Classes¶

Classifier¶

class freesasa.Classifier¶

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 config-files with a custom classifier.

If initialized without arguments the default classifier is used.

Derived classifiers must 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.

__init__()¶

Constructor.

If no file is provided the default classifier is used.

Parameters

fileName (str) – Name of file with classifier configuration.

Raises

IOError – Problem opening/reading file
Exception – Problem parsing provided configuration or initializing defaults

__new__(**kwargs)¶: Create and return a new object. See help(type) for accurate signature.

classify()¶

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

Class name

Return type

str

static getStandardClassifier()¶

Get a standard classifier (ProtOr, OONS or NACCESS)

Parameters: type (str) – The type, can have values 'protor', 'oons' or 'naccess'
Returns: The requested classifier
Return type: Classifier
Raises: Exception – If type not recognized

radius()¶

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.

Return type

float

Parameters¶

class freesasa.Parameters¶

Stores parameter values to be used by calculation.

Default parameters are

Parameters.defaultParameters = {
    '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
}

Variables: defaultParamers (dict) – The default parameters

__init__()¶

Initializes Parameters object.

Parameters: param (dict) – optional argument to specify parameter-values, see Parameters.defaultParameters.
Raises: AssertionError – Invalid parameter values supplied

__new__(**kwargs)¶: Create and return a new object. See help(type) for accurate signature.

algorithm()¶

Get algorithm.

Returns: Name of algorithm
Return type: str

nPoints()¶

Get number of test points in Shrake & Rupley algorithm.

Returns: Number of points.
Return type: int

nSlices()¶

Get the number of slices per atom in Lee & Richards algorithm.

Returns: Number of slices.
Return type: int

nThreads()¶

Get the number of threads to use in calculations.

Returns: Number of threads.
Return type: int

probeRadius()¶

Get probe radius.

Returns: Probe radius in Å
Return type: float

setAlgorithm()¶

Set algorithm.

Parameters

alg (str) – algorithm name, only allowed values are
:py:data:`freesasa.ShrakeRupley` and :py:data:`freesasa.LeeRichards`

Raises

AssertionError – unknown algorithm specified

setNPoints()¶

Set number of test points in Shrake & Rupley algorithm.

Parameters: n (int) – Number of points (> 0).
Raises: AssertionError – n <= 0.

setNSlices()¶

Set the number of slices per atom in Lee & Richards algorithm.

Parameters: n (int) – Number of slices (> 0)
Raises: AssertionError – n <= 0

setNThreads()¶

Set the number of threads to use in calculations.

Parameters: n (int) – Number of points (> 0)
Raises: AssertionError – n <= 0

setProbeRadius()¶

Set probe radius.

Parameters: r (float) – probe radius in Å (>= 0)
Raises: AssertionError – r < 0

Result¶

class freesasa.Result¶

Stores results from SASA calculation.

The type of object returned by freesasa.calc(), not intended to be used outside of that context.

atomArea()¶

SASA for a given atom.

Parameters: i (int) – index of atom.
Returns: SASA of atom i in Å^2.
Return type: float
Raises: AssertionError – If no results have been associated with the object or if index is out of bounds

nAtoms()¶

Number of atoms in the results.

Returns: Number of atoms.
Return type: int

residueAreas()¶

Get SASA for all residues including relative areas if available for the classifier used.

Returns dictionary of results where first dimension is chain label and the second dimension residue number. I.e. result["A"]["5"] gives the ResidueArea of residue number 5 in chain A.

Relative areas are normalized to 1, but can be > 1 for residues in unusual conformations or at the ends of chains.

Returns: dictionary
Raises: AssertionError – If no results or structure has been associated with the object.

totalArea()¶

Total SASA.

Returns: The total area in Å^2.
Raises: AssertionError – If no results have been associated with the object.

ResidueArea¶

class freesasa.ResidueArea¶

Stores absolute and relative areas for a residue

Variables

residueType (str) – Type of Residue
residueNumber (str) – Residue number
hasRelativeAreas (bool) – False if there was noe reference area to calculate relative areas from
total (float) – Total SASA of residue
polar (float) – Polar SASA
apolar (float) – Apolar SASA
mainChain (float) – Main chain SASA
sideChain (float) – Side chain SASA
relativeTotal (float) – Relative total SASA
relativePolar (float) – Relative polar SASA
relativeApolar (float) – Relative Apolar SASA
relativeMainChain (float) – Relative main chain SASA
relativeSideChain (float) – Relative side chain SASA

Structure¶

class freesasa.Structure¶

Represents a protein structure, including its atomic radii.

Initialized from PDB-file. Calculates atomic radii using default classifier, or custom one provided as argument to initalizer.

