Functions

calc

Calculate SASA of Structure

calcBioPDB

Calc SASA from BioPython PDB structure.

calcCoord

Calculate SASA for a set of coordinates and radii

classifyResults

Break SASA result down into classes.

getVerbosity

Get global verbosity

selectArea

Sum SASA result over a selection of atoms

setVerbosity

Set global verbosity
freesasa.calc()

Calculate SASA of Structure

Parameters

  • structure – Structure to be used

  • parameters – Parameters to use (if not specified defaults are used)

Returns

The results

Return type

Result

Raises

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

freesasa.calcBioPDB()

Calc SASA from BioPython PDB structure.

Usage:

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

Experimental, not thorougly tested yet

Parameters

  • bioPDBStructure – A Bio.PDB structure

  • parameters – A Parameters object (uses default if none specified)

  • classifier – A Classifier object (uses default if none specified)

  • options (dict) – Options supported are ‘hetatm’, ‘skip-unknown’ and ‘halt-at-unknown’ (uses Structure.defaultOptions if none specified

Returns

A Result object, a dictionary with classes defined by the classifier and associated areas, and a dictionary of the type returned by Result.residueAreas().

Raises

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

freesasa.calcCoord()

Calculate SASA for a set of coordinates and radii

Parameters

  • coord (list) – array of size 3*N with atomic coordinates (x1, y1, z1, x2, y2, z2, …, x_N, y_N, z_N).

  • radii (list) – array of size N with atomic radii (r_1, r_2, …, r_N).

  • parameters – Parameters to use (if not specified, defaults are used)

Raises

  • AssertionError – mismatched array-sizes

  • Exception – Out of memory

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

freesasa.classifyResults()

Break SASA result down into classes.

Parameters

  • result – Result from SASA calculation.

  • structure – Structure used in calculation.

  • classifier – Classifier to use (if not specified default is used).

Returns

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

Return type

dict

Raises

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

freesasa.getVerbosity()

Get global verbosity

Returns

Verbosity silent, nowarnings or normal

Return type

int

freesasa.setVerbosity()

Set global verbosity

Parameters

verbosity (int) – Can have values silent, nowarnings or normal

Raises

AssertionError – if verbosity has illegal value

freesasa.selectArea()

Sum SASA result over a selection of atoms

Parameters

  • commands (list) – A list of commands with selections using Pymol syntax, e.g. "s1, resn ala+arg" or "s2, chain A and resi 1-5". See select-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.

Return type

dict

Raises

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

freesasa.structureArray()

Create array of structures from PDB file.

Split PDB file into several structures by either by treating chains separately and/or by treating each MODEL as a separate structure and/or grouping chains.

Parameters

  • fileName (str) – The PDB file.

  • options (dict) – Specification for how to read the PDB-file (see Structure.defaultStructureArrayOptions for options and default value).

  • classifier – Classifier to assign atoms radii, default is used if none specified.

Returns

An array of Structure

Return type

list

Raises

  • 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

freesasa.structureFromBioPDB()

Create a freesasa structure from a Bio.PDB structure

Experimental, not thorougly tested yet. Structures generated this way will not preserve whitespace in residue numbers, etc, as in Structure.

Parameters

  • bioPDBStructure – a Bio.PDB structure

  • classifier – an optional Classifier to specify atomic radii

  • options (dict) – Options supported are ‘hetatm’, ‘skip-unknown’ and ‘halt-at-unknown’

Returns

The structure

Return type

Structure

Raises

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