Module protkit.properties.hydrophobicity
Implements class Hydrophobicity to calculate the hydrophobicity and
hydrophobicity class of a residue, chain, protein or sequence.
Hydrophobicity is calculated based on the Kyte-Doolittle scale.
For chains, the hydrophobicity is the sum of the hydrophobicity values of the residues in the chain. For proteins, the hydrophobicity is the sum of the hydrophobicity values of the chains in the protein.
Calculated values can be added as attributes to the respective objects.
For more information, see: https://en.wikipedia.org/wiki/Hydrophobicity_scales#Kyte%E2%80%93Doolittle_scale
The Kyte-Doolittle scale was defined in: Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
Also see: https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html
Expand source code
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors: Fred Senekal (FS)
# Contact: fred@silicogenesis.com
# License: GPLv3
"""
Implements class `Hydrophobicity` to calculate the hydrophobicity and
hydrophobicity class of a residue, chain, protein or sequence.
Hydrophobicity is calculated based on the Kyte-Doolittle scale.
For chains, the hydrophobicity is
the sum of the hydrophobicity values of the residues in the chain. For
proteins, the hydrophobicity is the sum of the hydrophobicity values of
the chains in the protein.
Calculated values can be added as attributes to the respective objects.
For more information, see:
https://en.wikipedia.org/wiki/Hydrophobicity_scales#Kyte%E2%80%93Doolittle_scale
The Kyte-Doolittle scale was defined in:
Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the
hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
Also see:
https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html
"""
from typing import List
from protkit.structure.residue import Residue
from protkit.structure.chain import Chain
from protkit.structure.protein import Protein
from protkit.seq.sequence import Sequence
class Hydrophobicity:
