Classifier

Interface for classifying atoms as polar/apolar and determining their radius based on atom name and residue name. More...

Typedefs
typedef struct freesasa_classifier	freesasa_classifier
	Classifier struct. More...

Enumerations
enum	freesasa_atom_class { FREESASA_ATOM_APOLAR = 0 , FREESASA_ATOM_POLAR = 1 , FREESASA_ATOM_UNKNOWN = 2 }
	Atom classes. More...

Functions
freesasa_classifier *	freesasa_classifier_from_file (FILE *file)
	Generate a classifier from a config-file. More...
void	freesasa_classifier_free (freesasa_classifier *classifier)
	Frees a classifier object. More...
double	freesasa_classifier_radius (const freesasa_classifier *classifier, const char *res_name, const char *atom_name)
	Use a classifier to determine the radius of a given atom. More...
freesasa_atom_class	freesasa_classifier_class (const freesasa_classifier *classifier, const char *res_name, const char *atom_name)
	Use a classifier to determine the class of a given atom. More...
const char *	freesasa_classifier_class2str (freesasa_atom_class atom_class)
	Names for freesasa_atom_class. More...
const char *	freesasa_classifier_name (const freesasa_classifier *classifier)
	The name of a classifier. More...

Variables
const freesasa_classifier	freesasa_protor_classifier
	ProtOr classifier. More...
const freesasa_classifier	freesasa_naccess_classifier
	NACCESS classifier. More...
const freesasa_classifier	freesasa_oons_classifier
	OONS classifier. More...

Detailed Description

Interface for classifying atoms as polar/apolar and determining their radius based on atom name and residue name.

Typedef Documentation

freesasa_classifier

typedef struct freesasa_classifier freesasa_classifier

Classifier struct.

Struct that can be used to determine classes (polar/apolar) and radii of atoms. Initiated from freesasa_classifier_from_file(). The classifiers freesasa_default_classifier, freesasa_protor_classifier, freesasa_naccess_classifier and freesasa_classifier are const classifiers that can be used directly.

Definition at line 374 of file freesasa.h.

Enumeration Type Documentation

freesasa_atom_class

enum freesasa_atom_class

Atom classes.

Atoms can be of the classes Apolar, Polar or Unknown.

Definition at line 163 of file freesasa.h.

Function Documentation

freesasa_classifier_from_file()

freesasa_classifier * freesasa_classifier_from_file

(

FILE *

file

)

Generate a classifier from a config-file.

Input file format described in Classifier configuration files

Return value is dynamically allocated, should be freed with freesasa_classifier_free().

Parameters

file	File containing configuration

Returns

The generated classifier. NULL if there were problems parsing or reading the file or memory allocation problem.

See also

Classifier configuration files

freesasa_classifier_free()

void freesasa_classifier_free

(

freesasa_classifier *

classifier

)

Frees a classifier object.

Parameters

classifier

The classifier.

freesasa_classifier_radius()

double freesasa_classifier_radius	(	const freesasa_classifier *	classifier,
		const char *	res_name,
		const char *	atom_name
	)

Use a classifier to determine the radius of a given atom.

Parameters

classifier	The classifier.
res_name	The residue name (ALA/VAL/U/C/...)
atom_name	The atom name (CA/N/CB/...)

Returns

The radius, negative if atom unknown.

freesasa_classifier_class()

freesasa_atom_class freesasa_classifier_class	(	const freesasa_classifier *	classifier,
		const char *	res_name,
		const char *	atom_name
	)

Use a classifier to determine the class of a given atom.

Parameters

classifier	The classifier.
res_name	The residue name (ALA/VAL/U/C/...)
atom_name	The atom name (CA/N/CB/...)

Returns

The class.

freesasa_classifier_class2str()

const char * freesasa_classifier_class2str

(

freesasa_atom_class

atom_class

)

Names for freesasa_atom_class.

Parameters

atom_class

The class.

Returns

Name of class.

freesasa_classifier_name()

const char * freesasa_classifier_name

(

const freesasa_classifier *

classifier

)

The name of a classifier.

Parameters

classifier

The classifier.

Returns

The name of the classifier.

Variable Documentation

freesasa_protor_classifier

const freesasa_classifier freesasa_protor_classifier

extern

ProtOr classifier.

Classifier using ProtOr radii and classes.

freesasa_naccess_classifier

const freesasa_classifier freesasa_naccess_classifier

extern

NACCESS classifier.

Classifier using NACCESS radii and classes.

freesasa_oons_classifier

const freesasa_classifier freesasa_oons_classifier

extern

OONS classifier.

Classifier using OONS radii and classes.