Map from Atom identifiers to contained values class. More...

#include <AtomID_Map.hh>

Public Types
typedef utility::vector1< T >	AtomMap

typedef utility::vector1< AtomMap >	ResidueMap

typedef T	value_type

typedef AtomMap::reference	reference

typedef AtomMap::const_reference	const_reference

typedef AtomMap::size_type	size_type

typedef T	Value

typedef AtomMap::Reference	Reference

typedef AtomMap::ConstReference	ConstReference

typedef platform::Size	Size

Public Member Functions
	AtomID_Map ()
	Default constructor with no arguments (PyRosetta workaround) More...

	AtomID_Map (Value const &default_value_a)
	Default constructor. More...

	AtomID_Map (Size const n_res)
	Number of residues constructor. More...

	AtomID_Map (Size const n_res, Value const &default_value_a)
	Number of residues constructor. More...

	AtomID_Map (AtomID_Map const &)=default

AtomID_Map &	operator= (AtomID_Map const &)=default

	~AtomID_Map ()=default
	Destructor. More...

void	resize (Size const n_res)
	Resize to a given number of residues. More...

void	resize (Size const i_res, Size const n_atom)
	Resize the number of atoms of a residue and use the default fill value. More...

void	resize (Size const i_res, Size const n_atom, Value const &value)
	Resize the number of atoms of a residue and use a specified fill value. More...

void	fill ()
	Fill the map with the default fill value. More...

void	fill_with (Value const &value)
	Fill the map with a specified fill value. More...

void	fill_with (Size const seqpos, Value const &value)
	Fill the map at position seqpos with a specified fill value. More...

value_type	get (AtomID const &id) const
	Get the value for an AtomID: Extend the map if necessary, filling with the default value Phil changing this to be a non-resizing function. More...

void	set (AtomID const &id, Value const &value)
	Set the value for an AtomID: Extend the map if necessary, filling with the default value. More...

void	finalize ()
	Finalize after sizing all the vectors. More...

void	shrink ()
	Shrink the vectors to remove unused capacity. More...

void	swap (AtomID_Map &s)
	swap( AtomID_Map ) More...

void	clear ()
	Clear the map. More...

void	clear (Value const &default_value_a)
	Clear the map and set a new default value. More...

void	update_sequence_numbering (Size const new_size, utility::vector1< Size > const &old2new)

Size	size () const
	Size. More...

Size	n_residue () const
	Number of residues (size) More...

Size	n_atom (Size const i_res) const
	Number of atoms in a residue. More...

bool	empty () const
	Empty? More...

Value const &	default_value () const
	Default value. More...

void	default_value (Value const &default_value_a)
	Set default value. More...

bool	all_default ()
	Set default value. More...

bool	has (AtomID const &id) const
	Is an element with this AtomID present? More...

ConstReference	operator[] (AtomID const &id) const
	AtomID_Map[ atom_id ] const. More...

Reference	operator[] (AtomID const &id)
	AtomID_Map[ atom_id ]. More...

ConstReference	operator() (AtomID const &id) const
	AtomID_Map( atom_id ) const. More...

Reference	operator() (AtomID const &id)
	AtomID_Map( atom_id ) More...

ConstReference	operator() (Size const i_res, Size const i_atom) const
	AtomID_Map( i_res, i_atom ) const. More...

Reference	operator() (Size const i_res, Size const i_atom)
	AtomID_Map( i_res, i_atom ) More...

AtomMap const &	operator[] (Size const i_res) const
	AtomID_Map[ i_res ] const. More...

AtomMap &	operator[] (Size const i_res)
	AtomID_Map[ i_res ]. More...

AtomMap const &	operator() (Size const i_res) const
	AtomID_Map( i_res ) const. More...

AtomMap &	operator() (Size const i_res)
	AtomID_Map( i_res ) More...

Private Attributes
Value	default_value_
	Default value. More...

ResidueMap	res_map_
	Map from Atom identifiers to values. More...

