core::import_pose::libraries::ChunkSet Class Reference

#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

ChunkSet() [1/2]

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

ChunkSet() [2/2]

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
	)

~ChunkSet()

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

overridedefault

Member Function Documentation

check_fold_tree_OK()

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(), core::pose::Pose::num_jump(), core::pose::Pose::size(), and core::kinematics::FoldTree::upstream_jump_residue().

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

filter_atom_id_map_with_mask()

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

filter_poses_have_same_sequence_and_variants()

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

private

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

get_atom_id_domain_map_for_rosetta_library_chunk()

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::pose::atom_id_to_named_atom_id(), core::pose::toolbox::AtomLevelDomainMap::get_domain(), core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN, core::pose::toolbox::AtomLevelDomainMap::show(), core::id::to_string(), and core::pose::TR().

get_atom_id_map()

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 core::pose::toolbox::AtomID_Mapper::calculate_atom_id_map().

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

insert_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().

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

insert_protein_chunk_into_pose()

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(), protocols::stepwise::modeler::protein::contains_protein(), core::pose::copydofs::copy_dofs(), core::pose::Pose::fold_tree(), core::chemical::is_canonical_L_aa_or_gly(), core::pose::Pose::jump(), core::pose::MiniPose::sequence(), and core::pose::Pose::set_jump().

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

mini_pose()

core::pose::MiniPoseOP const core::import_pose::libraries::ChunkSet::mini_pose

(

Size const

idx

)

const

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

num_chunks()

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().

res_map()

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().

set_user_input()

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

inline

References user_input_.

setup_atom_id_mapper_to_vanilla_chunk_pose()

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

private

setup_atom_id_mask()

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

private

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

setup_atom_id_mask_and_mapper()

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

private

user_input()

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

inline

References user_input_.

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

Member Data Documentation

atom_id_mapper_to_vanilla_chunk_pose_

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

private

atom_id_mask_

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

private

mini_pose_list_

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

private

Referenced by num_chunks().

res_map_

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

private

Referenced by res_map().

user_input_

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

private

Referenced by set_user_input(), and user_input().

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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