Default options are

Structure.defaultOptions = {
    'hetatm' : False,          # False: skip HETATM
                               # True: include HETATM

    'hydrogen' : False,        # False: ignore hydrogens
                               # True: include hydrogens

    'join-models' : False,     # False: Only use the first MODEL
                               # True: Include all MODELs

    'skip-unknown' : False,    # False: Guess radius for unknown atoms
                               #     based on element
                               # True: Skip unknown atoms

    'halt-at-unknown' : False  # False: set radius for unknown atoms,
                               #    that can not be guessed to 0.
                               # True: Throw exception on unknown atoms.
}

Variables: defaultOptions – Default options for reading structure from PDB.

__init__()¶

Constructor

If a PDB file is provided, the structure will be constructed based on the file. If not, this simply initializes an empty structure with the given classifier and options. Atoms will then have to be added manually using :py:meth:.Structure.addAtom()`.

Parameters

fileName (str) – PDB file (if None empty structure generated).
classifier – An optional Classifier to calculate atomic radii, uses default if none provided. This classifier will also be used in calls to Structure.addAtom() but only if it’s the default classifier, one of the standard classifiers from Classifier.getStandardClassifier(), or defined by a config-file (i.e. if it uses the underlying C API).
options (dict) – specify which atoms and models to include, default is Structure.defaultOptions

Raises

IOError – Problem opening/reading file.
Exception – Problem parsing PDB file or calculating atomic radii.
Exception – If option ‘halt-at-unknown’ selected and unknown atom encountered.

__new__(**kwargs)¶: Create and return a new object. See help(type) for accurate signature.

addAtom()¶

Add atom to structure.

This function is meant to be used if the structure was not initialized from a PDB. The options and classifier passed to the constructor for the Structure will be used (see the documentation of the constructor for restrictions). The radii set by the classifier can be overriden by calling Structure.setRadiiWithClassifier() afterwards.

There are no restraints on string lengths for the arguments, but the atom won’t be added if the classifier doesn’t recognize the atom and also cannot deduce its element from the atom name.

Parameters

atomName (str) – atom name (e.g. “CA”)
residueName (str) – residue name (e.g. “ALA”)
residueNumber (str or int) – residue number (e.g. ‘12’) or integer. Some PDBs have residue-numbers that aren’t regular numbers. Therefore treated as a string primarily.
chainLabel (str) – 1-character string with chain label (e.g. ‘A’) x,y,z (float): coordinates

Raises

Exception – Residue-number invalid
AssertionError –

addAtoms()¶

Add multiple atoms to structure.

Parameters

atomNames (list) – list of atom name (e.g. [“CA”])
residueNames (list) – list of residue name (e.g. [“ALA”])
residueNumbers (list) – list of residue number (e.g. [‘12’]) or integer. Some PDBs have residue-numbers that aren’t regular numbers. Therefore treated as a string primarily.
chainLabels (list) – list of 1-character string with chain label (e.g. [‘A’]) xs,ys,zs (list): list of coordinates

Raises

AssertionError – inconsistent size of input args

atomName()¶

Get atom name

Parameters: i (int) – Atom index.
Returns: Atom name as 4-character string.
Return type: str
Raises: AssertionError – if index out of range or Structure not properly initialized.

chainLabel()¶

Get chain label for given atom.

Parameters: i (int) – Atom index.
Returns: Chain label as 1-character string.
Return type: str
Raises: AssertionError – if index out of range or Structure not properly initialized

coord()¶

Get coordinates of given atom.

Parameters: i (int) – Atom index.
Returns: array of x, y, and z coordinates
Return type: list
Raises: AssertionError – if index out of range or Structure not properly initialized

nAtoms()¶

Number of atoms.

Returns: Number of atoms
Return type: int
Raises: AssertionError – if not properly initialized

radius()¶

Radius of atom.

Parameters: i (int) – Index of atom.
Returns: Radius in Å.
Return type: float
Raises: AssertionError – if index out of bounds, object not properly initalized.

residueName()¶

Get residue name of given atom.

Parameters: i (int) – Atom index.
Returns: Residue name as 3-character string.
Return type: str
Raises: AssertionError – if index out of range or Structure not properly initialized

residueNumber()¶

Get residue number for given atom.

Residue number will include the insertion code if there is one.

Parameters: i (int) – Atom index.
Returns: Residue number as 5-character string (last character is either whitespace or insertion code)
Return type: str
Raises: AssertionError – if index out of range or Structure not properly initialized

setRadii()¶

Set atomic radii from an array

Parameters: radiusArray (list) – Array of atomic radii in Ångström, should have nAtoms() elements.
Raises: AssertionError – if radiusArray has wrong dimension, structure not properly initialized, or if the array contains negative radii (not properly classified?)

setRadiiWithClassifier()¶

Assign radii to atoms in structure using a classifier.

Parameters: classifier – A Classifier to use to calculate radii.
Raises: AssertionError – if structure not properly initialized

setRadius()¶

Set radius for a given atom

Parameters

atomIndex (int) – Index of atom
radius (float) – Value of radius

Raises

AssertionError – if index out of bounds, radius negative, or structure not properly initialized