline

References res_map_.

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::check_fold_tree_OK().

void core::import_pose::libraries::ChunkSet::set_user_input ( bool const & setting )

inline

References user_input_.

void core::import_pose::libraries::ChunkSet::setup_atom_id_mapper_to_vanilla_chunk_pose ( core::pose::Pose const & pose )

private

References atom_id_mapper_to_vanilla_chunk_pose_.

Referenced by setup_atom_id_mask_and_mapper().

void core::import_pose::libraries::ChunkSet::setup_atom_id_mask ( core::pose::Pose const & pose )

private

References atom_id_mask_, core::conformation::Residue::is_virtual(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by setup_atom_id_mask_and_mapper().

void core::import_pose::libraries::ChunkSet::setup_atom_id_mask_and_mapper ( core::pose::Pose const & pose )

private

References setup_atom_id_mapper_to_vanilla_chunk_pose(), and setup_atom_id_mask().

bool core::import_pose::libraries::ChunkSet::user_input ( ) const

inline

References user_input_.

Referenced by get_atom_id_domain_map_for_rosetta_library_chunk(), core::import_pose::libraries::RNA_ChunkLibrary::initialize_random_chunks(), insert_chunk_into_pose(), insert_protein_chunk_into_pose(), core::import_pose::libraries::RNA_ChunkLibrary::insert_random_protein_chunks(), and core::import_pose::libraries::RNA_ChunkLibrary::single_user_input_chunk().

Member Data Documentation

core::pose::toolbox::AtomID_MapperCOP core::import_pose::libraries::ChunkSet::atom_id_mapper_to_vanilla_chunk_pose_

private

Referenced by get_atom_id_map(), and setup_atom_id_mapper_to_vanilla_chunk_pose().

std::map< core::id::AtomID, bool > core::import_pose::libraries::ChunkSet::atom_id_mask_

private

Referenced by filter_atom_id_map_with_mask(), and setup_atom_id_mask().

utility::vector1< core::pose::MiniPoseOP > core::import_pose::libraries::ChunkSet::mini_pose_list_

private

Referenced by check_fold_tree_OK(), filter_poses_have_same_sequence_and_variants(), get_atom_id_domain_map_for_rosetta_library_chunk(), get_atom_id_map(), insert_chunk_into_pose(), insert_protein_chunk_into_pose(), mini_pose(), and num_chunks().

core::pose::ResMap core::import_pose::libraries::ChunkSet::res_map_

private

Referenced by check_fold_tree_OK(), get_atom_id_map(), and res_map().

bool core::import_pose::libraries::ChunkSet::user_input_

private

Referenced by set_user_input(), and user_input().

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

src/core/import_pose/libraries/ChunkSet.hh
src/core/import_pose/libraries/ChunkSet.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation