# -*- 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 computing the quasi sequence order descriptors based on the
given protein sequence. We can obtain two types of descriptors: Sequence-order-coupling
number and quasi-sequence-order descriptors. Two distance matrixes between 20 amino acids
are employed. You can freely use and distribute it. If you have any problem, please contact
us immediately.
References:
[1]:Kuo-Chen Chou. Prediction of Protein Subcellar Locations by Incorporating
Quasi-Sequence-Order Effect. Biochemical and Biophysical Research Communications
2000, 278, 477-483.
[2]: Kuo-Chen Chou and Yu-Dong Cai. Prediction of Protein sucellular locations by
GO-FunD-PseAA predictor, Biochemical and Biophysical Research Communications,
2004, 320, 1236-1239.
[3]:Gisbert Schneider and Paul wrede. The Rational Design of Amino Acid
Sequences by Artifical Neural Networks and Simulated Molecular Evolution: Do
Novo Design of an Idealized Leader Cleavge Site. Biophys Journal, 1994, 66,
335-344.
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com
##############################################################################################
"""
# Core Library modules
import math
import string
AALetter = [
"A",
"R",
"N",
"D",
"C",
"E",
"Q",
"G",
"H",
"I",
"L",
"K",
"M",
"F",
"P",
"S",
"T",
"W",
"Y",
"V",
]
## Distance is the Schneider-Wrede physicochemical distance matrix used by Chou et. al.
_Distance1 = {
"GW": 0.923,
"GV": 0.464,
"GT": 0.272,
"GS": 0.158,
"GR": 1.0,
"GQ": 0.467,
"GP": 0.323,
"GY": 0.728,
"GG": 0.0,
"GF": 0.727,
"GE": 0.807,
"GD": 0.776,
"GC": 0.312,
"GA": 0.206,
"GN": 0.381,
"GM": 0.557,
"GL": 0.591,
"GK": 0.894,
"GI": 0.592,
"GH": 0.769,
"ME": 0.879,
"MD": 0.932,
"MG": 0.569,
"MF": 0.182,
"MA": 0.383,
"MC": 0.276,
"MM": 0.0,
"ML": 0.062,
"MN": 0.447,
"MI": 0.058,
"MH": 0.648,
"MK": 0.884,
"MT": 0.358,
"MW": 0.391,
"MV": 0.12,
"MQ": 0.372,
"MP": 0.285,
"MS": 0.417,
"MR": 1.0,
"MY": 0.255,
"FP": 0.42,
"FQ": 0.459,
"FR": 1.0,
"FS": 0.548,
"FT": 0.499,
"FV": 0.252,
"FW": 0.207,
"FY": 0.179,
"FA": 0.508,
"FC": 0.405,
"FD": 0.977,
"FE": 0.918,
"FF": 0.0,
"FG": 0.69,
"FH": 0.663,
"FI": 0.128,
"FK": 0.903,
"FL": 0.131,
"FM": 0.169,
"FN": 0.541,
"SY": 0.615,
"SS": 0.0,
"SR": 1.0,
"SQ": 0.358,
"SP": 0.181,
"SW": 0.827,
"SV": 0.342,
"ST": 0.174,
"SK": 0.883,
"SI": 0.478,
"SH": 0.718,
"SN": 0.289,
"SM": 0.44,
"SL": 0.474,
