Module protkit.properties.charge
Implements class Charge to calculate the charge of a residue,
chain, protein or sequence.
Charge values related to residues are defined at: https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html#charge
Expand source code
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors: Fred Senekal (FS)
# Contact: fred@silicogenesis.com
# License: GPLv3
"""
Implements class `Charge` to calculate the charge of a residue,
chain, protein or sequence.
Charge values related to residues are defined at:
https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html#charge
"""
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 Charge:
# Charges of residues as defined by IMGT.
# See: https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html#charge
# Positively charged: R, H, K
# Negatively charged: D, E
# Neutral: A, C, F, G, I, L, M, N, P, Q, S, T, V, W, Y
# As noted by IMGT: The sulfhydryl group of cystein and
# phenolic hydroxyl group of tyrosine show some degree of pH-dependent ionization.
NEUTRAL = 0
POSITIVE = 1
NEGATIVE = -1
RESIDUE_CHARGE = {
"ALA": 0,
"ARG": 1,
"ASN": 0,
"ASP": -1,
"CYS": 0,
"GLN": 0,
"GLU": -1,
"GLY": 0,
"HIS": 1, # Note: The charge of histidine is pH-dependent. A value of 1 is used here, but 0.1 is also common.
"ILE": 0,
"LEU": 0,
"LYS": 1,
"MET": 0,
"PHE": 0,
"PRO": 0,
"SER": 0,
"THR": 0,
"TRP": 0,
"TYR": 0,
"VAL": 0,
"A": 0,
"R": 1,
"N": 0,
"D": -1,
"C": 0,
"Q": 0,
"E": -1,
"G": 0,
"H": 1,
"I": 0,
"L": 0,
"K": 1,
"M": 0,
"F": 0,
"P": 0,
"S": 0,
"T": 0,
"W": 0,
"Y": 0
}
@staticmethod
def charge_of_residue(residue: Residue,
assign_attribute: bool = False,
key: str = "charge") -> int:
"""
Returns the charge of a residue.
Args:
residue (Residue): The residue for which to determine the charge.
assign_attribute (bool): Whether to assign the charge to the residue.
key (str): The key to use for the attribute.
Returns:
int: The charge of the residue.
"""
charge = Charge.RESIDUE_CHARGE.get(residue.residue_type, Charge.NEUTRAL)
if assign_attribute:
residue.set_attribute(key, charge)
return charge
@staticmethod
def charge_of_chain(chain: Chain,
assign_attribute: bool = False,
key: str = "charge") -> int:
"""
Returns the charge of a chain.
Args:
chain (Chain): The chain for which to determine the charge.
assign_attribute (bool): Whether to assign the charge to the chain.
key (str): The key to use for the attribute.
Returns:
int: The charge of the chain.
"""
charge = sum([Charge.charge_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues])
if assign_attribute:
chain.set_attribute(key, charge)
return charge
@staticmethod
def charge_of_protein(protein: Protein,
assign_attribute: bool = False,
key: str = "charge") -> int:
"""
Returns the charge of a protein.
Args:
protein (Protein): The protein for which to determine the charge.
assign_attribute (bool): Whether to assign the charge to the protein.
key (str): The key to use for the attribute.
Returns:
int: The charge of the protein.
"""
charge = sum([Charge.charge_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains])
if assign_attribute:
protein.set_attribute(key, charge)
return charge
@staticmethod
def charge_of_sequence(sequence: Sequence,
assign_attribute: bool = False,
key: str = "charge") -> int:
"""
Returns the charge of a sequence.
Args:
sequence (Sequence): The sequence for which to determine the charge.
assign_attribute (bool): Whether to assign the charge to the sequence.
key (str): The key to use for the attribute.
Returns:
int: The charge of the sequence.