# Hydrophobicity values on the Kyte-Doolittle scale.
HYDROPHOBICITY = {
"ALA": 1.8,
"ARG": -4.5,
"ASN": -3.5,
"ASP": -3.5,
"CYS": 2.5,
"GLN": -3.5,
"GLU": -3.5,
"GLY": -0.4,
"HIS": -3.2,
"ILE": 4.5,
"LEU": 3.8,
"LYS": -3.9,
"MET": 1.9,
"PHE": 2.8,
"PRO": -1.6,
"SER": -0.8,
"THR": -0.7,
"TRP": -0.9,
"TYR": -1.3,
"VAL": 4.2,
"A": 1.8,
"R": -4.5,
"N": -3.5,
"D": -3.5,
"C": 2.5,
"Q": -3.5,
"E": -3.5,
"G": -0.4,
"H": -3.2,
"I": 4.5,
"L": 3.8,
"K": -3.9,
"M": 1.9,
"F": 2.8,
"P": -1.6,
"S": -0.8,
"T": -0.7,
"W": -0.9,
"Y": -1.3,
"V": 4.2
}
# Hydrophobicity classes as assigned by IMGT. See
# https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html?
# The classes are:
# Hydrophobic: I, V, L, F, C, M, A, W
# Neutral: G, T, S, Y, P, H
# Hydrophilic: N, D, Q, E, K, R
# Note that IMGT assigns Tryptophan (-0.9 on the Kyte-Doolittle scale) to the
# hydrophobic class, while it is often considered to be neutral.
# Also note that Histidine (-3.2 on the Kyte-Doolittle scale) is considered to be
# neutral by IMGT, while it is often considered to be hydrophilic.
UNDEFINED = 0
HYDROPHOBIC = 1
NEUTRAL = 2
HYDROPHILIC = 3
HYDROPHOBICITY_CLASS_STRING = [
"Undefined",
"Hydrophobic",
"Neutral",
"Hydrophilic"
]
HYDROPHOBICITY_CLASS = {
"ALA": HYDROPHOBIC,
"ARG": HYDROPHILIC,
"ASN": HYDROPHILIC,
"ASP": HYDROPHILIC,
"CYS": HYDROPHOBIC,
"GLN": HYDROPHILIC,
"GLU": HYDROPHILIC,
"GLY": NEUTRAL,
"HIS": NEUTRAL,
"ILE": HYDROPHOBIC,
"LEU": HYDROPHOBIC,
"LYS": HYDROPHILIC,
"MET": HYDROPHOBIC,
"PHE": HYDROPHOBIC,
"PRO": NEUTRAL,
"SER": NEUTRAL,
"THR": NEUTRAL,
"TRP": HYDROPHOBIC,
"TYR": NEUTRAL,
"VAL": HYDROPHOBIC,
"A": HYDROPHOBIC,
"R": HYDROPHILIC,
"N": HYDROPHILIC,
"D": HYDROPHILIC,
"C": HYDROPHOBIC,
"Q": HYDROPHILIC,
"E": HYDROPHILIC,
"G": NEUTRAL,
"H": NEUTRAL,
"I": HYDROPHOBIC,
"L": HYDROPHOBIC,
"K": HYDROPHILIC,
"M": HYDROPHOBIC,
"F": HYDROPHOBIC,
"P": NEUTRAL,
"S": NEUTRAL,
"T": NEUTRAL,
"W": HYDROPHOBIC,
"Y": NEUTRAL,
"V": HYDROPHOBIC
}
@staticmethod
def hydrophobicity_of_residue(residue: Residue,
assign_attribute: bool = False,
key: str = "hydrophobicity") -> float:
"""
Returns the hydrophobicity value of the residue.
Args:
residue (Residue): The residue for which the hydrophobicity value will be returned.
assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the residue.
key (str): The name of the attribute that will be added to the residue.
Returns:
float: The hydrophobicity value of the residue.
"""
hydrophobicity = Hydrophobicity.HYDROPHOBICITY.get(residue.residue_type, 0.0)
if assign_attribute:
residue.set_attribute(key, hydrophobicity)
return hydrophobicity
@staticmethod
def hydrophobicity_class_of_residue(residue: Residue,
assign_attribute: bool = False,
key: str = "hydrophobicity_class") -> int:
"""
Returns the hydrophobicity class of the residue.
Args:
residue (Residue): The residue for which the hydrophobicity class will be returned.
assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the residue.
key (str): The name of the attribute that will be added to the residue.
Returns:
int: The hydrophobicity class of the residue.
"""
hydrophobicity_class = Hydrophobicity.HYDROPHOBICITY_CLASS.get(residue.residue_type, Hydrophobicity.UNDEFINED)
if assign_attribute:
residue.set_attribute(key, hydrophobicity_class)
return hydrophobicity_class
@staticmethod
def hydrophobicity_of_chain(chain: Chain,
assign_attribute: bool = False,
key: str = "hydrophobicity") -> float:
"""
Returns the hydrophobicity value of the chain.
Args:
chain (Chain): The chain for which the hydrophobicity value will be returned.
assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the chain.
key (str): The name of the attribute that will be added to the chain.
Returns:
float: The hydrophobicity value of the chain.
"""
hydrophobicity = sum(Hydrophobicity.hydrophobicity_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues)
if assign_attribute:
chain.set_attribute(key, hydrophobicity)
return hydrophobicity
@staticmethod
def hydrophobicity_classes_of_chain(chain: Chain,
assign_attribute: bool = False,
key: str = "hydrophobicity_class") -> List[int]:
"""
Returns the hydrophobicity class of the chain.
Args:
chain (Chain): The chain for which the hydrophobicity class will be returned.
assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the chain.
key (str): The name of the attribute that will be added to the chain.
Returns:
list: The hydrophobicity classes of the residues of the chain.
"""
hydrophobicity_classes = [Hydrophobicity.hydrophobicity_class_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues]
if assign_attribute:
chain.set_attribute(key, hydrophobicity_classes)
return hydrophobicity_classes
@staticmethod
def hydrophobicity_of_protein(protein: Protein,
assign_attribute: bool = False,
key: str = "hydrophobicity") -> float:
"""
Returns the hydrophobicity value of the protein.
Args:
protein (Protein): The protein for which the hydrophobicity value will be returned.
assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the protein.
key (str): The name of the attribute that will be added to the protein.
Returns
float: The hydrophobicity value of the protein.
"""
hydrophobicity = sum(Hydrophobicity.hydrophobicity_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains)
if assign_attribute:
protein.set_attribute(key, hydrophobicity)
return hydrophobicity
@staticmethod
def hydrophobicity_classes_of_protein(protein: Protein,
assign_attribute: bool = False,
key: str = "hydrophobicity_class") -> List[List[int]]:
"""
Returns the hydrophobicity classes of the residues of the protein.
