BTK::Monomer< AtomType > Class Template Reference

A minimal monomer object. More...

#include <monomer.h>

Inheritance diagram for BTK::Monomer< AtomType >:

[legend]Collaboration diagram for BTK::Monomer< AtomType >:

[legend]List of all members.

Public Types
typedef std::set< GROUP_VARIANT::index_t >	group_variant_container_t
STL-required container type definitions.
typedef base_type::value_type	value_type
typedef base_type::reference	reference
typedef base_type::const_reference	const_reference
typedef base_type::pointer	pointer
typedef base_type::const_pointer	const_pointer
typedef base_type::size_type	size_type
typedef base_type::iterator	iterator
typedef base_type::const_iterator	const_iterator
atom versions of standard STL typedefs
typedef value_type	atom_type
typedef iterator	atom_iterator
typedef const_iterator	const_atom_iterator
Public Member Functions
	Monomer (size_type s=0)
	see std::vector(s)
template<typename AtomIterator>	Monomer (AtomIterator first, AtomIterator last, self_type *prev_monomer=0, self_type *next_monomer=0, const AtomGroupConcept::group_variant_container_t &modifiers=group_variant_container_t())
	see std::vector(first,last)
template<typename T2>	Monomer (const Monomer< T2 > &source)
	~Monomer ()
template<typename T2> self_type &	operator= (const Monomer< T2 > &rhs)
virtual GROUP::index_t	group_index () const
virtual int	group_num () const
void	set_group_num (int x)
virtual const std::string &	group_name3 () const
virtual char	group_name1 () const
virtual const AtomGroupConcept::group_variant_container_t &	group_variant_codes () const
size_type	size () const
	Replication of std::vector function (see std::vector documentation).
iterator	begin ()
const_iterator	begin () const
iterator	end ()
const_iterator	end () const
reference	operator[] (size_type i)
const_reference	operator[] (size_type i) const
reference	front ()
const_reference	front () const
reference	back ()
const_reference	back () const
Special 'atom_' versions of std::vector functions
size_type	atom_size () const
	atom versions of std::vector function names
atom_iterator	atom_begin ()
	atom versions of std::vector function names
const_atom_iterator	atom_begin () const
	atom versions of std::vector function names
atom_iterator	atom_end ()
	atom versions of std::vector function names
const_atom_iterator	atom_end () const
	atom versions of std::vector function names
reference	atom (size_type i)
	atom versions of std::vector function names
const_reference	atom (size_type i) const
	atom versions of std::vector function names
reference	atom_back ()
	atom versions of std::vector function names
const_reference	atom_back () const
	atom versions of std::vector function names
reference	atom_front ()
	atom versions of std::vector function names
const_reference	atom_front () const
	atom versions of std::vector function names
Protected Member Functions
void	clear ()
	Replication of std::vector function (see std::vector documentation).
void	resize (size_type s)
void	reserve (size_type s)
void	push_back (const value_type &x)
iterator	insert (iterator pos, const value_type &x)
void	insert (iterator pos, size_type s, const value_type &x)
void	insert (iterator pos, InputIterator first, InputIterator last)
iterator	erase (iterator pos)
iterator	erase (iterator first, iterator last)
void	shallow_push_back (value_type *x)
void	shallow_insert (iterator pos, const_iterator first, const_iterator last)
void	deep_copy (const SharedVectorBase< T2 > &source)
void	shallow_copy (const self_type &source)

---

Detailed Description

template<typename AtomType>
class BTK::Monomer< AtomType >

A minimal monomer object.

