freesasa.Classifier Class Reference

Assigns class and radius to atom by residue and atom name. More...

Public Member Functions
def	__cinit__
	Constructor. More...
def	__dealloc__ (self)
	The destructor.
def	classify (self, residueName, atomName)
	Class of atom. More...
def	radius (self, residueName, atomName)
	Radius of atom. More...

Detailed Description

Assigns class and radius to atom by residue and atom name.

Subclasses derived from Classifier can be used to define custom atomic radii and/or classes. Can also be initialized from a configuration file with a custom classifier.

Wraps a C freesasa_classifier. If initialized without arguments the default classifier is used.

Residue names should be of the format "ALA","ARG", etc.

Atom names should be of the format "CA", "N", etc.

Definition at line 222 of file freesasa.pyx.

Member Function Documentation

def freesasa.Classifier.__cinit__	(		self,
			fileName = None
	)

Constructor.

If no file is provided the default classifier is used.

See also

Classifier configuration files.

Parameters

fileName

Name of file with classifier configuration.

Exceptions

IOError	Problem opening/reading file
Exception	Problem parsing provided configuration or initializing defaults

Definition at line 235 of file freesasa.pyx.

def freesasa.Classifier.classify	(		self,
			residueName,
			atomName
	)

Class of atom.

Depending on the configuration these classes can be anything, but typically they will be 'Polar' and 'Apolar'. Unrecognized atoms will get the class 'Unknown'.

Parameters

residueName	(str) Residue name ("ALA","ARG",...).
atomName	(str) Atom name ("CA","C",...).

Returns

A string describing the class

Definition at line 262 of file freesasa.pyx.

def freesasa.Classifier.radius	(		self,
			residueName,
			atomName
	)

Radius of atom.

This allows the classifier to be used to calculate the atomic radii used in calculations. Unknown atoms will get a negative radius.

Parameters

residueName	(str) Residue name ("ALA", "ARG", ...).
atomName	(str) Atom name ("CA", "C", ...).

Returns

The radius in Å.

Definition at line 277 of file freesasa.pyx.

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

• freesasa.pyx