Introduction

This package provides Python bindings for the FreeSASA C Library.

It can be installed using

pip install freesasa

Binaries are available for Python 3.7-3.11 for Mac OS X and Windows, in addition to the source distribution.

Basic calculations

Using defaults everywhere a simple calculation can be carried out as follows (assuming the file 1ubq.pdb is available)

import freesasa

structure = freesasa.Structure("1ubq.pdb")
result = freesasa.calc(structure)
area_classes = freesasa.classifyResults(result, structure)

print "Total : %.2f A2" % result.totalArea()
for key in area_classes:
    print key, ": %.2f A2" % area_classes[key]

Which would give the following output

Total : 4804.06 A2
Polar : 2504.22 A2
Apolar : 2299.84 A2

The following does a high precision L&R calculation

result = freesasa.calc(structure,
                       freesasa.Parameters({'algorithm' : freesasa.LeeRichards,
                                            'n-slices' : 100}))

Using the results from a calculation we can also integrate SASA over a selection of atoms, using a subset of the Pymol selection syntax:

selections = freesasa.selectArea(('alanine, resn ala', 'r1_10, resi 1-10'),
                                 structure, result)
for key in selections:
    print key, ": %.2f A2" % selections[key]

which gives the output

alanine : 120.08 A2
r1_10 : 634.31 A2

Customizing atom classification

This uses the NACCESS parameters (the file naccess.config is available in the share/ directory of the repository).

classifier = freesasa.Classifier("naccess.config")
structure = freesasa.Structure("1ubq.pdb", classifier)
result = freesasa.calc(structure)
area_classes = freesasa.classifyResults(result, structure, classifier)

Classification can be customized also by extending the Classifier interface. The code below is an illustration of a classifier that classes nitrogens separately, and assigns radii based on element only (and crudely).

import freesasa
import re

class DerivedClassifier(freesasa.Classifier):
    # this must be set explicitly in all derived classifiers
    purePython = True

    def classify(self, residueName, atomName):
        if re.match('\s*N', atomName):
            return 'Nitrogen'
        return 'Not-nitrogen'

    def radius(self, residueName, atomName):
        if re.match('\s*N',atomName): # Nitrogen
            return 1.6
        if re.match('\s*C',atomName): # Carbon
            return 1.7
        if re.match('\s*O',atomName): # Oxygen
            return 1.4
        if re.match('\s*S',atomName): # Sulfur
            return 1.8
        return 0;                     # everything else (Hydrogen, etc)

classifier = DerivedClassifier()

# use the DerivedClassifier to calculate atom radii
structure = freesasa.Structure("1ubq.pdb", classifier)
result = freesasa.calc(structure)

# use the DerivedClassifier to classify atoms
area_classes = freesasa.classifyResults(result,structure,classifier)

Of course, this example is somewhat contrived, if we only want the integrated area of nitrogen atoms, the simpler choice would be

selection = freesasa.selectArea('nitrogen, symbol n', structure, result)

However, extending Classifier, as illustrated above, allows classification to arbitrary complexity and also lets us redefine the radii used in the calculation.

Bio.PDB

FreeSASA can also calculate the SASA of a Bio.PDB structure from BioPython

from Bio.PDB import PDBParser
parser = PDBParser()
structure = parser.get_structure("Ubiquitin", "1ubq.pdb")
result, sasa_classes = freesasa.calcBioPDB(structure)

If one needs more control over the analysis the structure can be converted to a Structure using structureFromBioPDB() and the calculation can be performed the normal way using this structure.

Writing a FreeSASA PDB

Here is a simple example on how to turn a calculated result into a PDB file.

import freesasa

structure = freesasa.Structure('2ubq.pdb')
result = freesasa.calc(structure)
result.write_pdb('2ubq.sasa.pdb')

This only works if the input file was parsed with Freesasa.Structure().