BTK::Polymer< MonomerType > Class Template Reference

Polymer is a class for representing polymeric molecules. More...

#include <polymer.h>

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[legend]List of all members.

Public Types
typedef boost::function< void(atom_iterator, atom_iterator)	build_strategy_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
specially named STL-types
typedef value_type	monomer_type
typedef iterator	monomer_iterator
typedef const_iterator	const_monomer_iterator
typedef base_molecule_type::value_type	atom_type
typedef base_molecule_type::iterator	atom_iterator
typedef base_molecule_type::const_iterator	const_atom_iterator
typedef base_molecule_type::reference	atom_reference
typedef base_molecule_type::const_reference	const_atom_reference
Public Member Functions
	Polymer (size_type s=0, build_strategy_t build_strategy=0)
template<typename AtomIterator>	Polymer (AtomIterator first, AtomIterator last, build_strategy_t build_strategy=0)
	Construct a polymer from an stl container of atoms.
	Polymer (const self_type &source)
template<typename T2>	Polymer (const Polymer< T2 > &source)
	~Polymer ()
self_type &	operator= (const self_type &rhs)
template<typename T2> self_type &	operator= (const Polymer< T2 > &rhs)
const std::string &	name () const
void	set_name (const std::string &name)
char	chain_id () const
void	set_chain_id (char chain_id)
size_type	atom_size () const
atom_iterator	atom_begin ()
const_atom_iterator	atom_begin () const
atom_iterator	atom_end ()
const_atom_iterator	atom_end () const
atom_reference	atom (size_type i)
const_atom_reference	atom (size_type i) const
atom_reference	atom_back ()
const_atom_reference	atom_back () const
atom_reference	atom_front ()
const_atom_reference	atom_front () const
void	monomer_push_back (const monomer_type &m)
build_strategy_t	build_strategy () 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
size_type	monomer_size () const
	atom versions of standard STL function names
iterator	monomer_begin ()
	atom versions of standard STL function names
const_iterator	monomer_begin () const
	atom versions of standard STL function names
iterator	monomer_end ()
	atom versions of standard STL function names
const_iterator	monomer_end () const
	atom versions of standard STL function names
reference	monomer (size_type i)
	atom versions of standard STL function names
const_reference	monomer (size_type i) const
	atom versions of standard STL function names
reference	monomer_back ()
	atom versions of standard STL function names
const_reference	monomer_back () const
	atom versions of standard STL function names
reference	monomer_front ()
	atom versions of standard STL function names
const_reference	monomer_front () const
	atom versions of standard STL function names
Protected Member Functions
template<typename AtomIterator> void	add_monomer (AtomIterator first, AtomIterator last, const AtomGroupConcept::group_variant_container_t &modifiers)
template<typename AtomIterator> void	create_monomers (AtomIterator first, AtomIterator last)
void	sync_molecule_to_monomers ()
	Create a molecule that contains a shared copy of the atoms in all monomers of this polymer.
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)

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Detailed Description

template<typename MonomerType>
class BTK::Polymer< MonomerType >

Polymer is a class for representing polymeric molecules.

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Member Typedef Documentation

template<typename MonomerType> typedef base_molecule_type::iterator BTK::Polymer< MonomerType >::atom_iterator

template<typename MonomerType> typedef base_molecule_type::reference BTK::Polymer< MonomerType >::atom_reference

template<typename MonomerType> typedef base_molecule_type::value_type BTK::Polymer< MonomerType >::atom_type

template<typename MonomerType> typedef boost::function<void(atom_iterator,atom_iterator) BTK::Polymer< MonomerType >::build_strategy_t)

template<typename MonomerType> typedef base_molecule_type::const_iterator BTK::Polymer< MonomerType >::const_atom_iterator

template<typename MonomerType> typedef base_molecule_type::const_reference BTK::Polymer< MonomerType >::const_atom_reference

template<typename MonomerType> typedef base_type::const_iterator BTK::Polymer< MonomerType >::const_iterator

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef const_iterator BTK::Polymer< MonomerType >::const_monomer_iterator

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef base_type::const_pointer BTK::Polymer< MonomerType >::const_pointer

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef base_type::const_reference BTK::Polymer< MonomerType >::const_reference

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef base_type::iterator BTK::Polymer< MonomerType >::iterator

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef iterator BTK::Polymer< MonomerType >::monomer_iterator

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef value_type BTK::Polymer< MonomerType >::monomer_type

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef base_type::pointer BTK::Polymer< MonomerType >::pointer

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef base_type::reference BTK::Polymer< MonomerType >::reference

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef base_type::size_type BTK::Polymer< MonomerType >::size_type

Reimplemented from BTK::MonomerContainer< MonomerType >.

template<typename MonomerType> typedef base_type::value_type BTK::Polymer< MonomerType >::value_type

Reimplemented from BTK::MonomerContainer< MonomerType >.

