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

#include <AtomID_Map.fwd.hh>

Collaboration diagram for core::id::AtomID_Map< T >:

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 ()
	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...

ConstReference	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	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.

Definition at line 24 of file AtomID_Map.fwd.hh.

Member Typedef Documentation

template<typename T>

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

Definition at line 55 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 61 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 67 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 60 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 66 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 56 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 68 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 62 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 65 of file AtomID_Map.hh.

template<typename T>

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

Definition at line 59 of file AtomID_Map.hh.

Constructor & Destructor Documentation

template<typename T>

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

inlineexplicit

Default constructor with no arguments (PyRosetta workaround)

Definition at line 76 of file AtomID_Map.hh.

template<typename T>

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

inlineexplicit

Default constructor.

Definition at line 84 of file AtomID_Map.hh.

template<typename T>

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

inlineexplicit

Number of residues constructor.

Definition at line 92 of file AtomID_Map.hh.

template<typename T>

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

inlineexplicit

Number of residues constructor.

Definition at line 102 of file AtomID_Map.hh.

template<typename T>

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

inline

Destructor.

Definition at line 113 of file AtomID_Map.hh.

Member Function Documentation

template<typename T>

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

inline

Clear the map.

Definition at line 256 of file AtomID_Map.hh.

Referenced by core::conformation::build_tree(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_res_hydrophobic_sasa(), core::kinematics::AtomTree::clear(), core::conformation::Conformation::clear(), protocols::sasa_scores::compute_residue_sasas_for_sasa_scores(), 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::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator().

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.

Definition at line 266 of file AtomID_Map.hh.

template<typename T>

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

inline

Default value.

Definition at line 333 of file AtomID_Map.hh.

template<typename T>

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

inline

Set default value.

Definition at line 342 of file AtomID_Map.hh.

template<typename T>

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

inline

Empty?

Definition at line 324 of file AtomID_Map.hh.

template<typename T>

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

inline

Fill the map with the default fill value.

Definition at line 150 of file AtomID_Map.hh.

template<typename T>

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

inline

Fill the map with a specified fill value.

Definition at line 164 of file AtomID_Map.hh.

Referenced by core::conformation::Conformation::reset_move_data().

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.

Definition at line 178 of file AtomID_Map.hh.

template<typename T>

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

inline

Finalize after sizing all the vectors.

Definition at line 217 of file AtomID_Map.hh.

template<typename T>

ConstReference 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.

Definition at line 191 of file AtomID_Map.hh.

Referenced by core::pack::figure_out_repackable_residues(), core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), core::scoring::methods::DipolarCouplingEnergy::setup_for_minimizing(), and core::scoring::methods::ChemicalShiftAnisotropyEnergy::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?

Definition at line 351 of file AtomID_Map.hh.

Referenced by core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::DipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::eval_atom_derivative(), and core::kinematics::AtomTree::has().

template<typename T>

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

inline

Number of atoms in a residue.

Definition at line 315 of file AtomID_Map.hh.

Referenced by protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::sic_dock::xyzStripeHashPose::init_with_pose(), and core::scoring::packing::initialize_AtomID_Map().

template<typename T>

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

inline

Number of residues (size)

Definition at line 306 of file AtomID_Map.hh.

Referenced by protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), and protocols::sic_dock::xyzStripeHashPose::init_with_pose().

template<typename T>

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

inline

AtomID_Map( atom_id ) const.

Definition at line 385 of file AtomID_Map.hh.

template<typename T>

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

inline

AtomID_Map( atom_id )

Definition at line 394 of file AtomID_Map.hh.

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.

Definition at line 403 of file AtomID_Map.hh.

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 )

Definition at line 412 of file AtomID_Map.hh.

template<typename T>

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

inline

AtomID_Map( i_res ) const.

Definition at line 439 of file AtomID_Map.hh.

template<typename T>

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

inline

AtomID_Map( i_res )

Definition at line 448 of file AtomID_Map.hh.

template<typename T>

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

inline

AtomID_Map[ atom_id ] const.

Definition at line 367 of file AtomID_Map.hh.

template<typename T>

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

inline

AtomID_Map[ atom_id ].

Definition at line 376 of file AtomID_Map.hh.

template<typename T>

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

inline

AtomID_Map[ i_res ] const.

Definition at line 421 of file AtomID_Map.hh.

template<typename T>

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

inline

AtomID_Map[ i_res ].

Definition at line 430 of file AtomID_Map.hh.

template<typename T>

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

inline

Resize to a given number of residues.

Definition at line 123 of file AtomID_Map.hh.

Referenced by core::conformation::build_tree(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::kinematics::AtomTree::delete_seqpos(), 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::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), and core::conformation::Conformation::residues_append().

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.

Definition at line 132 of file AtomID_Map.hh.

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.

Definition at line 141 of file AtomID_Map.hh.

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.

Definition at line 205 of file AtomID_Map.hh.

Referenced by protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::fldsgn::topology::calc_delta_sasa(), protocols::toolbox::SelectResiduesByLayer::calc_rsd_sasa(), protocols::toolbox::task_operations::LayerOperations::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(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::conformation::setup_corresponding_atoms(), core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), core::scoring::methods::DipolarCouplingEnergy::setup_for_minimizing(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::setup_for_minimizing(), protocols::swa::protein::setup_protein_backbone_atom_id_map(), protocols::swa::protein::setup_protein_CA_atom_id_map(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::simple_moves::SuperimposeMover::superimpose(), and protocols::fldsgn::MatchResidues::superimpose_comb().

template<typename T>

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

inline

Shrink the vectors to remove unused capacity.

Definition at line 226 of file AtomID_Map.hh.

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

template<typename T>

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

inline

Size.

Definition at line 297 of file AtomID_Map.hh.

Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::kinematics::AtomTree::AtomTree(), core::kinematics::AtomTree::find_root_from_atom_pointer(), core::scoring::packing::initialize_AtomID_Map(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::kinematics::AtomTree::replace_tree(), core::kinematics::AtomTree::size(), core::kinematics::AtomTree::update_atom_ids_from_atom_pointer(), and core::id::AtomID_Map< core::id::core::id::AtomID >::update_sequence_numbering().

template<typename T>

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

inline

swap( AtomID_Map )

Definition at line 238 of file AtomID_Map.hh.

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

Definition at line 278 of file AtomID_Map.hh.

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