myenv/lib/python3.10/site-packages/Bio/SeqUtils/ProtParamData.py

# Copyright 2003 Yair Benita.  All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Indices to be used with ProtParam."""

# Turn black code style off
# fmt: off

# Hydrophobicity

# Kyte & Doolittle index of hydrophobicity
# J. Mol. Biol. 157:105-132(1982).
# "KyteDoolittle"
kd = {"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}

# Aboderin hydrophobicity index
# International J. of Biochemistry, 2(11), 537-544.
# "Aboderin"
ab = {"A": 5.1, "R": 2.0, "N": 0.6, "D": 0.7, "C": 0.0,
      "Q": 1.4, "E": 1.8, "G": 4.1, "H": 1.6, "I": 9.3,
      "L": 10.0, "K": 1.3, "M": 8.7, "F": 9.6, "P": 4.9,
      "S": 3.1, "T": 3.5, "W": 9.2, "Y": 8.0, "V": 8.5}

# Abraham & Leo hydrophobicity index
# Proteins: Structure, Function and Genetics 2:130-152(1987).
# "AbrahamLeo"
al = {"A": 0.44, "R": -2.42, "N": -1.32, "D": -0.31, "C": 0.58,
      "Q": -0.71, "E": -0.34, "G": 0.0, "H": -0.01, "I": 2.46,
      "L": 2.46, "K": -2.45, "M": 1.1, "F": 2.54, "P": 1.29,
      "S": -0.84, "T": -0.41, "W": 2.56, "Y": 1.63, "V": 1.73}

# Argos hydrophobicity index
# European Journal of Biochemistry, 128(2-3), 565-575.
# "Argos"
ag = {"A": 0.61, "R": 0.6, "N": 0.06, "D": 0.46, "C": 1.07,
      "Q": 0.0, "E": 0.47, "G": 0.07, "H": 0.61, "I": 2.22,
      "L": 1.53, "K": 1.15, "M": 1.18, "F": 2.02, "P": 1.95,
      "S": 0.05, "T": 0.05, "W": 2.65, "Y": 1.88, "V": 1.32}

# Black & Mould hydrophobicity index
# Anal. Biochem. 193:72-82(1991).
# "BlackMould"
bm = {"A": 0.616, "R": 0.0, "N": 0.236, "D": 0.028, "C": 0.68,
      "Q": 0.251, "E": 0.043, "G": 0.501, "H": 0.165, "I": 0.943,
      "L": 0.943, "K": 0.283, "M": 0.738, "F": 1.0, "P": 0.711,
      "S": 0.359, "T": 0.45, "W": 0.878, "Y": 0.88, "V": 0.825}

# Bull & Breese hydrophobicity index
# Arch. Biochem. Biophys. 161:665-670(1974)
# "BullBreese"
bb = {"A": 0.61, "R": 0.69, "N": 0.89, "D": 0.61, "C": 0.36,
      "Q": 0.97, "E": 0.51, "G": 0.81, "H": 0.69, "I": -1.45,
      "L": -1.65, "K": 0.46, "M": -0.66, "F": -1.52, "P": -0.17,
      "S": 0.42, "T": 0.29, "W": -1.2, "Y": -1.43, "V": -0.75}

# Casari & Sippl hydrophobic potential
# Journal of molecular biology, 224(3), 725-732.
# "Casari"
cs = {"A": 0.2, "R": -0.7, "N": -0.5, "D": -1.4, "C": 1.9,
      "Q": -1.1, "E": -1.3, "G": -0.1, "H": 0.4, "I": 1.4,
      "L": 0.5, "K": -1.6, "M": 0.5, "F": 1.0, "P": -1.0,
      "S": -0.7, "T": -0.4, "W": 1.6, "Y": 0.5, "V": 0.7}

# Cid hydrophobicity index
# Protein engineering, 5(5), 373-375.
# "Cid"
ci = {"A": 0.02, "R": -0.42, "N": -0.77, "D": -1.04, "C": 0.77,
      "Q": -1.1, "E": -1.14, "G": -0.8, "H": 0.26, "I": 1.81,
      "L": 1.14, "K": -0.41, "M": 1.0, "F": 1.35, "P": -0.09,
      "S": -0.97, "T": -0.77, "W": 1.71, "Y": 1.11, "V": 1.13}

