Atom Class Template Reference

A minimal Atom class. More...

#include <atom.hpp>

Inheritance diagram for Atom:

List of all members.

Public Types
typedef base_type::dictionary	atom_dictionary
	The type of the atom dictionary.
typedef id_type	atom_id_type
	The type of the atom ID for this class (same as the ID type).
typedef chemical_type_system::element_dictionary	element_dictionary
	The type of the element dictionary.
typedef chemical_type_system::element_id_type	element_id_type
	The type of the element ID for this class.
typedef TS	chemical_type_system
	The type of the ChemicalTypeSystem for this class.
typedef base_type::dictionary	dictionary
	The type of the dictionary for this class.
typedef base_type::id_type	id_type
	The ID type for this class (same as the atom ID type).
Public Member Functions
	Atom ()
	Default constructor.
	Atom (BTK::MATH::BTKVector const &pos, atom_id_type type, element_id_type etype, int number=0, chemical_type_system const &ts=chemical_type_system())
	Construct from data.
	Atom (self_type const &src)
	Copy constructor.
virtual	~Atom ()
virtual dictionary const &	get_dictionary () const
virtual dictionary &	get_dictionary ()
element_id_type	element_type () const
	Get the element type.
void	set_element_type (element_id_type et)
	Set the element type.
std::string	element_name () const
	Get the element name.
int	number () const
	Get the atom number.
void	set_number (int number)
	Set the atom number.
BTK::MATH::BTKVector const &	position () const
	Get the atom position.
void	set_position (BTK::MATH::BTKVector const &position)
	Set the atom position.
bool	selected () const
	Is this atom selected?
void	select (bool s=true) const
	Set the selection flag for this atom.
virtual std::ostream &	print (std::ostream &os, int atom_number=1, int group_number=1, char chain_id= ' ', std::string const &group_name="", bool is_hetatom=false, char alt_loc= ' ', char i_code= ' ', double occupancy=1.0, double b_factor=1.0, std::string const &seg_id="", std::string const &element_name="", std::string const &charge="") const
	Print an atom to a stream, in PDB format.
self_type const &	operator= (self_type const &src)
	Assignment operator.
bool	operator== (self_type const &rhs) const
	Test atom equality.
bool	operator!= (self_type const &rhs) const
	Test atom inequality.

---

Detailed Description

template<typename TS = BTK::IO::DefaultTypeSystem>
class BTK::ATOMS::Atom< TS >

A minimal Atom class.

Todo:

Make this class abstract, so that decorated atoms cannot be used in mixed-type assignments.

This is a lightweight class that meets all of the requirements of the AtomConcept. It is intended to be a base class for further decoration and customization by the user of the library.

Element and atom types are enforced at compile time through the use of TypeSystem objects, which specify the atom and element ID types used by Atom, as well as the type dictionaries used to associate ID values to atom and element names. If not specified by the user, every Atom uses the DefaultTypeSystem object, which is a generic TypeSystem that provides dynamic name resolution for atom types.

---

Member Typedef Documentation

typedef TS chemical_type_system

The type of the ChemicalTypeSystem for this class.

Reimplemented from ChemicallyTypedObject< TS, TS::atom_dictionary >.

typedef base_type::dictionary dictionary

The type of the dictionary for this class.

Reimplemented from ChemicallyTypedObject< TS, TS::atom_dictionary >.

typedef base_type::id_type id_type

The ID type for this class (same as the atom ID type).

Reimplemented from ChemicallyTypedObject< TS, TS::atom_dictionary >.

typedef base_type::dictionary atom_dictionary

The type of the atom dictionary.

typedef id_type atom_id_type

The type of the atom ID for this class (same as the ID type).

typedef chemical_type_system::element_dictionary element_dictionary

The type of the element dictionary.

typedef chemical_type_system::element_id_type element_id_type

The type of the element ID for this class.

---

Constructor & Destructor Documentation

Atom

(

)

Default constructor.

Atom	(	BTK::MATH::BTKVector const &	pos,
		atom_id_type	type,
		element_id_type	etype,
		int	number = 0,
		chemical_type_system const &	ts = chemical_type_system()
	)

Construct from data.

Parameters:

	pos	The position of the atom.
	type	The type of the atom.
	element_type	The element type of the atom.
	number	The number/index of the atom.
	ts	An instance of the TypeSystem for this Atom class.

Atom

(

self_type const &

src

)

Copy constructor.

virtual ~Atom

(

)

[virtual]

---

Member Function Documentation

virtual dictionary const& get_dictionary

(

)

const [virtual]

Implements ChemicallyTypedObject< TS, TS::atom_dictionary >.

virtual dictionary& get_dictionary

(

)

[virtual]

Implements ChemicallyTypedObject< TS, TS::atom_dictionary >.

element_id_type element_type

(

)

const

Get the element type.

void set_element_type

(

element_id_type

et

)

Set the element type.

std::string element_name

(

)

const

Get the element name.

int number

(

)

const

Get the atom number.

void set_number

(

int

number

)

Set the atom number.

BTK::MATH::BTKVector const& position

(

)

const

Get the atom position.

void set_position

(

BTK::MATH::BTKVector const &

position

)

Set the atom position.

bool selected

(

)

const

Is this atom selected?

void select

(

bool

s = true

)

const

Set the selection flag for this atom.

virtual std::ostream& print	(	std::ostream &	os,
		int	atom_number = 1,
		int	group_number = 1,
		char	chain_id = ' ',
		std::string const &	group_name = "",
		bool	is_hetatom = false,
		char	alt_loc = ' ',
		char	i_code = ' ',
		double	occupancy = 1.0,
		double	b_factor = 1.0,
		std::string const &	seg_id = "",
		std::string const &	element_name = "",
		std::string const &	charge = ""
	)			const [virtual]

Print an atom to a stream, in PDB format.

Deprecated:

Todo:

Simplify the stream output system. PDB-formatted output should be relegated to specialized PDB classes, so that simple classes (like Atom) don't have to have complicated methods (like Atom::print()) that are only complex due to PDB output requirements.

self_type const& operator=

(

self_type const &

src

)

Assignment operator.

Todo:

The Atom class should be made abstract, and the assignment operator protected.

bool operator==

(

self_type const &

rhs

)

const

Test atom equality.

Two atoms are equivalent iff their types and positions are equivalent.

bool operator!=

(

self_type const &

rhs

)

const

Test atom inequality.

---

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

• atom.hpp

---