Module protkit.properties.surface_area
Implements class SurfaceArea to calculate the surface area of proteins.
The ASA or SASA was first described by Lee and Richards in 1971. Shrake and Rupley developed the rolling ball algorithm in 1973.
RASA can be calculated by dividing the ASA by the MaxASA. MasASA values were calculated by Miller et al. (1987).
Levy (2010) describes a method for defining interior, surface, support, core and rim residues of a protein based on ASA calculations.
Abbreviations:
ASA - Accessible Surface Area BASA - Buried Surface Area MaxASA - Maximum Accessible Surface Area RASA - Relative Accessible Surface Area = ASA / MaxASA SASA - Solvent Accessible Surface Area (same as ASA)
Papers referenced in this code:
Lee B., Richards F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. Vol. 55, pp. 279-400.
Levy E.D. (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J. Mol. Biol. Vol. 403, pp. 660-670.
Miller S., Janin J., Lesk A.M., Chothia C. (1987). Interior and surface of monomeric proteins. J. Mol. Biol. Vol. 196, pp. 641-656.
Mitternacht S. (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000 Research, 5:189.
Shrake A., Rupley J.A. (1973) Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. Vol. 79, pp. 351-371.
External packages used in this code:
FreeSASA - https://freesasa.github.io/ Provides C implementations of the Lee-Richards and Shrake-Rupley algorithms with implementation hooks for Python.
Expand source code
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors: Fred Senekal (FS)
# Contact: fred@silicogenesis.com
# License: GPLv3
"""
Implements class `SurfaceArea` to calculate the surface area of proteins.
The ASA or SASA was first described by Lee and Richards in 1971. Shrake and Rupley
developed the rolling ball algorithm in 1973.
RASA can be calculated by dividing the ASA by the MaxASA. MasASA values were calculated
by Miller et al. (1987).
Levy (2010) describes a method for defining interior, surface, support, core and rim
residues of a protein based on ASA calculations.
Abbreviations:
--------------
ASA - Accessible Surface Area
BASA - Buried Surface Area
MaxASA - Maximum Accessible Surface Area
RASA - Relative Accessible Surface Area = ASA / MaxASA
SASA - Solvent Accessible Surface Area (same as ASA)
Papers referenced in this code:
-------------------------------
Lee B., Richards F.M. (1971)
The interpretation of protein structures: estimation of static accessibility.
J. Mol. Biol. Vol. 55, pp. 279-400.
Levy E.D. (2010)
A simple definition of structural regions in proteins and its use in analyzing
interface evolution.
J. Mol. Biol. Vol. 403, pp. 660-670.
Miller S., Janin J., Lesk A.M., Chothia C. (1987).
Interior and surface of monomeric proteins.
J. Mol. Biol. Vol. 196, pp. 641-656.
Mitternacht S. (2016)
FreeSASA: An open source C library for solvent accessible surface area calculations.
F1000 Research, 5:189.
Shrake A., Rupley J.A. (1973)
Environment and exposure to solvent of protein atoms. Lysozyme and insulin.
J. Mol. Biol. Vol. 79, pp. 351-371.
External packages used in this code:
------------------------------------
FreeSASA - https://freesasa.github.io/
Provides C implementations of the Lee-Richards and Shrake-Rupley algorithms
with implementation hooks for Python.
"""
from typing import TYPE_CHECKING
from protkit.structure import Protein
class SurfaceArea:
MAX_ASA_MILLER = {
"ALA": 113.0,
"ARG": 241.0,
"ASN": 158.0,
"ASP": 151.0,
"CYS": 140.0,
"GLN": 189.0,
"GLU": 183.0,
"GLY": 85.0,
"HIS": 194.0,
"ILE": 182.0,
"LEU": 180.0,
"LYS": 211.0,
"MET": 204.0,
"PHE": 218.0,
"PRO": 143.0,
"SER": 122.0,
"THR": 146.0,
"TRP": 259.0,
"TYR": 229.0,
"VAL": 160.0
}
@staticmethod
def surface_area_of_protein(protein: Protein,
assign_attribute: bool = False,
key: str = "surface_area") -> float:
"""
Calculate the surface area of a protein.
Args:
protein (Protein): The protein object for which to calculate the surface area.
assign_attribute (bool): Whether to assign the surface area to the protein object.
key (str): The attribute key to use when assigning the surface area to the protein object.
Returns:
float: The surface area of the protein.