# Cowan hydrophobicity indices at ph 3.4 and 7.5
# Peptide Research 3:75-80(1990).
# "Cowan3.4" "Conwan7.5"
cw = {3.4 : {"A": 0.42, "R": -1.56, "N": -1.03, "D": -0.51, "C": 0.84,
             "Q": -0.96, "E": -0.37, "G": 0.0, "H": -2.28, "I": 1.81,
             "L": 1.8, "K": -2.03, "M": 1.18, "F": 1.74, "P": 0.86,
             "S": -0.64, "T": -0.26, "W": 1.46, "Y": 0.51, "V": 1.34},
      7.5 : {"A": 0.35, "R": -1.5, "N": -0.99, "D": -2.15, "C": 0.76,
             "Q": -0.93, "E": -1.95, "G": 0.0, "H": -0.65, "I": 1.83,
             "L": 1.8, "K": -1.54, "M": 1.1, "F": 1.69, "P": 0.84,
             "S": -0.63, "T": -0.27, "W": 1.35, "Y": 0.39, "V": 1.32}
      }

# Eisenberg Normalized consensus hydrophobicity scale
# J. Mol. Biol. 179:125-142(1984)
# "Eisenberg"
es = {"A": 0.62, "R": -2.53, "N": -0.78, "D": -0.9, "C": 0.29,
      "Q": -0.85, "E": -0.74, "G": 0.48, "H": -0.4, "I": 1.38,
      "L": 1.06, "K": -1.5, "M": 0.64, "F": 1.19, "P": 0.12,
      "S": -0.18, "T": -0.05, "W": 0.81, "Y": 0.26, "V": 1.08}

# Engelman Hydrophobic Transfer Free Energies
# Annual review of biophysics and biophysical chemistry, 15(1), 321-353.
# "Engelman"
eg = {"A": -1.6, "R": 12.3, "N": 4.8, "D": 9.2, "C": -2,
      "Q": 4.1, "E": 8.2, "G": -1, "H": 3, "I": -3.1,
      "L": -2.8, "K": 8.8, "M": -3.4, "F": -3.7, "P": 0.2,
      "S": -0.6, "T": -1.2, "W": -1.9, "Y": 0.7, "V": -2.6}

# Fasman hydrophobicity index
# (1989). Prediction of protein structure and the principles of protein conformation. Springer.
# "Fasman"
fs = {"A": -0.21, "R": 2.11, "N": 0.96, "D": 1.36, "C": -6.04,
      "Q": 1.52, "E": 2.3, "G": 0, "H": -1.23, "I": -4.81,
      "L": -4.68, "K": 3.88, "M": -3.66, "F": -4.65, "P": 0.75,
      "S": 1.74, "T": 0.78, "W": -3.32, "Y": -1.01, "V": -3.5}

# Fauchere Hydrophobicity scale
# Eur. J. Med. Chem. 18:369-375(1983).
# "Fauchere"
fc = {"A": 0.31, "R": -1.01, "N": -0.6, "D": -0.77, "C": 1.54,
      "Q": -0.22, "E": -0.64, "G": 0, "H": 0.13, "I": 1.8,
      "L": 1.7, "K": -0.99, "M": 1.23, "F": 1.79, "P": 0.72,
      "S": -0.04, "T": 0.26, "W": 2.25, "Y": 0.96, "V": 1.22}

# Goldsack & Chalifoux Free Energy of Mixing of the Hydrophobic Side Chains
# Journal of theoretical biology, 39(3), 645-651.
# "Goldsack"
gd = {"A": 0.75, "R": 0.75, "N": 0.69, "D": 0, "C": 1,
      "Q": 0.59, "E": 0, "G": 0, "H": 0, "I": 2.95,
      "L": 2.4, "K": 1.5, "M": 1.3, "F": 2.65, "P": 2.6,
      "S": 0, "T": 0.45, "W": 3, "Y": 2.85, "V": 1.7}

# Guy Hydrophobicity scale based on free energy of transfer (kcal/mole).
# Biophys J. 47:61-70(1985)
# "Guy"
gy = {"A": 0.1, "R": 1.91, "N": 0.48, "D": 0.78, "C": -1.42,
      "Q": 0.95, "E": 0.83, "G": 0.33, "H": -0.5, "I": -1.13,
      "L": -1.18, "K": 1.4, "M": -1.59, "F": -2.12, "P": 0.73,
      "S": 0.52, "T": 0.07, "W": -0.51, "Y": -0.21, "V": -1.27}