"""
charge = sum([Charge.RESIDUE_CHARGE.get(residue, Charge.NEUTRAL) for residue in sequence])
if assign_attribute:
sequence.set_attribute(key, charge)
return chargeClasses
class Charge-
Expand source code
class Charge: # Charges of residues as defined by IMGT. # See: https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html#charge # Positively charged: R, H, K # Negatively charged: D, E # Neutral: A, C, F, G, I, L, M, N, P, Q, S, T, V, W, Y # As noted by IMGT: The sulfhydryl group of cystein and # phenolic hydroxyl group of tyrosine show some degree of pH-dependent ionization. NEUTRAL = 0 POSITIVE = 1 NEGATIVE = -1 RESIDUE_CHARGE = { "ALA": 0, "ARG": 1, "ASN": 0, "ASP": -1, "CYS": 0, "GLN": 0, "GLU": -1, "GLY": 0, "HIS": 1, # Note: The charge of histidine is pH-dependent. A value of 1 is used here, but 0.1 is also common. "ILE": 0, "LEU": 0, "LYS": 1, "MET": 0, "PHE": 0, "PRO": 0, "SER": 0, "THR": 0, "TRP": 0, "TYR": 0, "VAL": 0, "A": 0, "R": 1, "N": 0, "D": -1, "C": 0, "Q": 0, "E": -1, "G": 0, "H": 1, "I": 0, "L": 0, "K": 1, "M": 0, "F": 0, "P": 0, "S": 0, "T": 0, "W": 0, "Y": 0 } @staticmethod def charge_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a residue. Args: residue (Residue): The residue for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the residue. key (str): The key to use for the attribute. Returns: int: The charge of the residue. """ charge = Charge.RESIDUE_CHARGE.get(residue.residue_type, Charge.NEUTRAL) if assign_attribute: residue.set_attribute(key, charge) return charge @staticmethod def charge_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a chain. Args: chain (Chain): The chain for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the chain. key (str): The key to use for the attribute. Returns: int: The charge of the chain. """ charge = sum([Charge.charge_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues]) if assign_attribute: chain.set_attribute(key, charge) return charge @staticmethod def charge_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a protein. Args: protein (Protein): The protein for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the protein. key (str): The key to use for the attribute. Returns: int: The charge of the protein. """ charge = sum([Charge.charge_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains]) if assign_attribute: protein.set_attribute(key, charge) return charge @staticmethod def charge_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a sequence. Args: sequence (Sequence): The sequence for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the sequence. key (str): The key to use for the attribute. Returns: int: The charge of the sequence. """ charge = sum([Charge.RESIDUE_CHARGE.get(residue, Charge.NEUTRAL) for residue in sequence]) if assign_attribute: sequence.set_attribute(key, charge) return chargeClass variables
var NEGATIVEvar NEUTRALvar POSITIVEvar RESIDUE_CHARGE
Static methods
def charge_of_chain(chain: Chain, assign_attribute: bool = False, key: str = 'charge') ‑> int-
Returns the charge of a chain.
Args
chain:Chain- The chain for which to determine the charge.
assign_attribute:bool- Whether to assign the charge to the chain.
key:str- The key to use for the attribute.
Returns
int- The charge of the chain.
Expand source code
@staticmethod def charge_of_chain(chain: Chain, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a chain. Args: chain (Chain): The chain for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the chain. key (str): The key to use for the attribute. Returns: int: The charge of the chain. """ charge = sum([Charge.charge_of_residue(residue, assign_attribute=assign_attribute, key=key) for residue in chain.residues]) if assign_attribute: chain.set_attribute(key, charge) return charge def charge_of_protein(protein: Protein, assign_attribute: bool = False, key: str = 'charge') ‑> int-
Returns the charge of a protein.
Args
protein:Protein- The protein for which to determine the charge.
assign_attribute:bool- Whether to assign the charge to the protein.
key:str- The key to use for the attribute.
Returns
int- The charge of the protein.
Expand source code
@staticmethod def charge_of_protein(protein: Protein, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a protein. Args: protein (Protein): The protein for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the protein. key (str): The key to use for the attribute. Returns: int: The charge of the protein. """ charge = sum([Charge.charge_of_chain(chain, assign_attribute=assign_attribute, key=key) for chain in protein.chains]) if assign_attribute: protein.set_attribute(key, charge) return charge def charge_of_residue(residue: Residue, assign_attribute: bool = False, key: str = 'charge') ‑> int-
Returns the charge of a residue.
Args
residue:Residue- The residue for which to determine the charge.
assign_attribute:bool- Whether to assign the charge to the residue.
key:str- The key to use for the attribute.
Returns
int- The charge of the residue.
Expand source code
@staticmethod def charge_of_residue(residue: Residue, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a residue. Args: residue (Residue): The residue for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the residue. key (str): The key to use for the attribute. Returns: int: The charge of the residue. """ charge = Charge.RESIDUE_CHARGE.get(residue.residue_type, Charge.NEUTRAL) if assign_attribute: residue.set_attribute(key, charge) return charge def charge_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = 'charge') ‑> int-
Returns the charge of a sequence.
Args
sequence:Sequence- The sequence for which to determine the charge.
assign_attribute:bool- Whether to assign the charge to the sequence.
key:str- The key to use for the attribute.
Returns
int- The charge of the sequence.
Expand source code
@staticmethod def charge_of_sequence(sequence: Sequence, assign_attribute: bool = False, key: str = "charge") -> int: """ Returns the charge of a sequence. Args: sequence (Sequence): The sequence for which to determine the charge. assign_attribute (bool): Whether to assign the charge to the sequence. key (str): The key to use for the attribute. Returns: int: The charge of the sequence. """ charge = sum([Charge.RESIDUE_CHARGE.get(residue, Charge.NEUTRAL) for residue in sequence]) if assign_attribute: sequence.set_attribute(key, charge) return charge