Args:
protein (Protein): The protein for which the hydrophobicity class will be returned.
assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the protein.
key (str): The name of the attribute that will be added to the protein.
Returns:
list: The hydrophobicity classes of the residues of the protein.
"""
hydrophobicity_classes = [Hydrophobicity.hydrophobicity_classes_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains]
if assign_attribute:
protein.set_attribute(key, hydrophobicity_classes)
return hydrophobicity_classes
@staticmethod
def hydrophobicity_of_sequence(sequence: Sequence,
assign_attribute: bool = False,
key: str = "hydrophobicity") -> float:
"""
Returns the hydrophobicity value of the sequence.
Args:
sequence (Sequence): The sequence for which the hydrophobicity value will be returned.
assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the sequence.
key (str): The name of the attribute that will be added to the sequence.
Returns:
float: The hydrophobicity value of the sequence.
"""
hydrophobicity = sum(Hydrophobicity.HYDROPHOBICITY.get(residue, 0.0) for residue in sequence)
if assign_attribute:
sequence.set_attribute(key, hydrophobicity)
return hydrophobicity
@staticmethod
def hydrophobicity_classes_of_sequence(sequence: Sequence,
assign_attribute: bool = False,
key: str = "hydrophobicity_class") -> List[int]:
"""
Returns the hydrophobicity classes of the residues of the sequence.
Args:
sequence (Sequence): The sequence for which the hydrophobicity class will be returned.
assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the sequence.
key (str): The name of the attribute that will be added to the sequence.
Returns:
list: The hydrophobicity classes of the residues of the sequence.
"""
hydrophobicity_classes = [Hydrophobicity.HYDROPHOBICITY_CLASS.get(residue, Hydrophobicity.UNDEFINED) for residue in sequence]
if assign_attribute:
sequence.set_attribute(key, hydrophobicity_classes)
return hydrophobicity_classesClasses
class Hydrophobicity-
Expand source code
class Hydrophobicity: # Hydrophobicity values on the Kyte-Doolittle scale. HYDROPHOBICITY = { "ALA": 1.8, "ARG": -4.5, "ASN": -3.5, "ASP": -3.5, "CYS": 2.5, "GLN": -3.5, "GLU": -3.5, "GLY": -0.4, "HIS": -3.2, "ILE": 4.5, "LEU": 3.8, "LYS": -3.9, "MET": 1.9, "PHE": 2.8, "PRO": -1.6, "SER": -0.8, "THR": -0.7, "TRP": -0.9, "TYR": -1.3, "VAL": 4.2, "A": 1.8, "R": -4.5, "N": -3.5, "D": -3.5, "C": 2.5, "Q": -3.5, "E": -3.5, "G": -0.4, "H": -3.2, "I": 4.5, "L": 3.8, "K": -3.9, "M": 1.9, "F": 2.8, "P": -1.6, "S": -0.8, "T": -0.7, "W": -0.9, "Y": -1.3, "V": 4.2 } # Hydrophobicity classes as assigned by IMGT. See # https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html? # The classes are: # Hydrophobic: I, V, L, F, C, M, A, W # Neutral: G, T, S, Y, P, H # Hydrophilic: N, D, Q, E, K, R # Note that IMGT assigns Tryptophan (-0.9 on the Kyte-Doolittle scale) to the # hydrophobic class, while it is often considered to be neutral. # Also note that Histidine (-3.2 on the Kyte-Doolittle scale) is considered to be # neutral by IMGT, while it is often considered to be hydrophilic. UNDEFINED = 0 HYDROPHOBIC = 1 NEUTRAL = 2 HYDROPHILIC = 3 HYDROPHOBICITY_CLASS_STRING = [ "Undefined", "Hydrophobic", "Neutral", "Hydrophilic" ] HYDROPHOBICITY_CLASS = { "ALA": HYDROPHOBIC, "ARG": HYDROPHILIC, "ASN": HYDROPHILIC, "ASP": HYDROPHILIC, "CYS": HYDROPHOBIC, "GLN": HYDROPHILIC, "GLU": HYDROPHILIC, "GLY": NEUTRAL, "HIS": NEUTRAL, "ILE": HYDROPHOBIC, "LEU": HYDROPHOBIC, "LYS": HYDROPHILIC, "MET": HYDROPHOBIC, "PHE": HYDROPHOBIC, "PRO": NEUTRAL, "SER": NEUTRAL, "THR": NEUTRAL, "TRP": HYDROPHOBIC, "TYR": NEUTRAL, "VAL": HYDROPHOBIC, "A": HYDROPHOBIC, "R": HYDROPHILIC, "N": HYDROPHILIC, "D": HYDROPHILIC, "C": HYDROPHOBIC, "Q": HYDROPHILIC, "E": HYDROPHILIC, "G": NEUTRAL, "H": NEUTRAL, "I": HYDROPHOBIC, "L": HYDROPHOBIC, "K": HYDROPHILIC, "M": HYDROPHOBIC, "F": HYDROPHOBIC, "P": NEUTRAL, "S": NEUTRAL, "T": NEUTRAL, "W": HYDROPHOBIC, "Y": NEUTRAL, "V": HYDROPHOBIC } @staticmethod def hydrophobicity_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the residue. Args: residue (Residue): The residue for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the residue. key (str): The name of the attribute that will be added to the residue. Returns: float: The hydrophobicity value of the residue. """ hydrophobicity = Hydrophobicity.HYDROPHOBICITY.get(residue.residue_type, 0.0) if assign_attribute: residue.set_attribute(key, hydrophobicity) return