PDBAtomDecorator Class Template Reference

A mixin-style atom decorator that provides support for PDB ATOM record data. More...

#include <pdb_atom_decorator.hpp>

Inheritance diagram for PDBAtomDecorator:


Public Types
typedef chemical_type_system::monomer_id_type	monomer_id_type
Public Member Functions
	IMPORT_ATOM_TYPES (base_type)
	PDBAtomDecorator (chemical_type_system const &cts, bool is_hetatom, int atom_number, atom_id_type atom_type, char alt_loc, monomer_id_type res_type, char chain_id, int res_number, char insert_code,::BTK::MATH::BTKVector const &position, double occupancy=1.0, double b_factor=1.0, std::string const &segment_id="", element_id_type element_type=element_id_type(), std::string charge="")
	Construct a PDBAtom from information in a PDB ATOM or HETATM record.
virtual std::ostream &	print (std::ostream &os, int atom_number, int group_number, char chain_id, std::string const &group_name) const
virtual std::ostream &	print (std::ostream &os) const
self_type const &	operator= (self_type const &rhs)
bool	operator== (self_type const &rhs) const
bool	operator!= (self_type const &rhs) const

int	res_number () const
	PDBAtom-specific access methods.
void	set_res_number (int num)
	PDBAtom-specific access methods.
monomer_id_type	res_type () const
	PDBAtom-specific access methods.
void	set_res_type (monomer_id_type type)
	PDBAtom-specific access methods.
std::string	res_name () const
	PDBAtom-specific access methods.
char	chain_id () const
	PDBAtom-specific access methods.
void	set_chain_id (char id)
	PDBAtom-specific access methods.
char	alt_loc () const
	PDBAtom-specific access methods.
void	set_alt_loc (char altloc)
	PDBAtom-specific access methods.
char	insert_code () const
	PDBAtom-specific access methods.
void	set_insert_code (char code)
	PDBAtom-specific access methods.
double	occupancy () const
	PDBAtom-specific access methods.
void	set_occupancy (double occ)
	PDBAtom-specific access methods.
double	b_factor () const
	PDBAtom-specific access methods.
void	set_b_factor (double bfactor)
	PDBAtom-specific access methods.
std::string const &	segment_id () const
	PDBAtom-specific access methods.
void	set_segment_id (std::string const &s_id)
	PDBAtom-specific access methods.
std::string const &	charge () const
	PDBAtom-specific access methods.
void	set_charge (std::string const &charge)
	PDBAtom-specific access methods.
bool	is_hetatom () const
	PDBAtom-specific access methods.
void	set_hetatom_flag (bool h)
	PDBAtom-specific access methods.

Detailed Description

template<typename BaseAtomType = BTK::ATOMS::Atom<>>
class BTK::ATOMS::PDBAtomDecorator< BaseAtomType >

A mixin-style atom decorator that provides support for PDB ATOM record data.

This is an atom decorator class that provides support for the storage and retrieval of data used in Brookhaven Protein Data Bank (PDB) ATOM records.

Because it is frequently necessary to use PDB I/O on a custom atom type (e.g. a previously-decorated Atom object), this object allows for the addition of PDB data to any atom type that conforms to the AtomConcept.

See pdb_atom.hpp for an example of atom decoration using this class.

Examples:: gyration_radius.cpp.

Member Typedef Documentation

typedef chemical_type_system::monomer_id_type monomer_id_type

Constructor & Destructor Documentation

PDBAtomDecorator ( )

Default constructor.

PDBAtomDecorator	(	::BTK::MATH::BTKVector const &	pos,
		atom_id_type	type,
		element_id_type	element_type,
		int	number = `0`,
		chemical_type_system const &	cts = `chemical_type_system()`
	)

Construct from position, types and number.

PDBAtomDecorator	(	chemical_type_system const &	cts,
		bool	is_hetatom,
		int	atom_number,
		atom_id_type	atom_type,
		char	alt_loc,
		monomer_id_type	res_type,
		char	chain_id,
		int	res_number,
		char	insert_code,
		::BTK::MATH::BTKVector const &	position,
		double	occupancy = `1.0`,
		double	b_factor = `1.0`,
		std::string const &	segment_id = `""`,
		element_id_type	element_type = `element_id_type()`,
		std::string	charge = `""`
	)

Construct a PDBAtom from information in a PDB ATOM or HETATM record.

PDBAtomDecorator ( self_type const & src )

Default copy constructor.

Called iff the base atom types are identical.

PDBAtomDecorator ( PDBAtomDecorator< AtomType > const & src )

Foreign atom type copy constructor.

Called iff the base atom types are different.