"SC": 0.185,
"SA": 0.1,
"SG": 0.17,
"SF": 0.622,
"SE": 0.812,
"SD": 0.801,
"YI": 0.23,
"YH": 0.678,
"YK": 0.904,
"YM": 0.268,
"YL": 0.219,
"YN": 0.512,
"YA": 0.587,
"YC": 0.478,
"YE": 0.932,
"YD": 1.0,
"YG": 0.782,
"YF": 0.202,
"YY": 0.0,
"YQ": 0.404,
"YP": 0.444,
"YS": 0.612,
"YR": 0.995,
"YT": 0.557,
"YW": 0.244,
"YV": 0.328,
"LF": 0.139,
"LG": 0.596,
"LD": 0.944,
"LE": 0.892,
"LC": 0.296,
"LA": 0.405,
"LN": 0.452,
"LL": 0.0,
"LM": 0.062,
"LK": 0.893,
"LH": 0.653,
"LI": 0.013,
"LV": 0.133,
"LW": 0.341,
"LT": 0.397,
"LR": 1.0,
"LS": 0.443,
"LP": 0.309,
"LQ": 0.376,
"LY": 0.205,
"RT": 0.808,
"RV": 0.914,
"RW": 1.0,
"RP": 0.796,
"RQ": 0.668,
"RR": 0.0,
"RS": 0.86,
"RY": 0.859,
"RD": 0.305,
"RE": 0.225,
"RF": 0.977,
"RG": 0.928,
"RA": 0.919,
"RC": 0.905,
"RL": 0.92,
"RM": 0.908,
"RN": 0.69,
"RH": 0.498,
"RI": 0.929,
"RK": 0.141,
"VH": 0.649,
"VI": 0.135,
"EM": 0.83,
"EL": 0.854,
"EN": 0.599,
"EI": 0.86,
"EH": 0.406,
"EK": 0.143,
"EE": 0.0,
"ED": 0.133,
"EG": 0.779,
"EF": 0.932,
"EA": 0.79,
"EC": 0.788,
"VM": 0.12,
"EY": 0.837,
"VN": 0.38,
"ET": 0.682,
"EW": 1.0,
"EV": 0.824,
"EQ": 0.598,
"EP": 0.688,
"ES": 0.726,
"ER": 0.234,
"VP": 0.212,
"VQ": 0.339,
"VR": 1.0,
"VT": 0.305,
"VW": 0.472,
"KC": 0.871,
"KA": 0.889,
"KG": 0.9,
"KF": 0.957,
"KE": 0.149,
"KD": 0.279,
"KK": 0.0,
"KI": 0.899,
"KH": 0.438,
"KN": 0.667,
"KM": 0.871,
"KL": 0.892,
"KS": 0.825,
"KR": 0.154,
"KQ": 0.639,
"KP": 0.757,
"KW": 1.0,
"KV": 0.882,
"KT": 0.759,
"KY": 0.848,
"DN": 0.56,
"DL": 0.841,
"DM": 0.819,
"DK": 0.249,
"DH": 0.435,
"DI": 0.847,
"DF": 0.924,
"DG": 0.697,
"DD": 0.0,
"DE": 0.124,
"DC": 0.742,
"DA": 0.729,
"DY": 0.836,
"DV": 0.797,
"DW": 1.0,
"DT": 0.649,
"DR": 0.295,
"DS": 0.667,
"DP": 0.657,
"DQ": 0.584,
"QQ": 0.0,
"QP": 0.272,
"QS": 0.461,
"QR": 1.0,
"QT": 0.389,
"QW": 0.831,
"QV": 0.464,
"QY": 0.522,
"QA": 0.512,
"QC": 0.462,
"QE": 0.861,
"QD": 0.903,
"QG": 0.648,
"QF": 0.671,
"QI": 0.532,
"QH": 0.765,
"QK": 0.881,
"QM": 0.505,
"QL": 0.518,
"QN": 0.181,
"WG": 0.829,
"WF": 0.196,
"WE": 0.931,
"WD": 1.0,
"WC": 0.56,
"WA": 0.658,
"WN": 0.631,
"WM": 0.344,
"WL": 0.304,
"WK": 0.892,
"WI": 0.305,
"WH": 0.678,
"WW": 0.0,
"WV": 0.418,
"WT": 0.638,
"WS": 0.689,
"WR": 0.968,
"WQ": 0.538,
"WP": 0.555,
"WY": 0.204,
"PR": 1.0,
"PS": 0.196,
"PP": 0.0,
"PQ": 0.228,
"PV": 0.244,
"PW": 0.72,
"PT": 0.161,
"PY": 0.481,
"PC": 0.179,
"PA": 0.22,
"PF": 0.515,