hydrophobicity @staticmethod def hydrophobicity_class_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> int: """ Returns the hydrophobicity class of the residue. Args: residue (Residue): The residue for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the residue. key (str): The name of the attribute that will be added to the residue. Returns: int: The hydrophobicity class of the residue. """ hydrophobicity_class = Hydrophobicity.HYDROPHOBICITY_CLASS.get(residue.residue_type, Hydrophobicity.UNDEFINED) if assign_attribute: residue.set_attribute(key, hydrophobicity_class) return hydrophobicity_class @staticmethod def hydrophobicity_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the chain. Args: chain (Chain): The chain for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the chain. key (str): The name of the attribute that will be added to the chain. Returns: float: The hydrophobicity value of the chain. """ hydrophobicity = sum(Hydrophobicity.hydrophobicity_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues) if assign_attribute: chain.set_attribute(key, hydrophobicity) return hydrophobicity @staticmethod def hydrophobicity_classes_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> List[int]: """ Returns the hydrophobicity class of the chain. Args: chain (Chain): The chain for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the chain. key (str): The name of the attribute that will be added to the chain. Returns: list: The hydrophobicity classes of the residues of the chain. """ hydrophobicity_classes = [Hydrophobicity.hydrophobicity_class_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues] if assign_attribute: chain.set_attribute(key, hydrophobicity_classes) return hydrophobicity_classes @staticmethod def hydrophobicity_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the protein. Args: protein (Protein): The protein for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the protein. key (str): The name of the attribute that will be added to the protein. Returns float: The hydrophobicity value of the protein. """ hydrophobicity = sum(Hydrophobicity.hydrophobicity_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains) if assign_attribute: protein.set_attribute(key, hydrophobicity) return hydrophobicity @staticmethod def hydrophobicity_classes_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> List[List[int]]: """ Returns the hydrophobicity classes of the residues of the protein. Args: protein (Protein): The protein for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the protein. key (str): The name of the attribute that will be added to the protein. Returns: list: The hydrophobicity classes of the residues of the protein. """ hydrophobicity_classes = [Hydrophobicity.hydrophobicity_classes_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains] if assign_attribute: protein.set_attribute(key, hydrophobicity_classes) return hydrophobicity_classes @staticmethod def hydrophobicity_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the sequence. Args: sequence (Sequence): The sequence for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the sequence. key (str): The name of the attribute that will be added to the sequence. Returns: float: The hydrophobicity value of the sequence. """ hydrophobicity = sum(Hydrophobicity.HYDROPHOBICITY.get(residue, 0.0) for residue in sequence) if assign_attribute: sequence.set_attribute(key, hydrophobicity) return hydrophobicity @staticmethod def hydrophobicity_classes_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> List[int]: """ Returns the hydrophobicity classes of the residues of the sequence. Args: sequence (Sequence): The sequence for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the sequence. key (str): The name of the attribute that will be added to the sequence. Returns: list: The hydrophobicity classes of the residues of the sequence. """ hydrophobicity_classes = [Hydrophobicity.HYDROPHOBICITY_CLASS.get(residue, Hydrophobicity.UNDEFINED) for residue in sequence] if assign_attribute: sequence.set_attribute(key, hydrophobicity_classes) return hydrophobicity_classesClass variables
var HYDROPHILICvar HYDROPHOBICvar HYDROPHOBICITYvar HYDROPHOBICITY_CLASSvar HYDROPHOBICITY_CLASS_STRINGvar NEUTRALvar UNDEFINED
Static methods
def hydrophobicity_class_of_residue(residue: Residue, assign_attribute: bool = False, key: str = 'hydrophobicity_class') ‑> int-
Returns the hydrophobicity class of the residue.
