A library to define the residual hydrophobicities

hydrophobicity.py

# coding=utf-8
"""
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'

# Refence:
#   Eisenberg D., Schwarz E., Komarony M., Wall R.
#   J. Mol. Biol. 179:125-142(1984).
HYDROPHOBICITIES = {
    'A':  0.620, 'R': -2.530, 'N': -0.780, 'D': -0.900, 'C':  0.290,
    'Q': -0.850, 'E': -0.740, 'G':  0.480, 'H': -0.400, 'I':  1.380,
    'L':  1.060, 'K': -1.500, 'M':  0.640, 'F':  1.190, 'P':  0.120,
    'S': -0.180, 'T': -0.050, 'W':  0.810, 'Y':  0.260, 'V':  1.080,
}

def get_hydrophobicity(sequence, average=False):
    """
    Get total (or average) residual hydrophobicity of the sequence
    """
    sequence = sequence.upper()
    nof = 0
    hydrophobicity = 0
    for c in sequence:
        if c in HYDROPHOBICITIES:
            hydrophobicity += HYDROPHOBICITIES[c]
            nof += 1
    if average:
        hydrophobicity /= float(nof)
    return hydrophobicity