---

Member Typedef Documentation

template<typename AtomType> typedef iterator BTK::Monomer< AtomType >::atom_iterator

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef value_type BTK::Monomer< AtomType >::atom_type

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef const_iterator BTK::Monomer< AtomType >::const_atom_iterator

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef base_type::const_iterator BTK::Monomer< AtomType >::const_iterator

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef base_type::const_pointer BTK::Monomer< AtomType >::const_pointer

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef base_type::const_reference BTK::Monomer< AtomType >::const_reference

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

typedef std::set<GROUP_VARIANT::index_t> BTK::AtomGroupConcept::group_variant_container_t [inherited]

:

template<typename AtomType> typedef base_type::iterator BTK::Monomer< AtomType >::iterator

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef base_type::pointer BTK::Monomer< AtomType >::pointer

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef base_type::reference BTK::Monomer< AtomType >::reference

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef base_type::size_type BTK::Monomer< AtomType >::size_type

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

template<typename AtomType> typedef base_type::value_type BTK::Monomer< AtomType >::value_type

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >, BTK::PeptideBB< AtomType >, and BTK::PeptideHeavyAtom< AtomType >.

---

Constructor & Destructor Documentation

template<typename AtomType> BTK::Monomer< AtomType >::Monomer (  size_type  s = 0  )  [inline]

see std::vector(s)

template<typename AtomType> template<typename AtomIterator> BTK::Monomer< AtomType >::Monomer (  AtomIterator  first, AtomIterator  last, self_type *  prev_monomer = 0, self_type *  next_monomer = 0, const AtomGroupConcept::group_variant_container_t &  modifiers = group_variant_container_t() )  [inline]

see std::vector(first,last)

template<typename AtomType> template<typename T2> BTK::Monomer< AtomType >::Monomer (  const Monomer< T2 > &  source  )  [inline]

template<typename AtomType> BTK::Monomer< AtomType >::~Monomer (   )  [inline]

---

Member Function Documentation

template<typename AtomType> const_reference BTK::AtomContainer< AtomType >::atom (  size_type  i  )  const [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> reference BTK::AtomContainer< AtomType >::atom (  size_type  i  )  [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> const_reference BTK::AtomContainer< AtomType >::atom_back (   )  const [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> reference BTK::AtomContainer< AtomType >::atom_back (   )  [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> const_atom_iterator BTK::AtomContainer< AtomType >::atom_begin (   )  const [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> atom_iterator BTK::AtomContainer< AtomType >::atom_begin (   )  [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> const_atom_iterator BTK::AtomContainer< AtomType >::atom_end (   )  const [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> atom_iterator BTK::AtomContainer< AtomType >::atom_end (   )  [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> const_reference BTK::AtomContainer< AtomType >::atom_front (   )  const [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> reference BTK::AtomContainer< AtomType >::atom_front (   )  [inline, inherited]

atom versions of std::vector function names

template<typename AtomType> size_type BTK::AtomContainer< AtomType >::atom_size (   )  const [inline, inherited]

atom versions of std::vector function names

const_reference BTK::SharedVectorBase< AtomType >::back (   )  const [inline, inherited]

Replication of std::vector function (see std::vector documentation).

reference BTK::SharedVectorBase< AtomType >::back (   )  [inline, inherited]

Replication of std::vector function (see std::vector documentation).

const_iterator BTK::SharedVectorBase< AtomType >::begin (   )  const [inline, inherited]

Replication of std::vector function (see std::vector documentation).

iterator BTK::SharedVectorBase< AtomType >::begin (   )  [inline, inherited]

Replication of std::vector function (see std::vector documentation).

void BTK::SharedVectorBase< AtomType >::clear (   )  [inline, protected, inherited]

Replication of std::vector function (see std::vector documentation).

void BTK::SharedVectorBase< AtomType >::deep_copy (  const SharedVectorBase< T2 > &  source  )  [protected, inherited]

const_iterator BTK::SharedVectorBase< AtomType >::end (   )  const [inline, inherited]

Replication of std::vector function (see std::vector documentation).

iterator BTK::SharedVectorBase< AtomType >::end (   )  [inline, inherited]

Replication of std::vector function (see std::vector documentation).

