analysis/Hsu.et.al.git/src/utils/georgiev_utils.py

import numpy as np


# This section of code is copied from ProFET (Ofer & Linial, DOI: 10.1093/bioinformatics/btv345)
# Original comment by the ProFET authors: 'Acquired from georgiev's paper of
# AAscales using helper script "GetTextData.py". + RegEx cleaning DOI: 10.1089/cmb.2008.0173'
gg_1 = {'Q': -2.54, 'L': 2.72, 'T': -0.65, 'C': 2.66, 'I': 3.1, 'G': 0.15, 'V': 2.64, 'K': -3.89, 'M': 1.89, 'F': 3.12, 'N': -2.02, 'R': -2.8, 'H': -0.39, 'E': -3.08, 'W': 1.89, 'A': 0.57, 'D': -2.46, 'Y': 0.79, 'S': -1.1, 'P': -0.58}
gg_2 = {'Q': 1.82, 'L': 1.88, 'T': -1.6, 'C': -1.52, 'I': 0.37, 'G': -3.49, 'V': 0.03, 'K': 1.47, 'M': 3.88, 'F': 0.68, 'N': -1.92, 'R': 0.31, 'H': 1, 'E': 3.45, 'W': -0.09, 'A': 3.37, 'D': -0.66, 'Y': -2.62, 'S': -2.05, 'P': -4.33}
gg_3 = {'Q': -0.82, 'L': 1.92, 'T': -1.39, 'C': -3.29, 'I': 0.26, 'G': -2.97, 'V': -0.67, 'K': 1.95, 'M': -1.57, 'F': 2.4, 'N': 0.04, 'R': 2.84, 'H': -0.63, 'E': 0.05, 'W': 4.21, 'A': -3.66, 'D': -0.57, 'Y': 4.11, 'S': -2.19, 'P': -0.02}
gg_4 = {'Q': -1.85, 'L': 5.33, 'T': 0.63, 'C': -3.77, 'I': 1.04, 'G': 2.06, 'V': 2.34, 'K': 1.17, 'M': -3.58, 'F': -0.35, 'N': -0.65, 'R': 0.25, 'H': -3.49, 'E': 0.62, 'W': -2.77, 'A': 2.34, 'D': 0.14, 'Y': -0.63, 'S': 1.36, 'P': -0.21}
gg_5 = {'Q': 0.09, 'L': 0.08, 'T': 1.35, 'C': 2.96, 'I': -0.05, 'G': 0.7, 'V': 0.64, 'K': 0.53, 'M': -2.55, 'F': -0.88, 'N': 1.61, 'R': 0.2, 'H': 0.05, 'E': -0.49, 'W': 0.72, 'A': -1.07, 'D': 0.75, 'Y': 1.89, 'S': 1.78, 'P': -8.31}
gg_6 = {'Q': 0.6, 'L': 0.09, 'T': -2.45, 'C': -2.23, 'I': -1.18, 'G': 7.47, 'V': -2.01, 'K': 0.1, 'M': 2.07, 'F': 1.62, 'N': 2.08, 'R': -0.37, 'H': 0.41, 'E': 0, 'W': 0.86, 'A': -0.4, 'D': 0.24, 'Y': -0.53, 'S': -3.36, 'P': -1.82}
gg_7 = {'Q': 0.25, 'L': 0.27, 'T': -0.65, 'C': 0.44, 'I': -0.21, 'G': 0.41, 'V': -0.33, 'K': 4.01, 'M': 0.84, 'F': -0.15, 'N': 0.4, 'R': 3.81, 'H': 1.61, 'E': -5.66, 'W': -1.07, 'A': 1.23, 'D': -5.15, 'Y': -1.3, 'S': 1.39, 'P': -0.12}
gg_8 = {'Q': 2.11, 'L': -4.06, 'T': 3.43, 'C': -3.49, 'I': 3.45, 'G': 1.62, 'V': 3.93, 'K': -0.01, 'M': 1.85, 'F': -0.41, 'N': -2.47, 'R': 0.98, 'H': -0.6, 'E': -0.11, 'W': -1.66, 'A': -2.32, 'D': -1.17, 'Y': 1.31, 'S': -1.21, 'P': -1.18}
gg_9 = {'Q': -1.92, 'L': 0.43, 'T': 0.34, 'C': 2.22, 'I': 0.86, 'G': -0.47, 'V': -0.21, 'K': -0.26, 'M': -2.05, 'F': 4.2, 'N': -0.07, 'R': 2.43, 'H': 3.55, 'E': 1.49, 'W': -5.87, 'A': -2.01, 'D': 0.73, 'Y': -0.56, 'S': -2.83, 'P': 0}
gg_10 = {'Q': -1.67, 'L': -1.2, 'T': 0.24, 'C': -3.78, 'I': 1.98, 'G': -2.9, 'V': 1.27, 'K': -1.66, 'M': 0.78, 'F': 0.73, 'N': 7.02, 'R': -0.99, 'H': 1.52, 'E': -2.26, 'W': -0.66, 'A': 1.31, 'D': 1.5, 'Y': -0.95, 'S': 0.39, 'P': -0.66}