Friends
template<typename TF >
void	swap (AtomID_Map< TF > &a, AtomID_Map< TF > &b)
	swap( AtomID_Map, AtomID_Map ) More...

bool	operator== (AtomID_Map const &a, AtomID_Map const &b)
	AtomID_Map == AtomID_Map. More...

bool	operator!= (AtomID_Map const &a, AtomID_Map const &b)
	AtomID_Map != AtomID_Map. More...

Detailed Description

template<typename T>
class core::id::AtomID_Map< T >

Map from Atom identifiers to contained values class.

Member Typedef Documentation

◆ AtomMap

template<typename T >

typedef utility::vector1< T > core::id::AtomID_Map< T >::AtomMap

◆ const_reference

template<typename T >

typedef AtomMap::const_reference core::id::AtomID_Map< T >::const_reference

◆ ConstReference

template<typename T >

typedef AtomMap::ConstReference core::id::AtomID_Map< T >::ConstReference

◆ reference

template<typename T >

typedef AtomMap::reference core::id::AtomID_Map< T >::reference

◆ Reference

template<typename T >

typedef AtomMap::Reference core::id::AtomID_Map< T >::Reference

◆ ResidueMap

template<typename T >

typedef utility::vector1< AtomMap > core::id::AtomID_Map< T >::ResidueMap

◆ Size

template<typename T >

typedef platform::Size core::id::AtomID_Map< T >::Size

◆ size_type

template<typename T >

typedef AtomMap::size_type core::id::AtomID_Map< T >::size_type

◆ Value

template<typename T >

typedef T core::id::AtomID_Map< T >::Value

◆ value_type

template<typename T >

typedef T core::id::AtomID_Map< T >::value_type

Constructor & Destructor Documentation

◆ AtomID_Map() [1/5]

template<typename T >

core::id::AtomID_Map< T >::AtomID_Map ( )

inlineexplicit

Default constructor with no arguments (PyRosetta workaround)

◆ AtomID_Map() [2/5]

template<typename T >

core::id::AtomID_Map< T >::AtomID_Map ( Value const & default_value_a )

inlineexplicit

Default constructor.

◆ AtomID_Map() [3/5]

template<typename T >

core::id::AtomID_Map< T >::AtomID_Map ( Size const n_res )

inlineexplicit

Number of residues constructor.

◆ AtomID_Map() [4/5]

template<typename T >

core::id::AtomID_Map< T >::AtomID_Map	(	Size const	n_res,
		Value const &	default_value_a
	)

inlineexplicit

Number of residues constructor.

◆ AtomID_Map() [5/5]

template<typename T >

core::id::AtomID_Map< T >::AtomID_Map ( AtomID_Map< T > const & )

default

◆ ~AtomID_Map()

template<typename T >

core::id::AtomID_Map< T >::~AtomID_Map ( )

inlinedefault

Destructor.

Member Function Documentation

◆ all_default()

template<typename T >

bool core::id::AtomID_Map< T >::all_default ( )

inline

Set default value.

References core::id::AtomID_Map< T >::default_value_, and core::id::AtomID_Map< T >::res_map_.

Referenced by protocols::stepwise::modeler::align::superimpose_pose_legacy().

◆ clear() [1/2]

template<typename T >

void core::id::AtomID_Map< T >::clear ( )

inline

Clear the map.

References core::id::AtomID_Map< T >::res_map_.

Referenced by core::conformation::build_tree(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::BuriedUnsatisfiedPolarsCalculator2(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_atom_sasa_sc(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa(), core::conformation::Conformation::clear(), core::kinematics::AtomTree::clear(), protocols::sasa_scores::compute_residue_sasas_for_sasa_scores(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute(), core::scoring::sasa::SasaCalc::init(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), core::conformation::Conformation::insert_conformation_by_jump(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), core::kinematics::AtomTree::replace_residue_subtree(), and protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::set_special_region().

◆ clear() [2/2]

template<typename T >

void core::id::AtomID_Map< T >::clear ( Value const & default_value_a )

inline

Clear the map and set a new default value.

