BTK::Molecule< AtomType > Class Template Reference

Generic molecule class. More...

#include <molecule.h>

Inheritance diagram for BTK::Molecule< AtomType >:

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

[legend]List of all members.

Public Types
typedef Molecule< AtomType >	self_type
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
	Molecule (size_type s=0)
	Construct a molecule of s default instances of AtomType.
template<typename AtomIterator>	Molecule (AtomIterator first, AtomIterator last)
	Construct a molecule from an iterator range over AtomType.
	Molecule (const self_type &source)
template<typename T2>	Molecule (const Molecule< T2 > &source)
	~Molecule ()
self_type &	operator= (const self_type &rhs)
template<typename T2> self_type &	operator= (const Molecule< T2 > &rhs)
virtual GROUP::index_t	group_index () const
const std::string &	name () const
void	set_name (const std::string &name)
char	chain_id () const
void	set_chain_id (char chain_id)
virtual const AtomGroupConcept::group_variant_container_t &	group_variant_codes () const
virtual const std::string &	group_name3 () const
virtual int	group_num () 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)

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Detailed Description

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

Generic molecule class.

Molecule is a rigid-body molecule class, meaning that it can represent molecules as fixed collections of atoms/points that may be translated, rotated and transformed like any other fixed set of points in space. You cannot rebuild or refold a Molecule object.

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Member Typedef Documentation

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

:

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

template<typename AtomType> typedef Molecule<AtomType> BTK::Molecule< AtomType >::self_type

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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

Reimplemented from BTK::AtomContainer< AtomType >.

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Constructor & Destructor Documentation

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

Construct a molecule of s default instances of AtomType.

template<typename AtomType> template<typename AtomIterator> BTK::Molecule< AtomType >::Molecule (  AtomIterator  first, AtomIterator  last )  [inline]

Construct a molecule from an iterator range over AtomType.

template<typename AtomType> BTK::Molecule< AtomType >::Molecule (  const self_type &  source  )  [inline]

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

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

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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).

template<typename AtomType> char BTK::Molecule< AtomType >::chain_id (   )  const [inline]

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::Molecule< AtomType >::group_index (   )  const [inline, virtual]

Reimplemented from BTK::AtomContainer< AtomType >.

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

Implements BTK::AtomGroupConcept. Reimplemented in BTK::BuildableMonomer< AtomType >, and BTK::Monomer< AtomType >.

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

Implements BTK::AtomGroupConcept. Reimplemented in BTK::Monomer< 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> const std::string& BTK::Molecule< AtomType >::name (   )  const [inline]

template<typename AtomType> template<typename T2> BTK::Molecule< AtomType >::self_type & BTK::Molecule< AtomType >::operator= (  const Molecule< T2 > &  rhs  )

Here is the call graph for this function:

template<typename AtomType> BTK::Molecule< AtomType >::self_type & BTK::Molecule< AtomType >::operator= (  const self_type &  rhs  )

Reimplemented from BTK::AtomContainer< AtomType >.

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::Molecule< AtomType >::set_chain_id (  char  chain_id  )  [inline]

template<typename AtomType> void BTK::Molecule< AtomType >::set_name (  const std::string &  name  )  [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).

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

• molecule.h
• molecule.hpp

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