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

#include <NamedAtomID_Map.hh>

Public Types
typedef std::map< std::string, T >	AtomMap

typedef utility::vector1< AtomMap >	ResidueMap

typedef T	value_type

typedef AtomMap::mapped_type	reference

typedef AtomMap::mapped_type const	const_reference

typedef AtomMap::size_type	size_type

typedef T	Value

typedef AtomMap::mapped_type	Reference

typedef AtomMap::mapped_type const	ConstReference

typedef platform::Size	Size

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

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

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

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

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

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

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

void	resize (Size const, Size const, Value const &)
	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...

ConstReference	get (NamedAtomID const &id) const
	Get the value for an NamedAtomID: Return default value if not present Phil changing this to be a non-resizing function. More...

void	set (NamedAtomID const &id, Value const &value)
	Set the value for an NamedAtomID: 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 (NamedAtomID_Map &s)
	swap( NamedAtomID_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 (NamedAtomID const &id) const
	Is an element with this NamedAtomID present? More...

ConstReference	operator[] (NamedAtomID const &id) const
	NamedAtomID_Map[ atom_id ] const. More...

Reference	operator[] (NamedAtomID const &id)
	NamedAtomID_Map[ atom_id ]. More...

ConstReference	operator() (NamedAtomID const &id) const
	NamedAtomID_Map( atom_id ) const. More...

Reference	operator() (NamedAtomID const &id)
	NamedAtomID_Map( atom_id ) More...

ConstReference	operator() (Size i_res, std::string const &atom) const
	NamedAtomID_Map( i_res, i_atom ) const. More...

Reference	operator() (Size i_res, std::string const &atom)
	NamedAtomID_Map( i_res, i_atom ) More...

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

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

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

AtomMap &	operator() (Size const i_res)
	NamedAtomID_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 (NamedAtomID_Map< TF > &a, NamedAtomID_Map< TF > &b)
	swap( NamedAtomID_Map, NamedAtomID_Map ) More...

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

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

Detailed Description

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

Map from Atom identifiers to contained values class.

Member Typedef Documentation

template<typename T>

typedef std::map< std::string, T > core::id::NamedAtomID_Map< T >::AtomMap

template<typename T>

typedef AtomMap::mapped_type const core::id::NamedAtomID_Map< T >::const_reference

template<typename T>

typedef AtomMap::mapped_type const core::id::NamedAtomID_Map< T >::ConstReference

template<typename T>

typedef AtomMap::mapped_type core::id::NamedAtomID_Map< T >::reference

template<typename T>

typedef AtomMap::mapped_type core::id::NamedAtomID_Map< T >::Reference

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

template<typename T>

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

Constructor & Destructor Documentation

template<typename T>

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

inlineexplicit

Default constructor with no arguments (PyRosetta workaround)

template<typename T>

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

inlineexplicit

Default constructor.

template<typename T>

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

inlineexplicit

Number of residues constructor.

template<typename T>

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

inlineexplicit

Number of residues constructor.

template<typename T>

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

inlinedefault

Destructor.

Member Function Documentation

template<typename T>

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

inline

Clear the map.

template<typename T>

void core::id::NamedAtomID_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::NamedAtomID_Map< T >::default_value ( ) const

inline

Default value.

template<typename T>

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

inline

Set default value.

template<typename T>

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

inline

Empty?

template<typename T>

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

inline

Fill the map with the default fill value.

template<typename T>

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

inline

Finalize after sizing all the vectors.

template<typename T>

ConstReference core::id::NamedAtomID_Map< T >::get ( NamedAtomID const & id ) const

inline

Get the value for an NamedAtomID: Return default value if not present Phil changing this to be a non-resizing function.

template<typename T>

bool core::id::NamedAtomID_Map< T >::has ( NamedAtomID const & id ) const

inline

Is an element with this NamedAtomID present?

template<typename T>

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

inline

Number of atoms in a residue.

template<typename T>

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

inline

Number of residues (size)

template<typename T>

ConstReference core::id::NamedAtomID_Map< T >::operator() ( NamedAtomID const & id ) const

inline

NamedAtomID_Map( atom_id ) const.

template<typename T>

Reference core::id::NamedAtomID_Map< T >::operator() ( NamedAtomID const & id )

inline

NamedAtomID_Map( atom_id )

template<typename T>

ConstReference core::id::NamedAtomID_Map< T >::operator()	(	Size	i_res,
		std::string const &	atom
	)		const

inline

NamedAtomID_Map( i_res, i_atom ) const.

template<typename T>

Reference core::id::NamedAtomID_Map< T >::operator()	(	Size	i_res,
		std::string const &	atom
	)

inline

NamedAtomID_Map( i_res, i_atom )

template<typename T>

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

inline

NamedAtomID_Map( i_res ) const.

template<typename T>

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

inline

NamedAtomID_Map( i_res )

template<typename T>

ConstReference core::id::NamedAtomID_Map< T >::operator[] ( NamedAtomID const & id ) const

inline

NamedAtomID_Map[ atom_id ] const.

template<typename T>

Reference core::id::NamedAtomID_Map< T >::operator[] ( NamedAtomID const & id )

inline

NamedAtomID_Map[ atom_id ].

template<typename T>

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

inline

NamedAtomID_Map[ i_res ] const.

template<typename T>

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

inline

NamedAtomID_Map[ i_res ].

template<typename T>

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

inline

Resize to a given number of residues.

template<typename T>

void core::id::NamedAtomID_Map< T >::resize	(	Size	const,
		Size	const
	)

inline

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

template<typename T>

void core::id::NamedAtomID_Map< T >::resize	(	Size	const,
		Size	const,
		Value const &
	)

inline

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

template<typename T>

void core::id::NamedAtomID_Map< T >::set	(	NamedAtomID const &	id,
		Value const &	value
	)

inline

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

template<typename T>

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

inline

Shrink the vectors to remove unused capacity.

Referenced by core::id::NamedAtomID_Map< NamedAtomID >::finalize().

template<typename T>

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

inline

Size.

Referenced by core::id::NamedAtomID_Map< NamedAtomID >::update_sequence_numbering().

template<typename T>

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

inline

swap( NamedAtomID_Map )

Referenced by core::id::NamedAtomID_Map< NamedAtomID >::update_sequence_numbering().

template<typename T>

void core::id::NamedAtomID_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()