# 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."""

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

# 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},
        "M": {"A": 13.34, "C": 1.0, "E": 1.0, "D": 1.0,
              "G": 1.0, "F": 1.0, "I": 1.0, "H": 58.28,
              "K": 1.0, "M": -1.88, "L": 1.0, "N": 1.0,
              "Q": -6.54, "P": 44.94, "S": 44.94, "R": -6.54,
              "T": -1.88, "W": 1.0, "V": 1.0, "Y": 24.68},
        "L": {"A": 1.0, "C": 1.0, "E": 1.0, "D": 1.0,
              "G": 1.0, "F": 1.0, "I": 1.0, "H": 1.0,
              "K": -7.49, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 33.60, "P": 20.26, "S": 1.0, "R": 20.26,
              "T": 1.0, "W": 24.68, "V": 1.0, "Y": 1.0},
        "N": {"A": 1.0, "C": -1.88, "E": 1.0, "D": 1.0,
              "G": -14.03, "F": -14.03, "I": 44.94, "H": 1.0,
              "K": 24.68, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": -6.54, "P": -1.88, "S": 1.0, "R": 1.0,
              "T": -7.49, "W": -9.37, "V": 1.0, "Y": 1.0},
        "Q": {"A": 1.0, "C": -6.54, "E": 20.26, "D": 20.26,
              "G": 1.0, "F": -6.54, "I": 1.0, "H": 1.0,
              "K": 1.0, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 20.26, "P": 20.26, "S": 44.94, "R": 1.0,
              "T": 1.0, "W": 1.0, "V": -6.54, "Y": -6.54},
        "P": {"A": 20.26, "C": -6.54, "E": 18.38, "D": -6.54,
              "G": 1.0, "F": 20.26, "I": 1.0, "H": 1.0,
              "K": 1.0, "M": -6.54, "L": 1.0, "N": 1.0,
              "Q": 20.26, "P": 20.26, "S": 20.26, "R": -6.54,
              "T": 1.0, "W": -1.88, "V": 20.26, "Y": 1.0},
        "S": {"A": 1.0, "C": 33.60, "E": 20.26, "D": 1.0,
              "G": 1.0, "F": 1.0, "I": 1.0, "H": 1.0,
              "K": 1.0, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 20.26, "P": 44.94, "S": 20.26, "R": 20.26,
              "T": 1.0, "W": 1.0, "V": 1.0, "Y": 1.0},
        "R": {"A": 1.0, "C": 1.0, "E": 1.0, "D": 1.0,
              "G": -7.49, "F": 1.0, "I": 1.0, "H": 20.26,
              "K": 1.0, "M": 1.0, "L": 1.0, "N": 13.34,
              "Q": 20.26, "P": 20.26, "S": 44.94, "R": 58.28,
              "T": 1.0, "W": 58.28, "V": 1.0, "Y": -6.54},
        "T": {"A": 1.0, "C": 1.0, "E": 20.26, "D": 1.0,
              "G": -7.49, "F": 13.34, "I": 1.0, "H": 1.0,
              "K": 1.0, "M": 1.0, "L": 1.0, "N": -14.03,
              "Q": -6.54, "P": 1.0, "S": 1.0, "R": 1.0,
              "T": 1.0, "W": -14.03, "V": 1.0, "Y": 1.0},
        "W": {"A": -14.03, "C": 1.0, "E": 1.0, "D": 1.0,
              "G": -9.37, "F": 1.0, "I": 1.0, "H": 24.68,
              "K": 1.0, "M": 24.68, "L": 13.34, "N": 13.34,
              "Q": 1.0, "P": 1.0, "S": 1.0, "R": 1.0,
              "T": -14.03, "W": 1.0, "V": -7.49, "Y": 1.0},
        "V": {"A": 1.0, "C": 1.0, "E": 1.0, "D": -14.03,
              "G": -7.49, "F": 1.0, "I": 1.0, "H": 1.0,
              "K": -1.88, "M": 1.0, "L": 1.0, "N": 1.0,
              "Q": 1.0, "P": 20.26, "S": 1.0, "R": 1.0,
              "T": -7.49, "W": 1.0, "V": 1.0, "Y": -6.54},
        "Y": {"A": 24.68, "C": 1.0, "E": -6.54, "D": 24.68,
              "G": -7.49, "F": 1.0, "I": 1.0, "H": 13.34,
              "K": 1.0, "M": 44.94, "L": 1.0, "N": 1.0,
              "Q": 1.0, "P": 13.34, "S": 1.0, "R": -15.91,
              "T": -7.49, "W": -9.37, "V": 1.0, "Y": 13.34},
        }

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