Radius_of_atom< NT, Atom > Class Template Reference

#include <atom_classifier.h>

Public Types
typedef Atom	Query_type
typedef std::string	Key_type
typedef NT	Value_type

Public Member Functions
	Radius_of_atom (const NT &radius, const unsigned &index)
	Radius_of_atom (std::stringstream &ss, unsigned index)

Static Public Member Functions
template<class Dictionary , class Vector_properties >
static unsigned	default_loader (Dictionary &dict, Vector_properties &vect)
static std::string	make_key (const Atom &atom)
template<class Dictionary >
static unsigned	add_classification (std::stringstream &ss, Dictionary &dict)
static void	handle_extra (std::stringstream &ss)
static int &	index_of_default ()

Detailed Description

template<class NT, class Atom>
class ESBTL::Radius_of_atom< NT, Atom >

A property class associating a radius to an atom.

Template Parameters

NT	is the number type used for the radius.
Atom	is the atom type.

Member Typedef Documentation

Key_type

typedef std::string Key_type

The type of the hash key

Query_type

typedef Atom Query_type

The type on which the queries are made,

Value_type

typedef NT Value_type

The number type of the property stored, here the radius.

Constructor & Destructor Documentation

Radius_of_atom() [1/2]

Radius_of_atom ( const NT &  radius, const unsigned &  index  )

inline

Constructor

Parameters

radius	is the radius associated to this property class.
index	is the index of the property.

Radius_of_atom() [2/2]

Radius_of_atom ( std::stringstream &  ss, unsigned  index  )

inline

Constructor

Parameters

ss	is a string stream containing information about the property. ss must contains the radius associated to index (ex: 1.4).
index	is the index of the property.

Member Function Documentation

add_classification()

static unsigned add_classification ( std::stringstream &  ss, Dictionary &  dict  )

inlinestatic

Function adding the classification of an atom type.

Template Parameters

Dictionary

an associative container, mapping a Query_type to the index of a property.

Parameters

ss	is a string stream containing the classification of an atom type. ss must contains in this order the residue name, the atom name and the index of the property (ex: ALA N 5)
dict	is the container mapping atoms to the index of a property.

default_loader()

static unsigned default_loader ( Dictionary &  dict, Vector_properties &  vect  )

inlinestatic

Function filling default radius of atoms. Current implementation uses radii from Tsai J, Taylor R, Chothia C, Gerstein M. J Mol Biol. 1999 Jul 2;290(1):253-66.

Template Parameters

Dictionary	an associative container, mapping a Query_type to the index of a property.
Vector_properties	is a vector storing the properties.

Parameters

dict	is the container mapping atoms to the index of a property.
vect	is a vector storing properties.

handle_extra()

static void handle_extra ( std::stringstream &  ss )

inlinestatic

Unused function in that class (but definition needed by the classifier).

Parameters

ss	a string stream.

index_of_default()

static int& index_of_default ( )

inlinestatic

Function indicating the index of the property assigned to an unknown atom type. By default this value is -1, which indicate to the classifier that unknown atoms are not expected.

make_key()

static std::string make_key ( const Atom &  atom )

inlinestatic

Function defining a unique identifier of an atom type.

Parameters

atom	is an atom.