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Constructor & Destructor Documentation

template<typename MonomerType> BTK::Polymer< MonomerType >::Polymer (  size_type  s = 0, build_strategy_t  build_strategy = 0 )

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template<typename MonomerType> template<typename AtomIterator> BTK::Polymer< MonomerType >::Polymer (  AtomIterator  first, AtomIterator  last, build_strategy_t  build_strategy = 0 )

Construct a polymer from an stl container of atoms. Polymer will copy the atoms in the list, divide them into their proper monomer groups, and store them internally.

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template<typename MonomerType> BTK::Polymer< MonomerType >::Polymer (  const self_type &  source  )

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template<typename MonomerType> template<typename T2> BTK::Polymer< MonomerType >::Polymer (  const Polymer< T2 > &  source  )

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template<typename MonomerType> BTK::Polymer< MonomerType >::~Polymer (   )  [inline]

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Member Function Documentation

template<typename MonomerType> template<typename AtomIterator> void BTK::Polymer< MonomerType >::add_monomer (  AtomIterator  first, AtomIterator  last, const AtomGroupConcept::group_variant_container_t &  modifiers )  [protected]

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template<typename MonomerType> const_atom_reference BTK::Polymer< MonomerType >::atom (  size_type  i  )  const [inline]

template<typename MonomerType> atom_reference BTK::Polymer< MonomerType >::atom (  size_type  i  )  [inline]

template<typename MonomerType> const_atom_reference BTK::Polymer< MonomerType >::atom_back (   )  const [inline]

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template<typename MonomerType> atom_reference BTK::Polymer< MonomerType >::atom_back (   )  [inline]

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template<typename MonomerType> const_atom_iterator BTK::Polymer< MonomerType >::atom_begin (   )  const [inline]

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template<typename MonomerType> atom_iterator BTK::Polymer< MonomerType >::atom_begin (   )  [inline]

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template<typename MonomerType> const_atom_iterator BTK::Polymer< MonomerType >::atom_end (   )  const [inline]

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template<typename MonomerType> atom_iterator BTK::Polymer< MonomerType >::atom_end (   )  [inline]

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template<typename MonomerType> const_atom_reference BTK::Polymer< MonomerType >::atom_front (   )  const [inline]

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template<typename MonomerType> atom_reference BTK::Polymer< MonomerType >::atom_front (   )  [inline]

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template<typename MonomerType> size_type BTK::Polymer< MonomerType >::atom_size (   )  const [inline]

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

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

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

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

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

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

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

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

template<typename MonomerType> build_strategy_t BTK::Polymer< MonomerType >::build_strategy (   )  const [inline]

template<typename MonomerType> char BTK::Polymer< MonomerType >::chain_id (   )  const [inline]

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

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

template<typename MonomerType> template<typename AtomIterator> void BTK::Polymer< MonomerType >::create_monomers (  AtomIterator  first, AtomIterator  last )  [protected]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

template<typename MonomerType> const_reference BTK::MonomerContainer< MonomerType >::monomer (  size_type  i  )  const [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> reference BTK::MonomerContainer< MonomerType >::monomer (  size_type  i  )  [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> const_reference BTK::MonomerContainer< MonomerType >::monomer_back (   )  const [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> reference BTK::MonomerContainer< MonomerType >::monomer_back (   )  [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> const_iterator BTK::MonomerContainer< MonomerType >::monomer_begin (   )  const [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> iterator BTK::MonomerContainer< MonomerType >::monomer_begin (   )  [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> const_iterator BTK::MonomerContainer< MonomerType >::monomer_end (   )  const [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> iterator BTK::MonomerContainer< MonomerType >::monomer_end (   )  [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> const_reference BTK::MonomerContainer< MonomerType >::monomer_front (   )  const [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> reference BTK::MonomerContainer< MonomerType >::monomer_front (   )  [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> void BTK::Polymer< MonomerType >::monomer_push_back (  const monomer_type &  m  )  [inline]

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template<typename MonomerType> size_type BTK::MonomerContainer< MonomerType >::monomer_size (   )  const [inline, inherited]

atom versions of standard STL function names

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template<typename MonomerType> const std::string& BTK::Polymer< MonomerType >::name (   )  const [inline]

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template<typename MonomerType> template<typename T2> BTK::Polymer< MonomerType >::self_type & BTK::Polymer< MonomerType >::operator= (  const Polymer< T2 > &  rhs  )

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template<typename MonomerType> BTK::Polymer< MonomerType >::self_type & BTK::Polymer< MonomerType >::operator= (  const self_type &  rhs  )

Atoms and monomers in rhs are deep-copied into this Polymer. No references to the original Polymer will remain in this Polymer. : Reimplemented from BTK::MonomerContainer< MonomerType >.

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

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

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

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

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

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

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

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

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

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

template<typename MonomerType> void BTK::Polymer< MonomerType >::set_chain_id (  char  chain_id  )  [inline]

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template<typename MonomerType> void BTK::Polymer< MonomerType >::set_name (  const std::string &  name  )  [inline]

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

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

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

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

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

template<typename MonomerType> void BTK::Polymer< MonomerType >::sync_molecule_to_monomers (   )  [protected]

Create a molecule that contains a shared copy of the atoms in all monomers of this polymer.

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

• polymer.h
• polymer.hpp

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