References core::id::AtomID_Map< T >::default_value_, and core::id::AtomID_Map< T >::res_map_.

◆ default_value() [1/2]

template<typename T >

Value const& core::id::AtomID_Map< T >::default_value ( ) const

inline

Default value.

References core::id::AtomID_Map< T >::default_value_.

Referenced by core::optimization::CartesianMinimizerMap::CartesianMinimizerMap(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), and protocols::nmr::rdc::RDCEnergy::setup_for_minimizing().

◆ default_value() [2/2]

template<typename T >

void core::id::AtomID_Map< T >::default_value ( Value const & default_value_a )

inline

Set default value.

References core::id::AtomID_Map< T >::default_value_.

◆ empty()

template<typename T >

bool core::id::AtomID_Map< T >::empty ( ) const

inline

Empty?

References core::id::AtomID_Map< T >::res_map_.

Referenced by protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), and protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions().

◆ fill()

template<typename T >

void core::id::AtomID_Map< T >::fill ( )

inline

Fill the map with the default fill value.

References core::id::AtomID_Map< T >::default_value_, and core::id::AtomID_Map< T >::res_map_.

◆ fill_with() [1/2]

template<typename T >

void core::id::AtomID_Map< T >::fill_with	(	Size const	seqpos,
		Value const &	value
	)

inline

Fill the map at position seqpos with a specified fill value.

References core::id::AtomID_Map< T >::res_map_.

◆ fill_with() [2/2]

template<typename T >

void core::id::AtomID_Map< T >::fill_with ( Value const & value )

inline

Fill the map with a specified fill value.

References core::id::AtomID_Map< T >::res_map_.

Referenced by protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::conformation::Conformation::reset_move_data(), core::pack::guidance_scoreterms::sap::sap_atom_sasa(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), and core::scoring::PoissonBoltzmannPotential::solve_pb().

◆ finalize()

template<typename T >

void core::id::AtomID_Map< T >::finalize ( )

inline

Finalize after sizing all the vectors.

References core::id::AtomID_Map< T >::shrink().

◆ get()

template<typename T >

value_type core::id::AtomID_Map< T >::get ( AtomID const & id ) const

inline

Get the value for an AtomID: Extend the map if necessary, filling with the default value Phil changing this to be a non-resizing function.

References core::id::AtomID_Map< T >::default_value_, and core::id::AtomID_Map< T >::res_map_.

Referenced by protocols::membrane::MPLipidAccessibility::apply(), protocols::nmr::pcs::PCSEnergy::eval_atom_derivative(), protocols::nmr::pre::PREEnergy::eval_atom_derivative(), protocols::nmr::rdc::RDCEnergy::eval_atom_derivative(), core::pack::figure_out_repackable_residues(), core::conformation::Conformation::fill_missing_atoms(), core::optimization::CartesianMinimizerMap::setup(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), core::energy_methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::energy_methods::DipolarCouplingEnergy::setup_for_minimizing(), and core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing().

◆ has()

template<typename T >

bool core::id::AtomID_Map< T >::has ( AtomID const & id ) const

inline

Is an element with this AtomID present?

References core::id::AtomID_Map< T >::res_map_, and core::id::AtomID_Map< T >::size().

Referenced by protocols::membrane::MPLipidAccessibility::apply(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat(), core::membrane::concave_shell(), protocols::nmr::pcs::PCSEnergy::eval_atom_derivative(), protocols::nmr::pre::PREEnergy::eval_atom_derivative(), protocols::nmr::rdc::RDCEnergy::eval_atom_derivative(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::energy_methods::DipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::kinematics::AtomTree::has(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and core::pose::set_bfactors_from_atom_id_map().

◆ n_atom()

template<typename T >

Size core::id::AtomID_Map< T >::n_atom ( Size const i_res ) const

inline

Number of atoms in a residue.

References core::id::AtomID_Map< T >::res_map_.