# Jones Hydrophobicity scale
# Journal of theoretical biology, 50(1), 167-183.
# "Jones"
jo = {"A": 0.87, "R": 0.85, "N": 0.09, "D": 0.66, "C": 1.52,
      "Q": 0, "E": 0.67, "G": 0.1, "H": 0.87, "I": 3.15,
      "L": 2.17, "K": 1.64, "M": 1.67, "F": 2.87, "P": 2.77,
      "S": 0.07, "T": 0.07, "W": 3.77, "Y": 2.67, "V": 1.87}

# Juretic Hydrophobicity scale
# Theoretical and computational chemistry, 5, 405-445.
# "Juretic"
ju = {"A": 1.1, "R": -5.1, "N": -3.5, "D": -3.6, "C": 2.5,
      "Q": -3.68, "E": -3.2, "G": -0.64, "H": -3.2, "I": 4.5,
      "L": 3.8, "K": -4.11, "M": 1.9, "F": 2.8, "P": -1.9,
      "S": -0.5, "T": -0.7, "W": -0.46, "Y": -1.3, "V": 4.2}

# Kidera Hydrophobicity Factors
# Journal of Protein Chemistry, 4(1), 23-55.
# "Kidera"
ki = {"A": -0.27, "R": 1.87, "N": 0.81, "D": 0.81, "C": -1.05,
      "Q": 1.1, "E": 1.17, "G": -0.16, "H": 0.28, "I": -0.77,
      "L": -1.1, "K": 1.7, "M": -0.73, "F": -1.43, "P": -0.75,
      "S": 0.42, "T": 0.63, "W": -1.57, "Y": -0.56, "V": -0.4}

# Miyazawa Hydrophobicity scale (contact energy derived from 3D data)
# Macromolecules 18:534-552(1985)
# "Miyazawa"
mi = {"A": 5.33, "R": 4.18, "N": 3.71, "D": 3.59, "C": 7.93,
      "Q": 3.87, "E": 3.65, "G": 4.48, "H": 5.1, "I": 8.83,
      "L": 8.47, "K": 2.95, "M": 8.95, "F": 9.03, "P": 3.87,
      "S": 4.09, "T": 4.49, "W": 7.66, "Y": 5.89, "V": 7.63}

# Parker Hydrophilicity scale derived from HPLC peptide retention times
# Biochemistry 25:5425-5431(1986)
# "Parker"
pa = {"A": 2.1, "R": 4.2, "N": 7, "D": 10, "C": 1.4,
      "Q": 6, "E": 7.8, "G": 5.7, "H": 2.1, "I": -8,
      "L": -9.2, "K": 5.7, "M": -4.2, "F": -9.2, "P": 2.1,
      "S": 6.5, "T": 5.2, "W": -10, "Y": -1.9, "V": -3.7}

# Ponnuswamy Hydrophobic characteristics of folded proteins
# Progress in biophysics and molecular biology, 59(1), 57-103.
# "Ponnuswamy"
po = {"A": 0.85, "R": 0.2, "N": -0.48, "D": -1.1, "C": 2.1,
      "Q": -0.42, "E": -0.79, "G": 0, "H": 0.22, "I": 3.14,
      "L": 1.99, "K": -1.19, "M": 1.42, "F": 1.69, "P": -1.14,
      "S": -0.52, "T": -0.08, "W": 1.76, "Y": 1.37, "V": 2.53}

# Rose Hydrophobicity scale
# Science 229:834-838(1985)
# "Rose"
ro = {"A": 0.74, "R": 0.64, "N": 0.63, "D": 0.62, "C": 0.91,
      "Q": 0.62, "E": 0.62, "G": 0.72, "H": 0.78, "I": 0.88,
      "L": 0.85, "K": 0.52, "M": 0.85, "F": 0.88, "P": 0.64,
      "S": 0.66, "T": 0.7, "W": 0.85, "Y": 0.76, "V": 0.86}

# Roseman Hydrophobicity scale
# J. Mol. Biol. 200:513-522(1988)
# "Roseman"
rm = {"A": 0.39, "R": -3.95, "N": -1.91, "D": -3.81, "C": 0.25,
      "Q": -1.3, "E": -2.91, "G": 0, "H": -0.64, "I": 1.82,
      "L": 1.82, "K": -2.77, "M": 0.96, "F": 2.27, "P": 0.99,
      "S": -1.24, "T": -1, "W": 2.13, "Y": 1.47, "V": 1.3}

