Polymer Class Template Reference

A Polymer is a chain of monomers that is also an atomic structure. More...

#include <polymer.hpp>

Inheritance diagram for Polymer:

List of all members.

Public Types
typedef base_type::chemical_type_system	chemical_type_system
typedef base_type::dictionary	dictionary
typedef base_type::id_type	id_type
typedef base_type::value_type	value_type
typedef base_type::iterator	iterator
typedef base_type::const_iterator	const_iterator
typedef base_type::reverse_iterator	reverse_iterator
typedef base_type::const_reverse_iterator	const_reverse_iterator
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::difference_type	difference_type
typedef base_type::size_type	size_type
typedef base_type::monomer_type	monomer_type
typedef base_type::monomer_iterator	monomer_iterator
typedef base_type::const_monomer_iterator	const_monomer_iterator
typedef base_type::reverse_monomer_iterator	reverse_monomer_iterator
typedef base_type::const_reverse_monomer_iterator	const_reverse_monomer_iterator
typedef base_type::structure_id_type	structure_id_type
typedef base_type::monomer_id_type	monomer_id_type
Type definitions required by the AtomicStructureConcept.
typedef monomer_type::atom_type	atom_type
	The atom type (the type of the atom held by the monomer objects).
typedef atom_type::id_type	atom_id_type
	THe atom ID type.
Required atom iterator types.
typedef UTILITY::GroupedElementIterator< monomer_iterator, typename monomer_type::atom_iterator, monomer_type, atom_type >	atom_iterator
typedef boost::reverse_iterator< atom_iterator >	reverse_atom_iterator
typedef UTILITY::GroupedElementIterator< const_monomer_iterator, typename monomer_type::const_atom_iterator, monomer_type const, atom_type const >	const_atom_iterator
typedef boost::reverse_iterator< const_atom_iterator >	const_reverse_atom_iterator
Public Member Functions
	Polymer (size_type s=0, monomer_type const &m=monomer_type(), char chain_id= ' ', structure_id_type t=structure_id_type())
	Construct a Polymer of a given size.
template<typename MonomerIterator>
	Polymer (MonomerIterator first, MonomerIterator last, char chain_id= ' ', structure_id_type t=structure_id_type())
	Construct a Polymer from a range of monomer objects.
	Polymer (self_type const &source)
virtual	~Polymer ()
virtual std::ostream &	print (std::ostream &os, size_type first_atom_num=1, size_type first_monomer_num=1) const
	Print the atoms in a Polymer to an output stream.
template<typename InputIterator>
void	insert (iterator p, InputIterator i, InputIterator j)
virtual dictionary const &	get_dictionary () const
virtual dictionary &	get_dictionary ()
void	swap (self_type &b)
self_type const &	operator= (self_type const &rhs)
bool	operator== (self_type const &rhs) const
bool	operator!= (self_type const &rhs) const
bool	operator< (self_type const &rhs) const
Methods required by the AtomicStructureConcept.
atom_iterator	structure_begin ()
	Get an atom_iterator (start of range).
const_atom_iterator	structure_begin () const
	Get an atom_iterator (start of range).
reverse_atom_iterator	structure_rbegin ()
	Get a reverse_atom_iterator.
const_reverse_atom_iterator	structure_rbegin () const
	Get a reverse_atom_iterator.
atom_iterator	structure_end ()
	Get a reverse_atom_iterator (end of range).
const_atom_iterator	structure_end () const
	Get an atom_iterator (end of range).
reverse_atom_iterator	structure_rend ()
	Get a reverse_atom_iterator (end of range).
const_reverse_atom_iterator	structure_rend () const
	Get a reverse_atom_iterator (end of range).
size_type	num_atoms () const
	Get the size of the Polymer, in atoms.
Methods required for the ChainConcept.
char	chain_id () const
	Get the current chain ID value.
void	set_chain_id (char chain_id)
	Set the current chain ID value.

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Detailed Description

template<typename MonomerType, typename ChemicalTypeSystemType = typename MonomerType::chemical_type_system, typename DictionaryType = typename ChemicalTypeSystemType::structure_dictionary, typename StorageStrategy = std::list<MonomerType>>
class BTK::MOLECULES::Polymer< MonomerType, ChemicalTypeSystemType, DictionaryType, StorageStrategy >

A Polymer is a chain of monomers that is also an atomic structure.

This class is a Sequence of objects that adhere to the MonomerConcept, (just like PolymerStructure), with the addition of methods thast allow iteration over atoms (as if the container were an AtomicStructure). This combination of features makes sense biochemically -- every polymer is a a chain of atoms, conceptually grouped into monomers.

More specifically, Polymer implements the ChainConcept and the AtomicStructureConcept. Thus, you can iterate over atoms and get/set the chain ID of a Polymer, but you cannot insert or delete individual atoms from a Polymer. As with the PolymerStructure, though, you may insert and delete monomer objects from a Polymer.

Examples:

gyration_radius.cpp.