"""
# Calculate the solvent accessible surface area using Lee Richards
# Note the import of the adaptor is done here to avoid circular imports.
from protkit.tools.freesasa_adaptor import FreeSASAAdaptor
freesasa_adaptor = FreeSASAAdaptor(algorithm=FreeSASAAdaptor.LEE_RICHARDS)
sasa = freesasa_adaptor.calculate_surface_area(list(protein.atoms))
if assign_attribute:
index = 0
protein_surface_area = 0
for chain in protein.chains:
chain_surface_area = 0
for residue in chain.residues:
residue_surface_area = 0
for atom in residue.atoms:
atom.set_attribute(key, sasa[index])
residue_surface_area += sasa[index]
index += 1
chain_surface_area += residue_surface_area
residue.set_attribute(key, residue_surface_area)
protein_surface_area += chain_surface_area
chain.set_attribute(key, chain_surface_area)
protein.set_attribute(key, protein_surface_area)
return protein_surface_area
else:
return sum(sasa)Classes
class SurfaceArea-
Expand source code
class SurfaceArea: MAX_ASA_MILLER = { "ALA": 113.0, "ARG": 241.0, "ASN": 158.0, "ASP": 151.0, "CYS": 140.0, "GLN": 189.0, "GLU": 183.0, "GLY": 85.0, "HIS": 194.0, "ILE": 182.0, "LEU": 180.0, "LYS": 211.0, "MET": 204.0, "PHE": 218.0, "PRO": 143.0, "SER": 122.0, "THR": 146.0, "TRP": 259.0, "TYR": 229.0, "VAL": 160.0 } @staticmethod def surface_area_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "surface_area") -> float: """ Calculate the surface area of a protein. Args: protein (Protein): The protein object for which to calculate the surface area. assign_attribute (bool): Whether to assign the surface area to the protein object. key (str): The attribute key to use when assigning the surface area to the protein object. Returns: float: The surface area of the protein. """ # Calculate the solvent accessible surface area using Lee Richards # Note the import of the adaptor is done here to avoid circular imports. from protkit.tools.freesasa_adaptor import FreeSASAAdaptor freesasa_adaptor = FreeSASAAdaptor(algorithm=FreeSASAAdaptor.LEE_RICHARDS) sasa = freesasa_adaptor.calculate_surface_area(list(protein.atoms)) if assign_attribute: index = 0 protein_surface_area = 0 for chain in protein.chains: chain_surface_area = 0 for residue in chain.residues: residue_surface_area = 0 for atom in residue.atoms: atom.set_attribute(key, sasa[index]) residue_surface_area += sasa[index] index += 1 chain_surface_area += residue_surface_area residue.set_attribute(key, residue_surface_area) protein_surface_area += chain_surface_area chain.set_attribute(key, chain_surface_area) protein.set_attribute(key, protein_surface_area) return protein_surface_area else: return sum(sasa)Class variables
var MAX_ASA_MILLER
Static methods
def surface_area_of_protein(protein: Protein, assign_attribute: bool = False, key: str = 'surface_area') ‑> float-
Calculate the surface area of a protein.
Args
protein:Protein- The protein object for which to calculate the surface area.
assign_attribute:bool- Whether to assign the surface area to the protein object.
key:str- The attribute key to use when assigning the surface area to the protein object.
Returns
float- The surface area of the protein.
Expand source code
@staticmethod def surface_area_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "surface_area") -> float: """ Calculate the surface area of a protein. Args: protein (Protein): The protein object for which to calculate the surface area. assign_attribute (bool): Whether to assign the surface area to the protein object. key (str): The attribute key to use when assigning the surface area to the protein object. Returns: float: The surface area of the protein. """ # Calculate the solvent accessible surface area using Lee Richards # Note the import of the adaptor is done here to avoid circular imports. from protkit.tools.freesasa_adaptor import FreeSASAAdaptor freesasa_adaptor = FreeSASAAdaptor(algorithm=FreeSASAAdaptor.LEE_RICHARDS) sasa = freesasa_adaptor.calculate_surface_area(list(protein.atoms)) if assign_attribute: index = 0 protein_surface_area = 0 for chain in protein.chains: chain_surface_area = 0 for residue in chain.residues: residue_surface_area = 0 for atom in residue.atoms: atom.set_attribute(key, sasa[index]) residue_surface_area += sasa[index] index += 1 chain_surface_area += residue_surface_area residue.set_attribute(key, residue_surface_area) protein_surface_area += chain_surface_area chain.set_attribute(key, chain_surface_area) protein.set_attribute(key, protein_surface_area) return protein_surface_area else: return sum(sasa)