Rosetta 3.4
Public Types | Public Member Functions | Friends
core::id::AtomID_Map< T > Class Template Reference

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

#include <AtomID_Map.hh>

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List of all members.

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)
 AtomID_Map (Value const &default_value_a)
 Default constructor.
 AtomID_Map (Size const n_res)
 Number of residues constructor.
 AtomID_Map (Size const n_res, Value const &default_value_a)
 Number of residues constructor.
 ~AtomID_Map ()
 Destructor.
void resize (Size const n_res)
 Resize to a given number of residues.
void resize (Size const i_res, Size const n_atom)
 Resize the number of atoms of a residue and use the default fill value.
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.
void fill ()
 Fill the map with the default fill value.
void fill_with (Value const &value)
 Fill the map with a specified fill value.
void fill_with (Size const seqpos, Value const &value)
 Fill the map at position seqpos with a specified fill value.
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.
void set (AtomID const &id, Value const &value)
 Set the value for an AtomID: Extend the map if necessary, filling with the default value.
void finalize ()
 Finalize after sizing all the vectors.
void shrink ()
 Shrink the vectors to remove unused capacity.
void swap (AtomID_Map &s)
 swap( AtomID_Map )
void clear ()
 Clear the map.
void clear (Value const &default_value_a)
 Clear the map and set a new default value.
void update_sequence_numbering (Size const new_size, utility::vector1< Size > const &old2new)
Size size () const
 Size.
Size n_residue () const
 Number of residues (size)
Size n_atom (Size const i_res) const
 Number of atoms in a residue.
bool empty () const
 Empty?
Value const & default_value () const
 Default value.
void default_value (Value const &default_value_a)
 Set default value.
bool has (AtomID const &id) const
 Is an element with this AtomID present?
ConstReference operator[] (AtomID const &id) const
 AtomID_Map[ atom_id ] const.
Reference operator[] (AtomID const &id)
 AtomID_Map[ atom_id ].
ConstReference operator() (AtomID const &id) const
 AtomID_Map( atom_id ) const.
Reference operator() (AtomID const &id)
 AtomID_Map( atom_id )
ConstReference operator() (Size const i_res, Size const i_atom) const
 AtomID_Map( i_res, i_atom ) const.
Reference operator() (Size const i_res, Size const i_atom)
 AtomID_Map( i_res, i_atom )
AtomMap const & operator[] (Size const i_res) const
 AtomID_Map[ i_res ] const.
AtomMapoperator[] (Size const i_res)
 AtomID_Map[ i_res ].
AtomMap const & operator() (Size const i_res) const
 AtomID_Map( i_res ) const.
AtomMapoperator() (Size const i_res)
 AtomID_Map( i_res )

Friends

template<typename TF >
void swap (AtomID_Map< TF > &a, AtomID_Map< TF > &b)
 swap( AtomID_Map, AtomID_Map )
bool operator== (AtomID_Map const &a, AtomID_Map const &b)
 AtomID_Map == AtomID_Map.
bool operator!= (AtomID_Map const &a, AtomID_Map const &b)
 AtomID_Map != AtomID_Map.

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 ( ) [inline, explicit]

Default constructor with no arguments (PyRosetta workaround)

template<typename T>
core::id::AtomID_Map< T >::AtomID_Map ( Value const &  default_value_a) [inline, explicit]

Default constructor.

template<typename T>
core::id::AtomID_Map< T >::AtomID_Map ( Size const  n_res) [inline, explicit]

Number of residues constructor.

template<typename T>
core::id::AtomID_Map< T >::AtomID_Map ( Size const  n_res,
Value const &  default_value_a 
) [inline, explicit]

Number of residues constructor.

template<typename T>
core::id::AtomID_Map< T >::~AtomID_Map ( ) [inline]

Destructor.


Member Function Documentation

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]

Default value.

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?

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 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.

template<typename T>
void core::id::AtomID_Map< T >::finalize ( ) [inline]

Finalize after sizing all the vectors.

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.

Referenced by core::pack::figure_out_repackable_residues(), and core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing().

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]

Number of atoms in a residue.

Referenced by core::scoring::packing::initialize_AtomID_Map().

template<typename T>
Size core::id::AtomID_Map< T >::n_residue ( ) const [inline]

Number of residues (size)

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

AtomID_Map( atom_id ) const.

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

AtomID_Map( i_res )

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>
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>
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  n_res) [inline]
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]
template<typename T>
void core::id::AtomID_Map< T >::shrink ( ) [inline]

Shrink the vectors to remove unused capacity.

Referenced by core::id::AtomID_Map< numeric::xyzVector< core::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().


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 )


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