Args
residue:Residue- The residue for which the hydrophobicity class will be returned.
assign_attribute:bool- If True, the hydrophobicity class will be added as an attribute to the residue.
key:str- The name of the attribute that will be added to the residue.
Returns
int- The hydrophobicity class of the residue.
Expand source code
@staticmethod def hydrophobicity_class_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> int: """ Returns the hydrophobicity class of the residue. Args: residue (Residue): The residue for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the residue. key (str): The name of the attribute that will be added to the residue. Returns: int: The hydrophobicity class of the residue. """ hydrophobicity_class = Hydrophobicity.HYDROPHOBICITY_CLASS.get(residue.residue_type, Hydrophobicity.UNDEFINED) if assign_attribute: residue.set_attribute(key, hydrophobicity_class) return hydrophobicity_class def hydrophobicity_classes_of_chain(chain: Chain, assign_attribute: bool = False, key: str = 'hydrophobicity_class') ‑> List[int]-
Returns the hydrophobicity class of the chain.
Args
chain:Chain- The chain for which the hydrophobicity class will be returned.
assign_attribute:bool- If True, the hydrophobicity class will be added as an attribute to the chain.
key:str- The name of the attribute that will be added to the chain.
Returns
list- The hydrophobicity classes of the residues of the chain.
Expand source code
@staticmethod def hydrophobicity_classes_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> List[int]: """ Returns the hydrophobicity class of the chain. Args: chain (Chain): The chain for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the chain. key (str): The name of the attribute that will be added to the chain. Returns: list: The hydrophobicity classes of the residues of the chain. """ hydrophobicity_classes = [Hydrophobicity.hydrophobicity_class_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues] if assign_attribute: chain.set_attribute(key, hydrophobicity_classes) return hydrophobicity_classes def hydrophobicity_classes_of_protein(protein: Protein, assign_attribute: bool = False, key: str = 'hydrophobicity_class') ‑> List[List[int]]-
Returns the hydrophobicity classes of the residues of the protein.
Args
protein:Protein- The protein for which the hydrophobicity class will be returned.
assign_attribute:bool- If True, the hydrophobicity class will be added as an attribute to the protein.
key:str- The name of the attribute that will be added to the protein.
Returns
list- The hydrophobicity classes of the residues of the protein.
Expand source code
@staticmethod def hydrophobicity_classes_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> List[List[int]]: """ Returns the hydrophobicity classes of the residues of the protein. Args: protein (Protein): The protein for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the protein. key (str): The name of the attribute that will be added to the protein. Returns: list: The hydrophobicity classes of the residues of the protein. """ hydrophobicity_classes = [Hydrophobicity.hydrophobicity_classes_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains] if assign_attribute: protein.set_attribute(key, hydrophobicity_classes) return hydrophobicity_classes def hydrophobicity_classes_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = 'hydrophobicity_class') ‑> List[int]-
Returns the hydrophobicity classes of the residues of the sequence.
Args
sequence:Sequence- The sequence for which the hydrophobicity class will be returned.
assign_attribute:bool- If True, the hydrophobicity class will be added as an attribute to the sequence.
key:str- The name of the attribute that will be added to the sequence.
Returns
list- The hydrophobicity classes of the residues of the sequence.
