# 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."""


# 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},
        }