# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
###############################################################################
This module is used for calculating the conjoint triad features only from the
protein sequence information. You can get 7*7*7=343 features.You can freely
use and distribute it. If you hava any problem, you could contact with us timely!
Reference:
Juwen Shen, Jian Zhang, Xiaomin Luo, Weiliang Zhu, Kunqian Yu, Kaixian Chen,
Yixue Li, Huanliang Jiang. Predicting proten-protein interactions based only
on sequences inforamtion. PNAS. 2007 (104) 4337-4341.
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com
###############################################################################
"""
import string
###############################################################################
AALetter = ["A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"]
# a Dipole scale (Debye): -, Dipole<1.0; +, 1.0<Dipole<2.0; ++, 2.0<Dipole<3.0; +++, Dipole>3.0; +'+'+', Dipole>3.0 with opposite orientation.
# b Volume scale (Å3): -, Volume<50; +, Volume> 50.
# c Cys is separated from class 3 because of its ability to form disulfide bonds.
_repmat = {1: ["A", 'G', 'V'], 2: ['I', 'L', 'F', 'P'], 3: ['Y', 'M', 'T', 'S'], 4: ['H', 'N', 'Q', 'W'], 5: ['R', 'K'],
6: ['D', 'E'], 7: ['C']}
###############################################################################
def _Str2Num(proteinsequence):
"""
translate the amino acid letter into the corresponding class based on the
given form.
"""
repmat = {}
for i in _repmat:
for j in _repmat[i]:
repmat[j] = i
res = proteinsequence
for i in repmat:
res = res.replace(i, str(repmat[i]))
return res
###############################################################################
[docs]def CalculateConjointTriad(proteinsequence):
"""
Calculate the conjoint triad features from protein sequence.
Useage:
res = CalculateConjointTriad(protein)
Input: protein is a pure protein sequence.
Output is a dict form containing all 343 conjoint triad features.
"""
res = {}
proteinnum = _Str2Num(proteinsequence)
for i in range(8):
for j in range(8):
for k in range(8):
temp = str(i) + str(j) + str(k)
res[temp] = proteinnum.count(temp)
return res
###############################################################################
if __name__ == "__main__":
protein = "ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"
print CalculateConjointTriad(protein)