iterator BTK::SharedVectorBase< AtomType >::erase (  iterator  first, iterator  last )  [inline, protected, inherited]

Replication of std::vector function (see std::vector documentation).

iterator BTK::SharedVectorBase< AtomType >::erase (  iterator  pos  )  [inline, protected, inherited]

Replication of std::vector function (see std::vector documentation).

const_reference BTK::SharedVectorBase< AtomType >::front (   )  const [inline, inherited]

Replication of std::vector function (see std::vector documentation).

reference BTK::SharedVectorBase< AtomType >::front (   )  [inline, inherited]

Replication of std::vector function (see std::vector documentation).

template<typename AtomType> virtual GROUP::index_t BTK::Monomer< AtomType >::group_index (   )  const [inline, virtual]

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >.

template<typename AtomType> virtual char BTK::Monomer< AtomType >::group_name1 (   )  const [inline, virtual]

Reimplemented in BTK::BuildableMonomer< AtomType >.

template<typename AtomType> virtual const std::string& BTK::Monomer< AtomType >::group_name3 (   )  const [inline, virtual]

Reimplemented from BTK::AtomContainer< AtomType >. Reimplemented in BTK::BuildableMonomer< AtomType >.

template<typename AtomType> virtual int BTK::Monomer< AtomType >::group_num (   )  const [inline, virtual]

Reimplemented from BTK::AtomContainer< AtomType >.

template<typename AtomType> virtual const AtomGroupConcept::group_variant_container_t& BTK::AtomContainer< AtomType >::group_variant_codes (   )  const [inline, virtual, inherited]

Implements BTK::AtomGroupConcept.

void BTK::SharedVectorBase< AtomType >::insert (  iterator  pos, InputIterator  first, InputIterator  last )  [protected, inherited]

Replication of std::vector function (see std::vector documentation).

void BTK::SharedVectorBase< AtomType >::insert (  iterator  pos, size_type  s, const value_type &  x )  [protected, inherited]

Replication of std::vector function (see std::vector documentation).

iterator BTK::SharedVectorBase< AtomType >::insert (  iterator  pos, const value_type &  x )  [inline, protected, inherited]

Replication of std::vector function (see std::vector documentation).

template<typename AtomType> template<typename T2> self_type& BTK::Monomer< AtomType >::operator= (  const Monomer< T2 > &  rhs  )  [inline]

Here is the call graph for this function:

const_reference BTK::SharedVectorBase< AtomType >::operator[] (  size_type  i  )  const [inline, inherited]

Replication of std::vector function (see std::vector documentation).

reference BTK::SharedVectorBase< AtomType >::operator[] (  size_type  i  )  [inline, inherited]

Replication of std::vector function (see std::vector documentation).

void BTK::SharedVectorBase< AtomType >::push_back (  const value_type &  x  )  [inline, protected, inherited]

Replication of std::vector function (see std::vector documentation).

void BTK::SharedVectorBase< AtomType >::reserve (  size_type  s  )  [inline, protected, inherited]

Replication of std::vector function (see std::vector documentation).

void BTK::SharedVectorBase< AtomType >::resize (  size_type  s  )  [inline, protected, inherited]

Replication of std::vector function (see std::vector documentation).

template<typename AtomType> void BTK::Monomer< AtomType >::set_group_num (  int  x  )  [inline]

void BTK::SharedVectorBase< AtomType >::shallow_copy (  const self_type &  source  )  [protected, inherited]

void BTK::SharedVectorBase< AtomType >::shallow_insert (  iterator  pos, const_iterator  first, const_iterator  last )  [inline, protected, inherited]

void BTK::SharedVectorBase< AtomType >::shallow_push_back (  value_type *  x  )  [inline, protected, inherited]

size_type BTK::SharedVectorBase< AtomType >::size (   )  const [inline, inherited]

Replication of std::vector function (see std::vector documentation).

---

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

• monomer.h

---