Referenced by protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), core::scoring::atomic_depth::atomic_depth(), core::scoring::atomic_depth::atoms_deeper_than(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsats_thorough_check(), core::scoring::calc_per_atom_sasa_sc(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::HolesFilter::compute(), core::scoring::APBSWrapper::count_atoms(), core::pose::xyzStripeHashPose::extract_pose_balls(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_atoms_within_radius(), protocols::simple_filters::BuriedUnsatHbondFilter::get_deep_apo_atoms(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_present_atoms(), core::scoring::sc::ElectrostaticSimilarityCalculator::get_present_atoms(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), core::scoring::packing::initialize_AtomID_Map(), core::id::AtomID_Map< T >::resize(), core::optimization::CartesianMinimizerMap::setup(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().

◆ n_residue()

template<typename T >

Size core::id::AtomID_Map< T >::n_residue ( ) const

inline

Number of residues (size)

References core::id::AtomID_Map< T >::res_map_.

Referenced by core::membrane::concave_shell(), core::scoring::APBSWrapper::count_atoms(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_atoms_within_radius(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_present_atoms(), and core::scoring::sc::ElectrostaticSimilarityCalculator::get_present_atoms().

◆ operator()() [1/6]

template<typename T >

Reference core::id::AtomID_Map< T >::operator() ( AtomID const & id )

inline

AtomID_Map( atom_id )

References core::id::AtomID_Map< T >::res_map_.

◆ operator()() [2/6]

template<typename T >

ConstReference core::id::AtomID_Map< T >::operator() ( AtomID const & id ) const

inline

AtomID_Map( atom_id ) const.

References core::id::AtomID_Map< T >::res_map_.

◆ operator()() [3/6]

template<typename T >

AtomMap& core::id::AtomID_Map< T >::operator() ( Size const i_res )

inline

AtomID_Map( i_res )

References core::id::AtomID_Map< T >::res_map_.

◆ operator()() [4/6]

template<typename T >

AtomMap const& core::id::AtomID_Map< T >::operator() ( Size const i_res ) const

inline

AtomID_Map( i_res ) const.

References core::id::AtomID_Map< T >::res_map_.

◆ operator()() [5/6]

template<typename T >

Reference core::id::AtomID_Map< T >::operator()	(	Size const	i_res,
		Size const	i_atom
	)

inline

AtomID_Map( i_res, i_atom )

References core::id::AtomID_Map< T >::res_map_.

◆ operator()() [6/6]

template<typename T >

ConstReference core::id::AtomID_Map< T >::operator()	(	Size const	i_res,
		Size const	i_atom
	)		const

inline

AtomID_Map( i_res, i_atom ) const.

References core::id::AtomID_Map< T >::res_map_.

◆ operator=()

template<typename T >

AtomID_Map& core::id::AtomID_Map< T >::operator= ( AtomID_Map< T > const & )

default

◆ operator[]() [1/4]

template<typename T >

Reference core::id::AtomID_Map< T >::operator[] ( AtomID const & id )

inline

AtomID_Map[ atom_id ].

References core::id::AtomID_Map< T >::res_map_.

◆ operator[]() [2/4]

template<typename T >

ConstReference core::id::AtomID_Map< T >::operator[] ( AtomID const & id ) const

inline

AtomID_Map[ atom_id ] const.

References core::id::AtomID_Map< T >::res_map_.

◆ operator[]() [3/4]

template<typename T >

AtomMap& core::id::AtomID_Map< T >::operator[] ( Size const i_res )

inline

AtomID_Map[ i_res ].

References core::id::AtomID_Map< T >::res_map_.

◆ operator[]() [4/4]

template<typename T >

AtomMap const& core::id::AtomID_Map< T >::operator[] ( Size const i_res ) const

inline

AtomID_Map[ i_res ] const.

References core::id::AtomID_Map< T >::res_map_.

◆ resize() [1/3]

template<typename T >

void core::id::AtomID_Map< T >::resize	(	Size const	i_res,
		Size const	n_atom
	)

inline

Resize the number of atoms of a residue and use the default fill value.

