mbapy.bio.peptide

This documentation provides a comprehensive overview of the AnimoAcid and Peptide classes, including their attributes, methods, parameters, return values, and usage examples. Kimi generated.

Class

AnimoAcid

Class Overview

The AnimoAcid class is designed to represent an amino acid with its respective properties, such as molecular weight, molecular formula, and protecting groups.

Members

aa_mwd

A dictionary containing the molecular weights of amino acids.

aa_3to1

A dictionary mapping three-letter amino acid codes to their one-letter codes.

aa_1to3

The inverse of aa_3to1, mapping one-letter codes to three-letter codes.

pg_mwd

A dictionary containing the molecular weights of protecting groups.

mfd

A dictionary containing the molecular formulas of amino acids and protecting groups.

all_mwd

A dictionary combining the molecular weights of amino acids and protecting groups.

Methods

init(self, repr: str, aa_repr_w: int = 3) -> None

Method Overview

Initializes an instance of the class with the given representation string.

Parameters
  • repr (str): The representation string of a peptide to initialize the instance with.
  • aa_repr_w (int, optional): The width of the amino acid representation (1 or 3 letters). Defaults to 3.
Exceptions
  • Raises ValueError if the representation string is not valid according to the amino acid and protecting group definitions.
Examples
aa = AnimoAcid('H-Ala-OH', 3)

check_is_aa(aa: str)

Method Overview

Checks if a given string is a valid amino acid or protecting group representation.

Parameters
  • aa (str): The string to check.
Returns
  • int: Returns 1 if the string is a valid one-letter amino acid code, 3 if it's a valid three-letter code, or 0 otherwise.
Examples
result = AnimoAcid.check_is_aa('A')  # Returns 1
result = AnimoAcid.check_is_aa('Ala')  # Returns 3

make_pep_repr(self, is_N_terminal: bool = False, is_C_terminal: bool = False, repr_w: int = 3, include_pg: bool = True)

Method Overview

Generates a PEP representation of the amino acid sequence.

Parameters
  • is_N_terminal (bool, optional): Whether the sequence is at the N-terminus. Defaults to False.
  • is_C_terminal (bool, optional): Whether the sequence is at the C-terminus. Defaults to False.
  • repr_w (int, optional): The width of the amino acid representation (1 or 3 letters). Defaults to 3.
  • include_pg (bool, optional): Whether to include protecting groups in the representation. Defaults to True.
Returns
  • str: The PEP representation of the amino acid sequence.
Examples
pep_repr = aa.make_pep_repr(is_N_terminal=True, is_C_terminal=True, repr_w=3)

calcu_mw(self, expand_mw_dict: Dict[str, float] = None)

Method Overview

Calculates the molecular weight of the peptide sequence.

Parameters
  • expand_mw_dict (Dict[str, float], optional): A dictionary containing the molecular weights of additional protecting groups. Defaults to None.
Returns
  • float: The calculated molecular weight of the peptide sequence.

get_molecular_formula_dict(self)

Method Overview

Returns a dictionary containing the molecular formula of the protein sequence.

Returns
  • dict: A dictionary containing the molecular formula.

get_molecular_formula(self, molecular_formula_dict: Dict[str, int] = None)

Method Overview

Generates the molecular formula from a given dictionary of element symbols and their counts.

Parameters
  • molecular_formula_dict (Dict[str, int], optional): A dictionary containing element symbols as keys and their counts as values. Defaults to None.
Returns
  • str: The molecular formula generated from the dictionary.

calcu_mass(self, molecular_formula: str = None, molecular_formula_dict: Dict[str, int] = None)

Method Overview

Calculates the mass of a molecule based on its molecular formula.

Parameters
  • molecular_formula (str, optional): The molecular formula of the molecule. Defaults to None.
  • molecular_formula_dict (Dict[str, int], optional): A dictionary representing the molecular formula of the molecule. Defaults to None.
Returns
  • float: The calculated mass of the molecule.

copy(self)

Method Overview

Creates a copy of the current instance.

Returns
  • A copy of the AnimoAcid object.

Peptide

Class Overview

The Peptide class represents a peptide, which is a sequence of AnimoAcid objects.

Methods

init(self, repr: str, aa_repr_w: int = 3) -> None

Method Overview

Initializes a Peptide object by splitting the input string and creating a list of AnimoAcid objects.

Parameters
  • repr (str): The representation string of the peptide.
  • aa_repr_w (int, optional): The width of the amino acid representation (1 or 3 letters). Defaults to 3.
Exceptions
  • Raises ValueError if the representation string is not valid according to the amino acid and protecting group definitions.

flatten(self, inplace: bool = False)

Method Overview

Flattens the list of AnimoAcid objects into a single list.

Parameters
  • inplace (bool, optional): If True, makes the change in place and returns self, otherwise returns the changed sequence only. Defaults to False.
Returns
  • The flattened list of AnimoAcid objects.

repr(self, repr_w: int = 3, include_pg: bool = True, include_dash: bool = True)

Method Overview

Returns a string representation of the Peptide object by joining the representations of each AnimoAcid object in the sequence.

Parameters
  • repr_w (int, optional): The width of the amino acid representation (1 or 3 letters). Defaults to 3.
  • include_pg (bool, optional): Whether to include protecting groups in the representation. Defaults to True.
  • include_dash (bool, optional): Whether to include dashes in the representation. Defaults to True.
Returns
  • str: The string representation of the Peptide object.

get_molecular_formula_dict(self)

Method Overview

Returns a dictionary representing the molecular formula of the Peptide object by summing the molecular formulas of each AnimoAcid object in the sequence.

Returns
  • dict: A dictionary representing the molecular formula.

get_molecular_formula(self, molecular_formula_dict: Dict[str, int] = None)

Method Overview

Returns a string representation of the molecular formula of the Peptide object by joining the elements of the molecular_formula_dict dictionary.

Parameters
  • molecular_formula_dict (Dict[str, int], optional): A dictionary representing the molecular formula, where the keys are the element symbols and the values are the corresponding counts. Defaults to None.
Returns
  • str: The molecular formula as a string.

calcu_mw(self, expand_mw_dict: Dict[str, float] = None)

Method Overview

Calculates the molecular weight of the Peptide object by summing the molecular weights of each AnimoAcid object in the sequence.

Parameters
  • expand_mw_dict (Optional[Dict[str, float]]): A dictionary containing the molecular weights of the protected group. Defaults to None.
Returns
  • float: The calculated molecular weight of the peptide.

calcu_mass(self, molecular_formula: str = None, molecular_formula_dict: Dict[str, int] = None)

Method Overview

Calculates the mass of the Peptide object by calling the calcu_mass method of the first AnimoAcid object in the sequence.

Parameters
  • molecular_formula (str, optional): The molecular formula of the molecule. Defaults to None.
  • molecular_formula_dict (Dict[str, int], optional): The dictionary representation of the molecular formula. Defaults to None.
Returns
  • float: The calculated mass of the molecule.

copy(self)

Method Overview

Creates a copy of the Peptide object by creating a new Peptide object and copying the list of AnimoAcid objects.

Returns
  • A copy of the Peptide object.

Examples

# Example usage of the Peptide class
pep = Peptide('H-Cys(Trt)-G(OtBu)', 3)
print(pep.repr(3, True, True))
print(pep.get_molecular_formula())
print(pep.calcu_mw())