utilities.py

"""Utilities"""

# List of ASCII characters to create new IDs when creating the final model
ascii_list = ['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k',
              'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z', 'A', 'B', 'C', 'D', 'E', 'F',
              'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '!',
              '"', '#', '$', '%', '&', "'", '(', ')', '*', '+', ',', '-', '.', '/', ':', ';', '<', '=', '>', '?', '@',
              '[', ']', '^', '_', '`', '{', '|', '}', '~']

# Dictionary to convert the amino acid sequence (from one to three code)
three_to_one = {'ALA':'A','ARG':'R','ASN':'N','ASP':'D','CYS':'C','GLU':'E','GLN':'Q','GLY':'G','HIS':'H',
           'ILE':'I','LEU':'L','LYS':'K','MET':'M','PHE':'F','PRO':'P','SER':'S','THR':'T','TRP':'W',
           'TYR':'Y','VAL':'V', 'UNK': 'X'}

# Dictionary to convert the amino acid sequence (from one to three code)
one_to_three = {'C': 'CYS', 'D': 'ASP', 'S': 'SER', 'Q': 'GLN', 'K': 'LYS', 'I': 'ILE', 'P': 'PRO', 'T': 'THR', 'F': 'PHE', 'N': 'ASN', 'G': 'GLY', 'H': 'HIS', 'L': 'LEU', 'R': 'ARG', 'W': 'TRP', 'A': 'ALA', 'V': 'VAL', 'E': 'GLU', 'Y': 'TYR', 'M': 'MET', 'X': 'UNK'}

# Possible residues list (protein, RNA or DNA)
res_list = ["ALA", "CYS", "ASP", "GLU", "PHE", "GLY", "HIS", "ILE", "LYS", "LEU", "MET", "ASN", "PRO", "GLN", "ARG",
           "SER", "THR", "VAL", "TRP", "TYR", "UNK", "  A", "  G", "  T", "  U", "  C", " DA", " DG", " DT", " DC"]


# Nucleic residues list (DNA or RNA)
nucleic_list = ["A", "G", "T", "U", "C", "DA", "DG", "DT", "DC"]