FreeSASA Python interface. More...

Data Structures
class	Classifier
	Assigns class and radius to atom by residue and atom name. More...

class	Parameters
	Stores parameter values to be used by calculation. More...

class	Result
	Stores results from SASA calculation. More...

class	Structure
	Represents a protein structure, including its atomic radii. More...

Functions
def	structureArray
	Create array of structures from PDB file. More...

def	calc
	Calculate SASA of Structure. More...

def	classifyResults
	Break SASA result down into classes. More...

def	selectArea (commands, structure, result)
	Sum SASA result over a selection of atoms. More...

def	setVerbosity (verbosity)
	Set global verbosity. More...

def	getVerbosity ()
	Get global verbosity. More...

def	structureFromBioPDB
	Create a freesasa structure from a Bio.PDB structure. More...

def	calcBioPDB
	Calc SASA from Bio.PDB structure. More...

Variables
string	ShrakeRupley = 'ShrakeRupley'
	Used to specify the algorithm by Shrake & Rupley.

string	LeeRichards = 'LeeRichards'
	Used to specify the algorithm by Lee & Richards.

string	polar = 'Polar'
	Used for classification.

string	apolar = 'Apolar'
	Used for classification.

	silent = FREESASA_V_SILENT
	int: Suppress all warnings and errors (used by setVerbosity())

	nowarnings = FREESASA_V_NOWARNINGS
	int: Suppress all warnings but not errors (used by setVerbosity())

	normal = FREESASA_V_NORMAL
	int: Normal verbosity (used by setVerbosity())

	debug = FREESASA_V_DEBUG
	int: Print debug messages (used by setVerbosity())

dictionary	defaultParameters
	The default values for calculation parameters. More...

dictionary	defaultStructureArrayOptions
	Default options for structureArray. More...

Detailed Description

FreeSASA Python interface.

Author: Simon Mitternacht

Copyright: MIT License

A minimal program would be something like

 structure = freesasa.Structure("1abc.pdb")
 result = freesasa.calc(structure)
 print "SASA = %f" % result.totalArea()

See documentation of the classes and functions for how to customize behavior

Function Documentation

def freesasa.structureArray	(	fileName,
		options = `defaultStructureArrayOptions`,
		classifier = `None`
	)

Create array of structures from PDB file.

Split PDB file into several structures by either by treating chains separately, by treating each MODEL as a separate structure, or both.

Parameters

fileName	(str) The PDB file.
options	(dict) Specification for how to read the PDB-file (see def value for options).
classifier	Classifier to assign atoms radii, default is used if none specified.

Exceptions

AssertionError	if fileName is None
AssertionError	if an option value is not recognized
AssertionError	if neither of the options 'separate-chains' and 'separate-models' are specified.
IOError	if can't open file
Exception	if there are problems parsing the input

Returns: An array of Structures

Definition at line 551 of file freesasa.pyx.

def freesasa.calc	(	structure,
		parameters = `None`
	)

Calculate SASA of Structure.

Parameters

structure	Structure to be used
parameters	Parameters to use (if not specified defaults are used)

Returns: A Result object

Exceptions

Exception something went wrong in calculation (see C library error messages)

Definition at line 581 of file freesasa.pyx.

def freesasa.classifyResults	(	result,
		structure,
		classifier = `None`
	)

Break SASA result down into classes.

Parameters

result	Result from sasa calculation.
structure	Structure used in calculation.
classifier	Classifier (if not specified default is used).

Returns: Dictionary with names of classes as keys and their SASA values as values.

Exceptions

Exception Problems with classification, see C library error messages (or Python exceptions if run with derived classifier).

Definition at line 599 of file freesasa.pyx.

def freesasa.selectArea	(	commands,
		structure,
		result
	)

Sum SASA result over a selection of atoms.

Parameters

commands	A list of commands with selections using Pymol syntax, e.g. `"s1, resn ala+arg"` or `"s2, chain A and resi 1-5"` (see Selection syntax).
structure	A Structure.
result	Result from sasa calculation on structure.

Returns: Dictionary with names of selections ("s1","s2",...) as keys, and the corresponding SASA values as values.

Exceptions

Exception Parser failed (typically syntax error), see library error messages.

Definition at line 620 of file freesasa.pyx.

def freesasa.setVerbosity ( verbosity )

Set global verbosity.

Parameters

verbosity Can have values freesasa.silent, freesasa.nowarnings or freesasa.normal

Exceptions

AssertionError if verbosity has illegal value

Definition at line 639 of file freesasa.pyx.

def freesasa.getVerbosity ( )

Get global verbosity.

Returns: Verbosity (freesasa.silent, freesasa.nowarnings or freesasa.normal)

Definition at line 646 of file freesasa.pyx.

def freesasa.structureFromBioPDB	(	bioPDBStructure,
		classifier = `None`,
		options = `Structure.defaultOptions`
	)

Create a freesasa structure from a Bio.PDB structure.

Remarks: Experimental, not thorougly tested yet

Parameters

bioPDBStructure	a Bio.PDB structure
classifier	an optional classifier to specify atomic radii
options	Options supported are 'hetatm', 'skip-unknown' and 'halt-at-unknown'

Returns: a freesasa.Structure

Exceptions

Exception if option 'halt-at-unknown' is selected and unknown atoms are encountered. Passes on exceptions from Structure.addAtom() and Structure.setRadiiWithClassifier().

Definition at line 662 of file freesasa.pyx.

def freesasa.calcBioPDB	(	bioPDBStructure,
		parameters = `Parameters()`,
		classifier = `None`,
		options = `Structure.defaultOptions`
	)

Calc SASA from Bio.PDB structure.

Usage

result, sasa_classes = calcBioPDB(structure, ...)

Remarks: Experimental, not thorougly tested yet

Parameters

bioPDBStructure	A Bio.PDB structure
parameters	A freesasa.Paremeters object
classifier	A freesasa.Classifier object
options	Options supported are 'hetatm', 'skip-unknown' and 'halt-at-unknown'

Returns: A freesasa.Result object and a dictionary with classes defined by the classifier and associated areas

Exceptions

Exception if unknown atom is encountered and the option 'halt-at-unknown' is active. Passes on exceptions from calc(), classifyResults() and structureFromBioPDB().

Definition at line 712 of file freesasa.pyx.

Variable Documentation

dictionary freesasa.defaultParameters

Initial value:

 = {
      'algorithm'    : LeeRichards, 
      'probe-radius' : freesasa_default_parameters.probe_radius,
      'n-points'     : freesasa_default_parameters.shrake_rupley_n_points,
      'n-slices'     : freesasa_default_parameters.lee_richards_n_slices,
      'n-threads'    : freesasa_default_parameters.n_threads 
 }

The default values for calculation parameters.

Definition at line 48 of file freesasa.pyx.

dictionary freesasa.defaultStructureArrayOptions

Initial value:

 = {
       'hetatm' : False, 
       'hydrogen' : False,
       'separate-chains' : True,
       'separate-models' : False
 }

Default options for structureArray.

Defined separately for Doxygen's sake.

Definition at line 524 of file freesasa.pyx.

Data Structures

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation