core::pose::toolbox::AtomID_Mapper Class Reference

#include <AtomID_Mapper.hh>

Inheritance diagram for core::pose::toolbox::AtomID_Mapper:

Public Member Functions
	AtomID_Mapper (core::pose::Pose const &pose, bool const map_to_vanilla_pose=false)
AtomID_MapperOP	clone () const
bool	has_atom_id (core::id::AtomID const &atom_id) const
void	renumber_after_variant_changes (core::pose::Pose const &pose)
utility::vector1 < core::id::AtomID > const &	atom_ids_in_res (Size const &n) const
std::map< core::id::AtomID, core::id::AtomID >	calculate_atom_id_map (core::pose::Pose const &target_pose, std::map< core::Size, core::Size > const &res_map, core::kinematics::FoldTree const &source_fold_tree, AtomID_MapperCOP source_mapper_to_vanilla=nullptr) const
core::id::AtomID const &	map_to_reference (core::id::AtomID const &atom_id) const
core::id::AtomID const &	map_from_reference (core::id::AtomID const &atom_id) const
bool	in_map_from_reference (core::id::AtomID const &atom_id) const
core::Size	nres () const

Private Member Functions
void	initialize (core::pose::Pose const &pose, bool const map_to_vanilla_pose)
void	initialize_from_pose (core::pose::Pose const &pose)

Private Attributes
std::map < core::id::NamedAtomID, core::id::AtomID >	named_atom_id_map_
std::string	sequence_
std::map< core::id::AtomID, core::id::AtomID >	map_to_reference_
std::map< core::id::AtomID, core::id::AtomID >	map_from_reference_
utility::vector1 < utility::vector1 < core::id::AtomID > >	atom_ids_in_res_

Constructor & Destructor Documentation

core::pose::toolbox::AtomID_Mapper::AtomID_Mapper	(	core::pose::Pose const &	pose,
		bool const	map_to_vanilla_pose = false
	)

Member Function Documentation

utility::vector1< core::id::AtomID > const& core::pose::toolbox::AtomID_Mapper::atom_ids_in_res ( Size const &  n ) const

inline

References atom_ids_in_res_.

std::map< AtomID, AtomID > core::pose::toolbox::AtomID_Mapper::calculate_atom_id_map	(	core::pose::Pose const &	target_pose,
		std::map< core::Size, core::Size > const &	res_map,
		core::kinematics::FoldTree const &	source_fold_tree,
		AtomID_MapperCOP	source_mapper_to_vanilla = nullptr
	)		const

References core::id::AtomID::atomno(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

Referenced by core::import_pose::libraries::ChunkSet::get_atom_id_map().

AtomID_MapperOP core::pose::toolbox::AtomID_Mapper::clone

(

)

const

bool core::pose::toolbox::AtomID_Mapper::has_atom_id

(

core::id::AtomID const &

atom_id

)

const

bool core::pose::toolbox::AtomID_Mapper::in_map_from_reference ( core::id::AtomID const &  atom_id ) const

inline

References map_from_reference_.

void core::pose::toolbox::AtomID_Mapper::initialize ( core::pose::Pose const &  pose, bool const  map_to_vanilla_pose  )

private

References core::chemical::ResidueTypeBase::base_name(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_protein(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), and core::pose::Pose::size().

void core::pose::toolbox::AtomID_Mapper::initialize_from_pose ( core::pose::Pose const &  pose )

private

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::sequence(), and core::pose::Pose::size().

AtomID const & core::pose::toolbox::AtomID_Mapper::map_from_reference

(

core::id::AtomID const &

atom_id

)

const

AtomID const & core::pose::toolbox::AtomID_Mapper::map_to_reference

(

core::id::AtomID const &

atom_id

)

const

core::Size core::pose::toolbox::AtomID_Mapper::nres ( ) const

inline

References atom_ids_in_res_.

void core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes

(

core::pose::Pose const &

pose

)

References core::chemical::ResidueType::atom_name(), core::scoring::methods::get_lower_cutpoint_partner_for_upper(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::chemical::ResidueType::is_coarse(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::sequence(), and core::pose::Pose::size().

Member Data Documentation

utility::vector1< utility::vector1< core::id::AtomID > > core::pose::toolbox::AtomID_Mapper::atom_ids_in_res_

private

Referenced by atom_ids_in_res(), and nres().

std::map< core::id::AtomID, core::id::AtomID > core::pose::toolbox::AtomID_Mapper::map_from_reference_

private

Referenced by in_map_from_reference().

std::map< core::id::AtomID, core::id::AtomID > core::pose::toolbox::AtomID_Mapper::map_to_reference_

private

std::map< core::id::NamedAtomID, core::id::AtomID > core::pose::toolbox::AtomID_Mapper::named_atom_id_map_

private

std::string core::pose::toolbox::AtomID_Mapper::sequence_

private

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

• src/core/pose/toolbox/AtomID_Mapper.hh
• src/core/pose/toolbox/AtomID_Mapper.cc