FreeSASA  2.0.1
Open source SASA calculations
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Public Member Functions | Static Public Attributes
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...
 

Static Public Attributes

 purePython = False
 

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.

Derived classifiers should set the member purePython to True

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

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

Definition at line 224 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
fileNameName of file with classifier configuration.
Exceptions
IOErrorProblem opening/reading file
ExceptionProblem parsing provided configuration or initializing defaults

Definition at line 238 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 272 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 285 of file freesasa.pyx.


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