FreeSASA  2.0.3
Open source SASA calculations
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Typedefs | Enumerations | Functions | Variables
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_classifierfreesasa_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

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 322 of file freesasa.h.

Enumeration Type Documentation

Atom classes.

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

Definition at line 155 of file freesasa.h.

Function Documentation

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
fileFile 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
void freesasa_classifier_free ( freesasa_classifier classifier)

Frees a classifier object.

Parameters
classifierThe classifier.
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
classifierThe classifier.
res_nameThe residue name (ALA/VAL/U/C/...)
atom_nameThe atom name (CA/N/CB/...)
Returns
The radius, negative if atom unknown.
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
classifierThe classifier.
res_nameThe residue name (ALA/VAL/U/C/...)
atom_nameThe atom name (CA/N/CB/...)
Returns
The class.
const char* freesasa_classifier_class2str ( freesasa_atom_class  atom_class)

Names for freesasa_atom_class.

Parameters
atom_classThe class.
Returns
Name of class.
const char* freesasa_classifier_name ( const freesasa_classifier classifier)

The name of a classifier.

Parameters
classifierThe classifier.
Returns
The name of the classifier.

Variable Documentation

const freesasa_classifier freesasa_protor_classifier

ProtOr classifier.

Classifier using ProtOr radii and classes.

const freesasa_classifier freesasa_naccess_classifier

NACCESS classifier.

Classifier using NACCESS radii and classes.

const freesasa_classifier freesasa_oons_classifier

OONS classifier.

Classifier using OONS radii and classes.