References core::id::AtomID_Map< T >::default_value_, core::id::AtomID_Map< T >::n_atom(), and core::id::AtomID_Map< T >::res_map_.

◆ resize() [2/3]

template<typename T >

void core::id::AtomID_Map< T >::resize	(	Size const	i_res,
		Size const	n_atom,
		Value const &	value
	)

inline

Resize the number of atoms of a residue and use a specified fill value.

References core::id::AtomID_Map< T >::n_atom(), and core::id::AtomID_Map< T >::res_map_.

◆ resize() [3/3]

template<typename T >

void core::id::AtomID_Map< T >::resize ( Size const n_res )

inline

Resize to a given number of residues.

References core::id::AtomID_Map< T >::res_map_.

Referenced by protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::conformation::build_tree(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::kinematics::AtomTree::delete_seqpos(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute(), core::scoring::hbonds::NPDHBondSet::get_weights_for_one_partner_hbonder(), core::scoring::hbonds::NPDHBondSet::get_weights_for_two_partner_hbonder(), core::scoring::packing::initialize_AtomID_Map(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), core::conformation::Conformation::insert_conformation_by_jump(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), core::conformation::Conformation::residues_append(), and core::io::pose_from_sfr::PoseFromSFRBuilder::setup().

◆ set()

template<typename T >

void core::id::AtomID_Map< T >::set	(	AtomID const &	id,
		Value const &	value
	)

inline

Set the value for an AtomID: Extend the map if necessary, filling with the default value.

References core::id::AtomID_Map< T >::default_value_, and core::id::AtomID_Map< T >::res_map_.

Referenced by protocols::loops::addScoresForLoopParts(), core::import_pose::libraries::RNA_ChunkLibrary::align_to_chunk(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsats_thorough_check(), protocols::fldsgn::topology::calc_delta_sasa(), protocols::forge::methods::calc_rsd_sasa(), core::select::util::SelectResiduesByLayer::calc_rsd_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), core::membrane::concave_shell(), core::pose::convert_from_std_map(), core::conformation::Conformation::fill_missing_atoms(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::tcr::orient_tcr_chain(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::set_special_region(), core::optimization::CartesianMinimizerMap::setup(), core::conformation::setup_corresponding_atoms(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), core::energy_methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::energy_methods::DipolarCouplingEnergy::setup_for_minimizing(), core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::fldsgn::MatchResidues::superimpose_comb(), core::scoring::superimpose_polymer_heavyatoms(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), and protocols::simple_moves::SuperimposeMover::superimposebb().

◆ shrink()

template<typename T >

void core::id::AtomID_Map< T >::shrink ( )

inline

Shrink the vectors to remove unused capacity.

References core::id::AtomID_Map< T >::res_map_.

Referenced by core::id::AtomID_Map< T >::finalize().

◆ size()

template<typename T >

Size core::id::AtomID_Map< T >::size ( ) const

inline

Size.

References core::id::AtomID_Map< T >::res_map_.

Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::scoring::atomic_depth::atomic_depth(), core::scoring::atomic_depth::atoms_deeper_than(), core::kinematics::AtomTree::AtomTree(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsats_thorough_check(), core::scoring::calc_per_atom_sasa_sc(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::kinematics::AtomTree::find_root_from_atom_pointer(), core::scoring::sasa::get_sc_bb_sasa(), core::scoring::sasa::get_sc_bb_sasa_per_res(), core::id::AtomID_Map< T >::has(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), core::scoring::packing::initialize_AtomID_Map(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), core::kinematics::AtomTree::replace_tree(), core::kinematics::AtomTree::size(), core::kinematics::AtomTree::update_atom_ids_from_atom_pointer(), and core::id::AtomID_Map< T >::update_sequence_numbering().

◆ swap()

template<typename T >

void core::id::AtomID_Map< T >::swap ( AtomID_Map< T > & s )

inline

swap( AtomID_Map )

References core::id::AtomID_Map< T >::res_map_.