Expand source code
@staticmethod def hydrophobicity_classes_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = "hydrophobicity_class") -> List[int]: """ Returns the hydrophobicity classes of the residues of the sequence. Args: sequence (Sequence): The sequence for which the hydrophobicity class will be returned. assign_attribute (bool): If True, the hydrophobicity class will be added as an attribute to the sequence. key (str): The name of the attribute that will be added to the sequence. Returns: list: The hydrophobicity classes of the residues of the sequence. """ hydrophobicity_classes = [Hydrophobicity.HYDROPHOBICITY_CLASS.get(residue, Hydrophobicity.UNDEFINED) for residue in sequence] if assign_attribute: sequence.set_attribute(key, hydrophobicity_classes) return hydrophobicity_classes def hydrophobicity_of_chain(chain: Chain, assign_attribute: bool = False, key: str = 'hydrophobicity') ‑> float-
Returns the hydrophobicity value of the chain.
Args
chain:Chain- The chain for which the hydrophobicity value will be returned.
assign_attribute:bool- If True, the hydrophobicity value will be added as an attribute to the chain.
key:str- The name of the attribute that will be added to the chain.
Returns
float- The hydrophobicity value of the chain.
Expand source code
@staticmethod def hydrophobicity_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the chain. Args: chain (Chain): The chain for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the chain. key (str): The name of the attribute that will be added to the chain. Returns: float: The hydrophobicity value of the chain. """ hydrophobicity = sum(Hydrophobicity.hydrophobicity_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues) if assign_attribute: chain.set_attribute(key, hydrophobicity) return hydrophobicity def hydrophobicity_of_protein(protein: Protein, assign_attribute: bool = False, key: str = 'hydrophobicity') ‑> float-
Returns the hydrophobicity value of the protein.
Args
protein:Protein- The protein for which the hydrophobicity value will be returned.
assign_attribute:bool- If True, the hydrophobicity value will be added as an attribute to the protein.
key:str- The name of the attribute that will be added to the protein.
Returns float: The hydrophobicity value of the protein.
Expand source code
@staticmethod def hydrophobicity_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the protein. Args: protein (Protein): The protein for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the protein. key (str): The name of the attribute that will be added to the protein. Returns float: The hydrophobicity value of the protein. """ hydrophobicity = sum(Hydrophobicity.hydrophobicity_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains) if assign_attribute: protein.set_attribute(key, hydrophobicity) return hydrophobicity def hydrophobicity_of_residue(residue: Residue, assign_attribute: bool = False, key: str = 'hydrophobicity') ‑> float-
Returns the hydrophobicity value of the residue.
Args
residue:Residue- The residue for which the hydrophobicity value will be returned.
assign_attribute:bool- If True, the hydrophobicity value will be added as an attribute to the residue.
key:str- The name of the attribute that will be added to the residue.
Returns
float- The hydrophobicity value of the residue.
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@staticmethod def hydrophobicity_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the residue. Args: residue (Residue): The residue for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the residue. key (str): The name of the attribute that will be added to the residue. Returns: float: The hydrophobicity value of the residue. """ hydrophobicity = Hydrophobicity.HYDROPHOBICITY.get(residue.residue_type, 0.0) if assign_attribute: residue.set_attribute(key, hydrophobicity) return hydrophobicity def hydrophobicity_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = 'hydrophobicity') ‑> float-
Returns the hydrophobicity value of the sequence.
Args
sequence:Sequence- The sequence for which the hydrophobicity value will be returned.
assign_attribute:bool- If True, the hydrophobicity value will be added as an attribute to the sequence.
key:str- The name of the attribute that will be added to the sequence.
Returns
float- The hydrophobicity value of the sequence.
Expand source code
@staticmethod def hydrophobicity_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = "hydrophobicity") -> float: """ Returns the hydrophobicity value of the sequence. Args: sequence (Sequence): The sequence for which the hydrophobicity value will be returned. assign_attribute (bool): If True, the hydrophobicity value will be added as an attribute to the sequence. key (str): The name of the attribute that will be added to the sequence. Returns: float: The hydrophobicity value of the sequence. """ hydrophobicity = sum(Hydrophobicity.HYDROPHOBICITY.get(residue, 0.0) for residue in sequence) if assign_attribute: sequence.set_attribute(key, hydrophobicity) return hydrophobicity