Module protkit.tools.freesasa_adaptor

Implements class FreeSASAAdaptor to calculate the accessible surface area (ASA) of proteins using the FreeSASA library.

#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors:  Fred Senekal (FS), Claudio Jardim (CJ)
# Contact:  fred@silicogenesis.com
# License:  GPLv3

"""
Implements class `FreeSASAAdaptor` to calculate the accessible surface area (ASA)
of proteins using the FreeSASA library.
"""

import freesasa
from typing import List
import numpy as np

from protkit.structure import Atom
from protkit.tasks.surface_area_calculator import SurfaceAreaCalculator
from protkit.properties.vdw_radius import VDWRadius


class FreeSASAAdaptor(SurfaceAreaCalculator):
    """
    Adapter class for the FreeSASA tool.

    This class provides concrete implementations of surface area calculations
    by interfacing with the FreeSASA library and updating Protein objects with
    the calculated surface properties.
    """
    LEE_RICHARDS = freesasa.LeeRichards
    SHRAKE_RUPLEY = freesasa.ShrakeRupley

    DEFAULT_PROBE_RADIUS = 1.4
    DEFAULT_LEE_RICHARDS_SLICES = 20
    DEFAULT_SHRAKE_RUPLEY_POINTS = 100
    DEFAULT_N_THREADS = 1

    def __init__(self,
                 algorithm: str = LEE_RICHARDS,
                 probe_radius: float = DEFAULT_PROBE_RADIUS,
                 n_points: int = DEFAULT_SHRAKE_RUPLEY_POINTS,
                 n_slices: int = DEFAULT_LEE_RICHARDS_SLICES,
                 n_threads: int = DEFAULT_N_THREADS):
        """
        Initialize the FreeSASA adaptor with the desired settings.

        Args:
            algorithm (str): The algorithm to use for surface area calculations.
                Options: LEE_RICHARDS, SHRAKE_RUPLEY
            probe_radius (float): The radius of the probe to use for surface area calculations.
            n_points (int): The number of points to use for the surface area calculations.
            n_slices (int): The number of slices to use for the surface area calculations.
            n_threads (int): The number of threads to use for the surface area calculations.
        """
        super().__init__()

        self._algorithm = algorithm
        self._probe_radius = probe_radius
        self._n_points = n_points
        self._n_slices = n_slices
        self._n_threads = n_threads

    def calculate_surface_area(self, atoms: List[Atom]) -> List[float]:
        """
        Calculate the accessible surface area of a protein using FreeSASA.

        Args:
            atoms (List[Atom]): A list of Atom objects whose surface area needs to be calculated.

        Returns:
            List[float]: A list of surface areas for each atom in the input list.
        """

        # Extract the atom coordinates and van der Waals radii
        num_atoms = len(atoms)
        atom_coordinates = np.array([(atom.x, atom.y, atom.z) for atom in atoms])
        vdw_radii = [VDWRadius.SURFACE_RADIUS.get(atom.element, 2.0) for atom in atoms]

        # Calculate the surface area of the protein
        parameters = freesasa.Parameters({
            'algorithm': self._algorithm,
            'probe-radius': self._probe_radius,
            'n-points': self._n_points,
            'n-slices': self._n_slices,
            'n-threads': self._n_threads
        })

        # Calculate the solvent accessible surface area
        result = freesasa.calcCoord(atom_coordinates.flatten(), vdw_radii, parameters=parameters)
        atom_sasa = [result.atomArea(i) for i in range(num_atoms)]

        # assert (sum(atom_sasa) == result.totalArea())
        # for i in range(len(vdw_radii)):
        #     atom_sasa[i] = result.atomArea(i)
        # atom_sasa_total = result.totalArea()

        # if self._assign_to_protein:
        #     protein.assign_list(list(protein.atoms), atom_sasa, "sasa")
        #     protein.set_attribute("sasa_total", atom_sasa_total)
        #
        #     for chain in protein.chains:
        #         for residue in chain.residues:
        #             residue.sum_attribute("sasa")
        #         chain.sum_attribute("sasa")

        return atom_sasa

Classes

class FreeSASAAdaptor (algorithm: str = 'LeeRichards', probe_radius: float = 1.4, n_points: int = 100, n_slices: int = 20, n_threads: int = 1)

Adapter class for the FreeSASA tool.

This class provides concrete implementations of surface area calculations by interfacing with the FreeSASA library and updating Protein objects with the calculated surface properties.

Initialize the FreeSASA adaptor with the desired settings.

Args

algorithm : str

The algorithm to use for surface area calculations. Options: LEE_RICHARDS, SHRAKE_RUPLEY

probe_radius : float

The radius of the probe to use for surface area calculations.

n_points : int

The number of points to use for the surface area calculations.

n_slices : int

The number of slices to use for the surface area calculations.

n_threads : int

The number of threads to use for the surface area calculations.

Expand source code

class FreeSASAAdaptor(SurfaceAreaCalculator):
    """
    Adapter class for the FreeSASA tool.

