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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

Constructor & Destructor Documentation

template<typename T>

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

inlineexplicit

Default constructor with no arguments (PyRosetta workaround)

template<typename T>

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

inlineexplicit

Default constructor.

template<typename T>

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

inlineexplicit

Number of residues constructor.

template<typename T>

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

inlineexplicit

Number of residues constructor.

template<typename T>

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

default

template<typename T>

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

inlinedefault

Destructor.

Member Function Documentation

template<typename T>

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

inline

Set default value.

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

template<typename T>

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

inline

Clear the 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(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator(), and protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::set_special_region().

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.

template<typename T>

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

inline

Default value.

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

template<typename T>

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

inline

Set default value.

template<typename T>

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

inline

Empty?

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

template<typename T>

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

inline

Fill the map with the default fill value.

template<typename T>

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

inline

Fill the map with a specified fill value.

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

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.

template<typename T>

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

inline

Finalize after sizing all the vectors.

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.

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

template<typename T>

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

inline

Is an element with this AtomID present?

Referenced by core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::energy_methods::DipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), protocols::nmr::rdc::RDCEnergy::eval_atom_derivative(), protocols::nmr::pcs::PCSEnergy::eval_atom_derivative(), protocols::nmr::pre::PREEnergy::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().

template<typename T>

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

inline

Number of atoms in a residue.

Referenced by 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::ElectrostaticSimilarityCalculator::get_present_atoms(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_present_atoms(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), core::scoring::packing::initialize_AtomID_Map(), core::optimization::CartesianMinimizerMap::setup(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().

template<typename T>

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

inline

Number of residues (size)

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

template<typename T>

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

inline

AtomID_Map( atom_id ) const.

template<typename T>

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

inline

AtomID_Map( atom_id )

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.

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 )

template<typename T>

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

inline

AtomID_Map( i_res ) const.

template<typename T>

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

inline

AtomID_Map( i_res )

template<typename T>

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

default

template<typename T>

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

inline

AtomID_Map[ atom_id ] const.

template<typename T>

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

inline

AtomID_Map[ atom_id ].

template<typename T>

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

inline

AtomID_Map[ i_res ] const.

template<typename T>

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

inline

AtomID_Map[ i_res ].

template<typename T>

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

inline

Resize to a given number of residues.

Referenced by 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::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::recompute(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), core::conformation::Conformation::residues_append(), and core::io::pose_from_sfr::PoseFromSFRBuilder::setup().

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.

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.

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.

Referenced by protocols::task_operations::SelectBySASAOperation::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsats_thorough_check(), protocols::fldsgn::topology::calc_delta_sasa(), core::select::util::SelectResiduesByLayer::calc_rsd_sasa(), protocols::forge::methods::calc_rsd_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), 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::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::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::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(), core::energy_methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::energy_methods::DipolarCouplingEnergy::setup_for_minimizing(), core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::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(), and protocols::simple_moves::SuperimposeMover::superimposebb().

template<typename T>

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

inline

Shrink the vectors to remove unused capacity.

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

template<typename T>

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

inline

Size.

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(), 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< Real >::update_sequence_numbering().

template<typename T>

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

inline

swap( AtomID_Map )

Referenced by core::id::AtomID_Map< Real >::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()

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