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core::id::AtomID_Map< T > Class Template Reference

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

#include <AtomID_Map.hh>

Public Types

typedef utility::vector1< T > AtomMap
 
typedef utility::vector1< AtomMapResidueMap
 
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_Mapoperator= (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...
 
AtomMapoperator[] (Size const i_res)
 AtomID_Map[ i_res ]. More...
 
AtomMap const & operator() (Size const i_res) const
 AtomID_Map( i_res ) const. More...
 
AtomMapoperator() (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
template<typename T>
void core::id::AtomID_Map< T >::clear ( )
inline
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
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
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
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
template<typename T>
bool core::id::AtomID_Map< T >::has ( AtomID const &  id) const
inline
template<typename T>
Size core::id::AtomID_Map< T >::n_atom ( Size const  i_res) const
inline
template<typename T>
Size core::id::AtomID_Map< T >::n_residue ( ) const
inline
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
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::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::scoring::methods::DipolarCouplingEnergy::setup_for_minimizing(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::scoring::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
template<typename T>
void core::id::AtomID_Map< T >::swap ( AtomID_Map< T > &  s)
inline
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().

Friends And Related Function Documentation

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

template<typename T>
Value core::id::AtomID_Map< T >::default_value_
private
template<typename T>
ResidueMap core::id::AtomID_Map< T >::res_map_
private

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