gg_11 = {'Q': 0.7, 'L': 0.67, 'T': -0.53, 'C': 1.98, 'I': 0.89, 'G': -0.98, 'V': 0.43, 'K': 5.86, 'M': 1.53, 'F': -0.56, 'N': 1.32, 'R': -4.9, 'H': -2.28, 'E': -1.62, 'W': -2.49, 'A': -1.14, 'D': 1.51, 'Y': 1.91, 'S': -2.92, 'P': 0.64}
gg_12 = {'Q': -0.27, 'L': -0.29, 'T': 1.91, 'C': -0.43, 'I': -1.67, 'G': -0.62, 'V': -1.71, 'K': -0.06, 'M': 2.44, 'F': 3.54, 'N': -2.44, 'R': 2.09, 'H': -3.12, 'E': -3.97, 'W': -0.3, 'A': 0.19, 'D': 5.61, 'Y': -1.26, 'S': 1.27, 'P': -0.92}
gg_13 = {'Q': -0.99, 'L': -2.47, 'T': 2.66, 'C': -1.03, 'I': -1.02, 'G': -0.11, 'V': -2.93, 'K': 1.38, 'M': -0.26, 'F': 5.25, 'N': 0.37, 'R': -3.08, 'H': -1.45, 'E': 2.3, 'W': -0.5, 'A': 1.66, 'D': -3.85, 'Y': 1.57, 'S': 2.86, 'P': -0.37}
gg_14 = {'Q': -1.56, 'L': -4.79, 'T': -3.07, 'C': 0.93, 'I': -1.21, 'G': 0.15, 'V': 4.22, 'K': 1.78, 'M': -3.09, 'F': 1.73, 'N': -0.89, 'R': 0.82, 'H': -0.77, 'E': -0.06, 'W': 1.64, 'A': 4.39, 'D': 1.28, 'Y': 0.2, 'S': -1.88, 'P': 0.17}
gg_15 = {'Q': 6.22, 'L': 0.8, 'T': 0.2, 'C': 1.43, 'I': -1.78, 'G': -0.53, 'V': 1.06, 'K': -2.71, 'M': -1.39, 'F': 2.14, 'N': 3.13, 'R': 1.32, 'H': -4.18, 'E': -0.35, 'W': -0.72, 'A': 0.18, 'D': -1.98, 'Y': -0.76, 'S': -2.42, 'P': 0.36}
gg_16 = {'Q': -0.18, 'L': -1.43, 'T': -2.2, 'C': 1.45, 'I': 5.71, 'G': 0.35, 'V': -1.31, 'K': 1.62, 'M': -1.02, 'F': 1.1, 'N': 0.79, 'R': 0.69, 'H': -2.91, 'E': 1.51, 'W': 1.75, 'A': -2.6, 'D': 0.05, 'Y': -5.19, 'S': 1.75, 'P': 0.08}
gg_17 = {'Q': 2.72, 'L': 0.63, 'T': 3.73, 'C': -1.15, 'I': 1.54, 'G': 0.3, 'V': -1.97, 'K': 0.96, 'M': -4.32, 'F': 0.68, 'N': -1.54, 'R': -2.62, 'H': 3.37, 'E': -2.29, 'W': 2.73, 'A': 1.49, 'D': 0.9, 'Y': -2.56, 'S': -2.77, 'P': 0.16}
gg_18 = {'Q': 4.35, 'L': -0.24, 'T': -5.46, 'C': -1.64, 'I': 2.11, 'G': 0.32, 'V': -1.21, 'K': -1.09, 'M': -1.34, 'F': 1.46, 'N': -1.71, 'R': -1.49, 'H': 1.87, 'E': -1.47, 'W': -2.2, 'A': 0.46, 'D': 1.38, 'Y': 2.87, 'S': 3.36, 'P': -0.34}
gg_19 = {'Q': 0.92, 'L': 1.01, 'T': -0.73, 'C': -1.05, 'I': -4.18, 'G': 0.05, 'V': 4.77, 'K': 1.36, 'M': 0.09, 'F': 2.33, 'N': -0.25, 'R': -2.57, 'H': 2.17, 'E': 0.15, 'W': 0.9, 'A': -4.22, 'D': -0.03, 'Y': -3.43, 'S': 2.67, 'P': 0.04}

# Package all georgiev parameters
georgiev_parameters = [gg_1, gg_2, gg_3, gg_4, gg_5, gg_6, gg_7, gg_8, gg_9,
                       gg_10, gg_11, gg_12, gg_13, gg_14, gg_15, gg_16, gg_17,
                       gg_18, gg_19]


def get_georgiev_params_for_aa(aa):
    return [gg[aa] for gg in georgiev_parameters]


def get_georgiev_params_for_seq(s):
    return np.concatenate([get_georgiev_params_for_aa(aa) for aa in s])


def seqs_to_georgiev(seqs):
    return np.stack([get_georgiev_params_for_seq(s) for s in seqs])