# Sweet Optimized Matchig Hydrophobicity (OMH)
# J. Mol. Biol. 171:479-488(1983).
# "Sweet
sw = {"A": -0.4, "R": -0.59, "N": -0.92, "D": -1.31, "C": 0.17,
      "Q": -0.91, "E": -1.22, "G": -0.67, "H": -0.64, "I": 1.25,
      "L": 1.22, "K": -0.67, "M": 1.02, "F": 1.92, "P": -0.49,
      "S": -0.55, "T": -0.28, "W": 0.5, "Y": 1.67, "V": 0.91}

# Tanford Hydrophobicity scale
# J. Am. Chem. Soc. 84:4240-4274(1962)
# "Tanford"
ta = {"A": 0.62, "R": -2.53, "N": -0.78, "D": -0.09, "C": 0.29,
      "Q": -0.85, "E": -0.74, "G": 0.48, "H": -0.4, "I": 1.38,
      "L": 1.53, "K": -1.5, "M": 0.64, "F": 1.19, "P": 0.12,
      "S": -0.18, "T": -0.05, "W": 0.81, "Y": 0.26, "V": 1.8}

# Wilson Hydrophobic constants derived from HPLC peptide retention times
# Biochem. J. 199:31-41(1981)
# "Wilson"
wi = {"A": -0.3, "R": -1.1, "N": -0.2, "D": -1.4, "C": 6.3,
      "Q": -0.2, "E": 0, "G": 1.2, "H": -1.3, "I": 4.3,
      "L": 6.6, "K": -3.6, "M": 2.5, "F": 7.5, "P": 2.2,
      "S": -0.6, "T": -2.2, "W": 7.9, "Y": 7.1, "V": 5.9}

# Zimmerman Hydrophobicity scale
# Journal of theoretical biology, 21(2), 170-201.
# "Zimmerman"
zi = {"A": 0.83, "R": 0.83, "N": 0.09, "D": 0.64, "C": 1.48,
      "Q": 0, "E": 0.65, "G": 0.1, "H": 1.1, "I": 3.07,
      "L": 2.52, "K": 1.6, "M": 1.4, "F": 2.75, "P": 2.7,
      "S": 0.14, "T": 0.54, "W": 0.31, "Y": 2.97, "V": 1.79}

gravy_scales = {"KyteDoolitle": kd, "Aboderin": ab,
                "AbrahamLeo": al, "Argos": ag,
                "BlackMould": bm, "BullBreese": bb,
                "Casari": cs, "Cid": ci,
                "Cowan3.4": cw[3.4], "Cowan7.5": cw[7.5],
                "Eisenberg": es, "Engelman": eg,
                "Fasman": fs, "Fauchere": fc,
                "GoldSack": gd, "Guy": gy,
                "Jones": jo, "Juretic": ju,
                "Kidera": ki, "Miyazawa": mi,
                "Parker": pa, "Ponnuswamy": po,
                "Rose": ro, "Roseman": rm,
                "Sweet": sw, "Tanford": ta,
                "Wilson": wi, "Zimmerman": zi}


# Flexibility
# Normalized flexibility parameters (B-values), average
# Vihinen M., Torkkila E., Riikonen P. Proteins. 19(2):141-9(1994).
Flex = {"A": 0.984, "C": 0.906, "E": 1.094, "D": 1.068,
        "G": 1.031, "F": 0.915, "I": 0.927, "H": 0.950,
        "K": 1.102, "M": 0.952, "L": 0.935, "N": 1.048,
        "Q": 1.037, "P": 1.049, "S": 1.046, "R": 1.008,
        "T": 0.997, "W": 0.904, "V": 0.931, "Y": 0.929}

# Hydrophilicity
# 1 Hopp & Wood
# Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).
hw = {"A": -0.5, "R": 3.0, "N": 0.2, "D": 3.0, "C": -1.0,
      "Q": 0.2, "E": 3.0, "G": 0.0, "H": -0.5, "I": -1.8,
      "L": -1.8, "K": 3.0, "M": -1.3, "F": -2.5, "P": 0.0,
      "S": 0.3, "T": -0.4, "W": -3.4, "Y": -2.3, "V": -1.5}

# Surface accessibility
# Vergoten G & Theophanides T, Biomolecular Structure and Dynamics,
# pg.138 (1997).
# 1 Emini Surface fractional probability
em = {"A": 0.815, "R": 1.475, "N": 1.296, "D": 1.283, "C": 0.394,
      "Q": 1.348, "E": 1.445, "G": 0.714, "H": 1.180, "I": 0.603,
      "L": 0.603, "K": 1.545, "M": 0.714, "F": 0.695, "P": 1.236,
      "S": 1.115, "T": 1.184, "W": 0.808, "Y": 1.089, "V": 0.606}