    This class provides concrete implementations of surface area calculations
    by interfacing with the FreeSASA library and updating Protein objects with
    the calculated surface properties.
    """
    LEE_RICHARDS = freesasa.LeeRichards
    SHRAKE_RUPLEY = freesasa.ShrakeRupley

    DEFAULT_PROBE_RADIUS = 1.4
    DEFAULT_LEE_RICHARDS_SLICES = 20
    DEFAULT_SHRAKE_RUPLEY_POINTS = 100
    DEFAULT_N_THREADS = 1

    def __init__(self,
                 algorithm: str = LEE_RICHARDS,
                 probe_radius: float = DEFAULT_PROBE_RADIUS,
                 n_points: int = DEFAULT_SHRAKE_RUPLEY_POINTS,
                 n_slices: int = DEFAULT_LEE_RICHARDS_SLICES,
                 n_threads: int = DEFAULT_N_THREADS):
        """
        Initialize the FreeSASA adaptor with the desired settings.

        Args:
            algorithm (str): The algorithm to use for surface area calculations.
                Options: LEE_RICHARDS, SHRAKE_RUPLEY
            probe_radius (float): The radius of the probe to use for surface area calculations.
            n_points (int): The number of points to use for the surface area calculations.
            n_slices (int): The number of slices to use for the surface area calculations.
            n_threads (int): The number of threads to use for the surface area calculations.
        """
        super().__init__()

        self._algorithm = algorithm
        self._probe_radius = probe_radius
        self._n_points = n_points
        self._n_slices = n_slices
        self._n_threads = n_threads

    def calculate_surface_area(self, atoms: List[Atom]) -> List[float]:
        """
        Calculate the accessible surface area of a protein using FreeSASA.

        Args:
            atoms (List[Atom]): A list of Atom objects whose surface area needs to be calculated.

        Returns:
            List[float]: A list of surface areas for each atom in the input list.
        """

        # Extract the atom coordinates and van der Waals radii
        num_atoms = len(atoms)
        atom_coordinates = np.array([(atom.x, atom.y, atom.z) for atom in atoms])
        vdw_radii = [VDWRadius.SURFACE_RADIUS.get(atom.element, 2.0) for atom in atoms]

        # Calculate the surface area of the protein
        parameters = freesasa.Parameters({
            'algorithm': self._algorithm,
            'probe-radius': self._probe_radius,
            'n-points': self._n_points,
            'n-slices': self._n_slices,
            'n-threads': self._n_threads
        })

        # Calculate the solvent accessible surface area
        result = freesasa.calcCoord(atom_coordinates.flatten(), vdw_radii, parameters=parameters)
        atom_sasa = [result.atomArea(i) for i in range(num_atoms)]

        # assert (sum(atom_sasa) == result.totalArea())
        # for i in range(len(vdw_radii)):
        #     atom_sasa[i] = result.atomArea(i)
        # atom_sasa_total = result.totalArea()

        # if self._assign_to_protein:
        #     protein.assign_list(list(protein.atoms), atom_sasa, "sasa")
        #     protein.set_attribute("sasa_total", atom_sasa_total)
        #
        #     for chain in protein.chains:
        #         for residue in chain.residues:
        #             residue.sum_attribute("sasa")
        #         chain.sum_attribute("sasa")

        return atom_sasa

Ancestors

• SurfaceAreaCalculator
• abc.ABC

Class variables

var DEFAULT_LEE_RICHARDS_SLICES

var DEFAULT_N_THREADS

var DEFAULT_PROBE_RADIUS

var DEFAULT_SHRAKE_RUPLEY_POINTS

var LEE_RICHARDS

var SHRAKE_RUPLEY

Methods

def calculate_surface_area(self, atoms: List[Atom]) ‑> List[float]

Calculate the accessible surface area of a protein using FreeSASA.

Args

atoms : List[Atom]

A list of Atom objects whose surface area needs to be calculated.

Returns

List[float]

A list of surface areas for each atom in the input list.

Expand source code

def calculate_surface_area(self, atoms: List[Atom]) -> List[float]:
    """
    Calculate the accessible surface area of a protein using FreeSASA.

    Args:
        atoms (List[Atom]): A list of Atom objects whose surface area needs to be calculated.

    Returns:
        List[float]: A list of surface areas for each atom in the input list.
    """

    # Extract the atom coordinates and van der Waals radii
    num_atoms = len(atoms)
    atom_coordinates = np.array([(atom.x, atom.y, atom.z) for atom in atoms])
    vdw_radii = [VDWRadius.SURFACE_RADIUS.get(atom.element, 2.0) for atom in atoms]

    # Calculate the surface area of the protein
    parameters = freesasa.Parameters({
        'algorithm': self._algorithm,
        'probe-radius': self._probe_radius,
        'n-points': self._n_points,
        'n-slices': self._n_slices,
        'n-threads': self._n_threads
    })

    # Calculate the solvent accessible surface area
    result = freesasa.calcCoord(atom_coordinates.flatten(), vdw_radii, parameters=parameters)
    atom_sasa = [result.atomArea(i) for i in range(num_atoms)]

    # assert (sum(atom_sasa) == result.totalArea())
    # for i in range(len(vdw_radii)):
    #     atom_sasa[i] = result.atomArea(i)
    # atom_sasa_total = result.totalArea()

    # if self._assign_to_protein:
    #     protein.assign_list(list(protein.atoms), atom_sasa, "sasa")
    #     protein.set_attribute("sasa_total", atom_sasa_total)
    #
    #     for chain in protein.chains:
    #         for residue in chain.residues:
    #             residue.sum_attribute("sasa")
    #         chain.sum_attribute("sasa")

    return atom_sasa

Inherited members

• SurfaceAreaCalculator:
  • calculate_surface_area_for_protein