biology

A utility module that allows access to the amino acid attributes needed for descriptors and encodings. The list of supported amino acids and post-translations are at the bottom of this page and the data for all attributes are under the peptidy.data.

Attributes:

Name	Type	Description
aromatic_aas	list	A list of aromatic amino acids retrieve based on Lobry,1994.
blosum62_scores	dict	A dictionary that contains the BLOSUM62 matrix.
descriptor_per_aas	dict	A dictionary that contains the all descriptor values per amino acid.
formulas	dict	A dictionary that contains the closed formulas of the amino acids.
hydrophobic_aas	list	A list of hydrophobic amino acids (Nelson & Cox, 2004).
instabilities	dict	A dictionary that contains the instability of amino acids pairs per Guruprasad, Reddy & Pandit, 1990.
n_h_acceptors	dict	A dictionary that contains the number of hydrogen acceptors per amino acid according to PubChem.
n_h_donors	dict	A dictionary that contains the number of hydrogen donors per amino acid according to PubChem.
n_rotatable_bonds	dict	A dictionary that contains the number of rotatable bonds in each amino acid (PubChem).
neg_pks	dict	A dictionary that contains the negative pKa values of the amino acids.
pos_pks	dict	A dictionary that contains the positive pKa values of the amino acids.
token2label	dict	A dictionary that contains the token to label mapping for label encoding. The amino acids are indexed from 1 to 20 in alphabetical order and the modifications are indexed from 21 to 28.
tpsas	dict	A dictionary that contains the topological polar surface area of the amino acids, as retrieved from Adhav & Saikrishnan, 2023.
weights	dict	A dictionary that contains the molecular weights of the amino acids.
x_logps	dict	A dictionary that contains the XLogP values of the amino acids per PubChem.

Supported Amino Acids, Post-translations, and Their Labels

{
    "A": 1,
    "C": 2,
    "D": 3,
    "E": 4,
    "F": 5,
    "G": 6,
    "H": 7,
    "I": 8,
    "K": 9,
    "L": 10,
    "M": 11,
    "N": 12,
    "P": 13,
    "Q": 14,
    "R": 15,
    "S": 16,
    "T": 17,
    "V": 18,
    "W": 19,
    "Y": 20,
    "S_p": 21,  # Phosphorylated Serine
    "T_p": 22,  # Phosphorylated Threonine
    "Y_p": 23,  # Phosphorylated Tyrosine
    "C_m": 24,  # Methylated Cysteine
    "R_m": 25,  # Methylated Arginine
    "R_d": 26,  # Dimethylated Arginine
    "R_s": 27,  # Symmetrically dimethylated Arginine
    "K_a": 28   # Acetylated Lysine
}