# 2 Janin Interior to surface transfer energy scale
ja = {"A": 0.28, "R": -1.14, "N": -0.55, "D": -0.52, "C": 0.97,
      "Q": -0.69, "E": -1.01, "G": 0.43, "H": -0.31, "I": 0.60,
      "L": 0.60, "K": -1.62, "M": 0.43, "F": 0.46, "P": -0.42,
      "S": -0.19, "T": -0.32, "W": 0.29, "Y": -0.15, "V": 0.60}


# A two dimensional dictionary for calculating the instability index.
# Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).
# It is based on dipeptide values; therefore, the value for the dipeptide DG
# is DIWV['D']['G'].
DIWV = {"A": {"A": 1.0, "C": 44.94, "E": 1.0, "D": -7.49,
              "G": 1.0, "F": 1.0, "I": 1.0, "H": -7.49,
              "K": 1.0, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 1.0, "P": 20.26, "S": 1.0, "R": 1.0,
              "T": 1.0, "W": 1.0, "V": 1.0, "Y": 1.0},
        "C": {"A": 1.0, "C": 1.0, "E": 1.0, "D": 20.26,
              "G": 1.0, "F": 1.0, "I": 1.0, "H": 33.60,
              "K": 1.0, "M": 33.60, "L": 20.26, "N": 1.0,
              "Q": -6.54, "P": 20.26, "S": 1.0, "R": 1.0,
              "T": 33.60, "W": 24.68, "V": -6.54, "Y": 1.0},
        "E": {"A": 1.0, "C": 44.94, "E": 33.60, "D": 20.26,
              "G": 1.0, "F": 1.0, "I": 20.26, "H": -6.54,
              "K": 1.0, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 20.26, "P": 20.26, "S": 20.26, "R": 1.0,
              "T": 1.0, "W": -14.03, "V": 1.0, "Y": 1.0},
        "D": {"A": 1.0, "C": 1.0, "E": 1.0, "D": 1.0,
              "G": 1.0, "F": -6.54, "I": 1.0, "H": 1.0,
              "K": -7.49, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 1.0, "P": 1.0, "S": 20.26, "R": -6.54,
              "T": -14.03, "W": 1.0, "V": 1.0, "Y": 1.0},
        "G": {"A": -7.49, "C": 1.0, "E": -6.54, "D": 1.0,
              "G": 13.34, "F": 1.0, "I": -7.49, "H": 1.0,
              "K": -7.49, "M": 1.0, "L": 1.0, "N": -7.49,
              "Q": 1.0, "P": 1.0, "S": 1.0, "R": 1.0,
              "T": -7.49, "W": 13.34, "V": 1.0, "Y": -7.49},
        "F": {"A": 1.0, "C": 1.0, "E": 1.0, "D": 13.34,
              "G": 1.0, "F": 1.0, "I": 1.0, "H": 1.0,
              "K": -14.03, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 1.0, "P": 20.26, "S": 1.0, "R": 1.0,
              "T": 1.0, "W": 1.0, "V": 1.0, "Y": 33.601},
        "I": {"A": 1.0, "C": 1.0, "E": 44.94, "D": 1.0,
              "G": 1.0, "F": 1.0, "I": 1.0, "H": 13.34,
              "K": -7.49, "M": 1.0, "L": 20.26, "N": 1.0,
              "Q": 1.0, "P": -1.88, "S": 1.0, "R": 1.0,
              "T": 1.0, "W": 1.0, "V": -7.49, "Y": 1.0},
        "H": {"A": 1.0, "C": 1.0, "E": 1.0, "D": 1.0,
              "G": -9.37, "F": -9.37, "I": 44.94, "H": 1.0,
              "K": 24.68, "M": 1.0, "L": 1.0, "N": 24.68,
              "Q": 1.0, "P": -1.88, "S": 1.0, "R": 1.0,
              "T": -6.54, "W": -1.88, "V": 1.0, "Y": 44.94},
        "K": {"A": 1.0, "C": 1.0, "E": 1.0, "D": 1.0,
              "G": -7.49, "F": 1.0, "I": -7.49, "H": 1.0,
              "K": 1.0, "M": 33.60, "L": -7.49, "N": 1.0,
              "Q": 24.64, "P": -6.54, "S": 1.0, "R": 33.60,
              "T": 1.0, "W": 1.0, "V": -7.49, "Y": 1.0},
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