---

Member Typedef Documentation

typedef base_type ::chemical_type_system chemical_type_system

Reimplemented from PolymerStructure.

typedef base_type ::dictionary dictionary

Reimplemented from PolymerStructure.

typedef base_type ::id_type id_type

Reimplemented from PolymerStructure.

typedef base_type ::value_type value_type

Reimplemented from PolymerStructure.

typedef base_type ::iterator iterator

Reimplemented from PolymerStructure.

typedef base_type ::const_iterator const_iterator

Reimplemented from PolymerStructure.

typedef base_type ::reverse_iterator reverse_iterator

Reimplemented from PolymerStructure.

typedef base_type ::const_reverse_iterator const_reverse_iterator

Reimplemented from PolymerStructure.

typedef base_type ::reference reference

Reimplemented from PolymerStructure.

typedef base_type ::const_reference const_reference

Reimplemented from PolymerStructure.

typedef base_type ::pointer pointer

Reimplemented from PolymerStructure.

typedef base_type ::const_pointer const_pointer

Reimplemented from PolymerStructure.

typedef base_type ::difference_type difference_type

Reimplemented from PolymerStructure.

typedef base_type ::size_type size_type

Reimplemented from PolymerStructure.

typedef base_type ::monomer_type monomer_type

Reimplemented from PolymerStructure.

typedef base_type ::monomer_iterator monomer_iterator

Reimplemented from PolymerStructure.

typedef base_type ::const_monomer_iterator const_monomer_iterator

Reimplemented from PolymerStructure.

typedef base_type ::reverse_monomer_iterator reverse_monomer_iterator

Reimplemented from PolymerStructure.

typedef base_type ::const_reverse_monomer_iterator const_reverse_monomer_iterator

Reimplemented from PolymerStructure.

typedef base_type ::structure_id_type structure_id_type

Reimplemented from PolymerStructure.

typedef base_type ::monomer_id_type monomer_id_type

Reimplemented from PolymerStructure.

typedef monomer_type::atom_type atom_type

The atom type (the type of the atom held by the monomer objects).

typedef atom_type::id_type atom_id_type

THe atom ID type.

typedef UTILITY:: GroupedElementIterator<monomer_iterator, typename monomer_type::atom_iterator, monomer_type, atom_type> atom_iterator

typedef boost::reverse_iterator<atom_iterator> reverse_atom_iterator

typedef UTILITY:: GroupedElementIterator<const_monomer_iterator, typename monomer_type::const_atom_iterator, monomer_type const, atom_type const> const_atom_iterator

typedef boost::reverse_iterator<const_atom_iterator> const_reverse_atom_iterator

---

Constructor & Destructor Documentation

Polymer	(	size_type	s = 0,
		monomer_type const &	m = monomer_type(),
		char	chain_id = ' ',
		structure_id_type	t = structure_id_type()
	)

Construct a Polymer of a given size.

Parameters:

	s	Size of the new Polymer.
	m	An instance of the MonomerType to copy into the new Polymer.
	chain_id	The chain ID value.
	t	The structure ID value (currently unused).

Polymer	(	MonomerIterator	first,
		MonomerIterator	last,
		char	chain_id = ' ',
		structure_id_type	t = structure_id_type()
	)

Construct a Polymer from a range of monomer objects.

Parameters:

	first	The start iterator of the monomer range.
	last	The end iterator of the monomer range.
	chain_id	The chain ID value.
	t	The structure ID value (currently unused).

Polymer

(

self_type const &

source

)

virtual ~Polymer

(

)

[virtual]

---

Member Function Documentation

atom_iterator structure_begin

(

)

Get an atom_iterator (start of range).

const_atom_iterator structure_begin

(

)

const

Get an atom_iterator (start of range).

reverse_atom_iterator structure_rbegin

(

)

Get a reverse_atom_iterator.

const_reverse_atom_iterator structure_rbegin

(

)

const

Get a reverse_atom_iterator.

atom_iterator structure_end

(

)

Get a reverse_atom_iterator (end of range).

const_atom_iterator structure_end

(

)

const

Get an atom_iterator (end of range).

reverse_atom_iterator structure_rend

(

)

Get a reverse_atom_iterator (end of range).

const_reverse_atom_iterator structure_rend

(

)

const

Get a reverse_atom_iterator (end of range).

size_type num_atoms

(

)

const

Get the size of the Polymer, in atoms.

Runs in linear time with the number of monomers in the Polymer.

virtual std::ostream& print	(	std::ostream &	os,
		size_type	first_atom_num = 1,
		size_type	first_monomer_num = 1
	)			const [virtual]

Print the atoms in a Polymer to an output stream.

Deprecated:

This interface will change when the simplified output system is completed in future versions of the library.

char chain_id

(

)

const

Get the current chain ID value.

void set_chain_id

(

char

chain_id

)

Set the current chain ID value.

void insert	(	iterator	p,
		InputIterator	i,
		InputIterator	j
	)

Reimplemented from BTKSequence< MonomerType, StorageStrategy >.

virtual dictionary const& get_dictionary

(

)

const [virtual]

Implements PolymerStructure.

virtual dictionary& get_dictionary

(

)

[virtual]

Implements PolymerStructure.

void swap

(

self_type &

b

)

self_type const& operator=

(

self_type const &

rhs

)

bool operator==

(

self_type const &

rhs

)

const

bool operator!=

(

self_type const &

rhs

)

const

bool operator<

(

self_type const &

rhs

)

const

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

• polymer.hpp

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