freesasa 2.0.3

Calculate solvent accessible surface areas of proteins

.. currentmodule:: freesasa

Introduction
============

This package provides Python bindings for the `FreeSASA C Library
<https://github.com/mittinatten/freesasa>`_.

It can be installed using

.. code::

pip install freesasa

Binaries are available for Python 2.7, 3.4, 3.5 and 3.6 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)

.. code:: python

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

.. code::

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

The following does a high precision L&R calculation

.. code:: python

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`_:

.. _selection syntax: http://freesasa.github.io/doxygen/Selection.html

.. code:: python

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

.. code::

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).

.. code:: python

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 :py:class:`.Classifier`
interface. The code below is an illustration of a classifier that
classes nitrogens separately, and assigns radii based on element only
(and crudely).

.. code:: python

import freesasa
import re

class DerivedClassifier(Classifier):
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

.. code:: python

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


However, extending :py:class:`.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

.. code:: python

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 :py:class:`.Structure` using :py:func:`.structureFromBioPDB()`
and the calculation can be performed the normal way using this
structure.