Referenced by core::id::AtomID_Map< T >::update_sequence_numbering().

◆ update_sequence_numbering()

template<typename T >

void core::id::AtomID_Map< T >::update_sequence_numbering	(	Size const	new_size,
		utility::vector1< Size > const &	old2new
	)

inline

Should move to .cc? if old2new[pos] == 0 , that position's mapping is lost if old2new[1...old_size] doesnt cover all of [1...new_size], the missed positions will have res_map_[pos].empty()

References core::id::AtomID_Map< T >::default_value_, core::id::AtomID_Map< T >::res_map_, core::id::AtomID_Map< T >::size(), and core::id::AtomID_Map< T >::swap().

Referenced by core::kinematics::AtomTree::update_sequence_numbering(), and core::conformation::Conformation::update_sequence_numbering().

Friends And Related Function Documentation

◆ operator!=

template<typename T >

bool operator!=	(	AtomID_Map< T > const &	a,
		AtomID_Map< T > const &	b
	)

friend

AtomID_Map != AtomID_Map.

◆ operator==

template<typename T >

bool operator==	(	AtomID_Map< T > const &	a,
		AtomID_Map< T > const &	b
	)

friend

AtomID_Map == AtomID_Map.

◆ swap

template<typename T >

template<typename TF >

void swap	(	AtomID_Map< TF > &	a,
		AtomID_Map< TF > &	b
	)

friend

swap( AtomID_Map, AtomID_Map )

Member Data Documentation

◆ default_value_

template<typename T >

Value core::id::AtomID_Map< T >::default_value_

private

Default value.

Referenced by core::id::AtomID_Map< T >::all_default(), core::id::AtomID_Map< T >::clear(), core::id::AtomID_Map< T >::default_value(), core::id::AtomID_Map< T >::fill(), core::id::AtomID_Map< T >::get(), core::id::AtomID_Map< T >::resize(), core::id::AtomID_Map< T >::set(), and core::id::AtomID_Map< T >::update_sequence_numbering().

◆ res_map_

template<typename T >

ResidueMap core::id::AtomID_Map< T >::res_map_

private

Map from Atom identifiers to values.

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

src/core/id/AtomID_Map.fwd.hh
src/core/id/AtomID_Map.hh

Public Types

Public Member Functions

Private Attributes

Friends

Detailed Description

template<typename T> class core::id::AtomID_Map< T >

Member Typedef Documentation

◆ AtomMap

◆ const_reference

◆ ConstReference

◆ reference

◆ Reference

◆ ResidueMap

◆ Size

◆ size_type

◆ Value

◆ value_type

Constructor & Destructor Documentation

◆ AtomID_Map() [1/5]

◆ AtomID_Map() [2/5]

◆ AtomID_Map() [3/5]

◆ AtomID_Map() [4/5]

◆ AtomID_Map() [5/5]

◆ ~AtomID_Map()

Member Function Documentation

◆ all_default()

◆ clear() [1/2]

◆ clear() [2/2]

◆ default_value() [1/2]

◆ default_value() [2/2]

◆ empty()

◆ fill()

◆ fill_with() [1/2]

◆ fill_with() [2/2]

◆ finalize()

◆ get()

◆ has()

◆ n_atom()

◆ n_residue()

◆ operator()() [1/6]

◆ operator()() [2/6]

◆ operator()() [3/6]

◆ operator()() [4/6]

◆ operator()() [5/6]

◆ operator()() [6/6]

◆ operator=()

◆ operator[]() [1/4]

◆ operator[]() [2/4]

◆ operator[]() [3/4]

◆ operator[]() [4/4]

◆ resize() [1/3]

◆ resize() [2/3]

◆ resize() [3/3]

◆ set()

◆ shrink()

◆ size()

◆ swap()

◆ update_sequence_numbering()

Friends And Related Function Documentation

◆ operator!=

◆ operator==

◆ swap

Member Data Documentation

◆ default_value_

◆ res_map_

template<typename T>
class core::id::AtomID_Map< T >