BTK::BuildableMonomer< AtomType > Class Template Reference

a class that implements the buildable concept for monomers More...

#include <buildable_monomer.h>

Inheritance diagram for BTK::BuildableMonomer< AtomType >:

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

[legend]List of all members.

Public Types
typedef self_type	buildable_monomer_types
typedef std::map< ATOM::index_t, pointer >	atom_index_map_t
typedef pattern_t::types::monomer_atom_idx_t	monomer_atom_idx_t
typedef std::set< GROUP_VARIANT::index_t >	group_variant_container_t
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
typedef value_type	atom_type
typedef iterator	atom_iterator
typedef const_iterator	const_atom_iterator
Public Member Functions
	BuildableMonomer (const BuildableMonomerFamilyPattern &family_pattern)
	minimal ctor
template<typename AtomIterator>	BuildableMonomer (AtomIterator first, AtomIterator last, self_type *prev_monomer, self_type *next_monomer, const AtomGroupConcept::group_variant_container_t &modifiers, const BuildableMonomerFamilyPattern &family_pattern)
	construct a monomer from an atom iterator
	BuildableMonomer (const self_type &source)
template<typename T2>	BuildableMonomer (const BuildableMonomer< T2 > &source)
self_type &	operator= (const self_type &rhs)
template<typename T2> self_type &	operator= (const BuildableMonomer< T2 > &rhs)
virtual GROUP::index_t	group_index () const
virtual const AtomGroupConcept::group_variant_container_t &	group_variants () const
virtual const std::string &	group_name3 () const
virtual char	group_name1 () const
void	insert_group_variant (GROUP_VARIANT::index_t v)
void	erase_group_variant (GROUP_VARIANT::index_t v)
double	torsion_angle (TORSION::index_t t) const
void	set_torsion_angle (TORSION::index_t t, double angle)
virtual bool	build_atom (const ATOM::index_t atom_index, bool is_bootstrap)
	attempt to build the atom indexed by atom_index
virtual int	group_num () const
void	set_group_num (int x)
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
Relative monomer atom lookup functions
reference	atom (monomer_atom_idx_t ma)
	Lookup an atom from this monomer or a relative monomer.
const_reference	atom (monomer_atom_idx_t ma) const
	Lookup an atom from this monomer or a relative monomer.
Atom lookup functions
reference	atom (ATOM::index_t atom_index)
	Lookup an atom from this monomer.
const_reference	atom (ATOM::index_t atom_index) const
	Lookup an atom from this monomer.
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::BuildableMonomer< AtomType >

a class that implements the buildable concept for monomers

This class serves as the base to peptide and nucleotide classes, but is not abstract. It's constructor takes a "Pattern" class argument which contains all of the data necessary to implement the pattern's build properties. The derived classes are simply more convenient.

Note that a lot of the code here is expected to work it's way up to a more general "BuildableGroupConcept" sort of class which can be shared with other buildable objects -- such as BuildableMolecules (which will handle ligands and heme groups, etc)

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Member Typedef Documentation

template<typename AtomType> typedef std::map<ATOM::index_t,pointer> BTK::BuildableMonomer< AtomType >::atom_index_map_t

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

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

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

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

template<typename AtomType> typedef self_type BTK::BuildableMonomer< AtomType >::buildable_monomer_types

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

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

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

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

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

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

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

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

Reimplemented from BTK::Monomer< AtomType >. Reimplemented in 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::BuildableMonomer< AtomType >::iterator

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

template<typename AtomType> typedef pattern_t::types::monomer_atom_idx_t BTK::BuildableMonomer< AtomType >::monomer_atom_idx_t

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

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

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

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

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

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

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

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

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Constructor & Destructor Documentation

template<typename AtomType> BTK::BuildableMonomer< AtomType >::BuildableMonomer (  const BuildableMonomerFamilyPattern &  family_pattern  )  [inline]

minimal ctor This ctor makes it easier for derived classes to be default constructable, not expected for practicle use.

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

construct a monomer from an atom iterator Parameters: family_pattern  Pattern class that contains all of the data describing how this object should be built

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

:

template<typename AtomType> template<typename T2> BTK::BuildableMonomer< AtomType >::BuildableMonomer (  const BuildableMonomer< T2 > &  source  )  [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::BuildableMonomer< AtomType >::atom (  ATOM::index_t  atom_index  )  const [inline]

Lookup an atom from this monomer.

template<typename AtomType> reference BTK::BuildableMonomer< AtomType >::atom (  ATOM::index_t  atom_index  )  [inline]

Lookup an atom from this monomer.

template<typename AtomType> const_reference BTK::BuildableMonomer< AtomType >::atom (  monomer_atom_idx_t  ma  )  const [inline]

Lookup an atom from this monomer or a relative monomer. Parameters: ma  make_pair(relative monomer count,atom index type)

template<typename AtomType> reference BTK::BuildableMonomer< AtomType >::atom (  monomer_atom_idx_t  ma  )  [inline]

Lookup an atom from this monomer or a relative monomer. Parameters: ma  make_pair(relative monomer count,atom index type)

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> virtual bool BTK::BuildableMonomer< AtomType >::build_atom (  const ATOM::index_t  atom_index, bool  is_bootstrap )  [inline, virtual]

attempt to build the atom indexed by atom_index Parameters: is_bootstrap  if true, build the atom and two neighboring atoms from scratch, (assumes no other atoms are built), use this option to "bootstrap" the build procedure Implements BTK::BuildableAtomGroupConcept.

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).

template<typename AtomType> void BTK::BuildableMonomer< AtomType >::erase_group_variant (  GROUP_VARIANT::index_t  v  )  [inline]

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

Reimplemented from BTK::Monomer< AtomType >.

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

Reimplemented from BTK::Monomer< AtomType >.

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

Reimplemented from BTK::Monomer< AtomType >.

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

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.

template<typename AtomType> virtual const AtomGroupConcept::group_variant_container_t& BTK::BuildableMonomer< AtomType >::group_variants (   )  const [inline, virtual]

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> void BTK::BuildableMonomer< AtomType >::insert_group_variant (  GROUP_VARIANT::index_t  v  )  [inline]

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

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

: 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::Monomer< AtomType >::set_group_num (  int  x  )  [inline, inherited]

template<typename AtomType> void BTK::BuildableMonomer< AtomType >::set_torsion_angle (  TORSION::index_t  t, double  angle )  [inline]

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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).

template<typename AtomType> double BTK::BuildableMonomer< AtomType >::torsion_angle (  TORSION::index_t  t  )  const [inline]

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

• buildable_monomer.h

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