"PG": 0.376,
"PD": 0.852,
"PE": 0.831,
"PK": 0.875,
"PH": 0.696,
"PI": 0.363,
"PN": 0.231,
"PL": 0.357,
"PM": 0.326,
"CK": 0.887,
"CI": 0.304,
"CH": 0.66,
"CN": 0.324,
"CM": 0.277,
"CL": 0.301,
"CC": 0.0,
"CA": 0.114,
"CG": 0.32,
"CF": 0.437,
"CE": 0.838,
"CD": 0.847,
"CY": 0.457,
"CS": 0.176,
"CR": 1.0,
"CQ": 0.341,
"CP": 0.157,
"CW": 0.639,
"CV": 0.167,
"CT": 0.233,
"IY": 0.213,
"VA": 0.275,
"VC": 0.165,
"VD": 0.9,
"VE": 0.867,
"VF": 0.269,
"VG": 0.471,
"IQ": 0.383,
"IP": 0.311,
"IS": 0.443,
"IR": 1.0,
"VL": 0.134,
"IT": 0.396,
"IW": 0.339,
"IV": 0.133,
"II": 0.0,
"IH": 0.652,
"IK": 0.892,
"VS": 0.322,
"IM": 0.057,
"IL": 0.013,
"VV": 0.0,
"IN": 0.457,
"IA": 0.403,
"VY": 0.31,
"IC": 0.296,
"IE": 0.891,
"ID": 0.942,
"IG": 0.592,
"IF": 0.134,
"HY": 0.821,
"HR": 0.697,
"HS": 0.865,
"HP": 0.777,
"HQ": 0.716,
"HV": 0.831,
"HW": 0.981,
"HT": 0.834,
"HK": 0.566,
"HH": 0.0,
"HI": 0.848,
"HN": 0.754,
"HL": 0.842,
"HM": 0.825,
"HC": 0.836,
"HA": 0.896,
"HF": 0.907,
"HG": 1.0,
"HD": 0.629,
"HE": 0.547,
"NH": 0.78,
"NI": 0.615,
"NK": 0.891,
"NL": 0.603,
"NM": 0.588,
"NN": 0.0,
"NA": 0.424,
"NC": 0.425,
"ND": 0.838,
"NE": 0.835,
"NF": 0.766,
"NG": 0.512,
"NY": 0.641,
"NP": 0.266,
"NQ": 0.175,
"NR": 1.0,
"NS": 0.361,
"NT": 0.368,
"NV": 0.503,
"NW": 0.945,
"TY": 0.596,
"TV": 0.345,
"TW": 0.816,
"TT": 0.0,
"TR": 1.0,
"TS": 0.185,
"TP": 0.159,
"TQ": 0.322,
"TN": 0.315,
"TL": 0.453,
"TM": 0.403,
"TK": 0.866,
"TH": 0.737,
"TI": 0.455,
"TF": 0.604,
"TG": 0.312,
"TD": 0.83,
"TE": 0.812,
"TC": 0.261,
"TA": 0.251,
"AA": 0.0,
"AC": 0.112,
"AE": 0.827,
"AD": 0.819,
"AG": 0.208,
"AF": 0.54,
"AI": 0.407,
"AH": 0.696,
"AK": 0.891,
"AM": 0.379,
"AL": 0.406,
"AN": 0.318,
"AQ": 0.372,
"AP": 0.191,
"AS": 0.094,
"AR": 1.0,
"AT": 0.22,
"AW": 0.739,
"AV": 0.273,
"AY": 0.552,
"VK": 0.889,
}
## Distance is the Grantham chemical distance matrix used by Grantham et. al.
_Distance2 = {
"GW": 0.923,
"GV": 0.464,
"GT": 0.272,
"GS": 0.158,
"GR": 1.0,
"GQ": 0.467,
"GP": 0.323,
"GY": 0.728,
"GG": 0.0,
"GF": 0.727,
"GE": 0.807,
"GD": 0.776,
"GC": 0.312,
"GA": 0.206,
"GN": 0.381,
"GM": 0.557,
"GL": 0.591,
"GK": 0.894,
"GI": 0.592,
"GH": 0.769,
"ME": 0.879,
"MD": 0.932,
"MG": 0.569,
"MF": 0.182,
"MA": 0.383,
"MC": 0.276,
"MM": 0.0,
"ML": 0.062,
"MN": 0.447,
"MI": 0.058,
"MH": 0.648,
"MK": 0.884,
"MT": 0.358,
"MW": 0.391,
"MV": 0.12,
"MQ": 0.372,
"MP": 0.285,
"MS": 0.417,
"MR": 1.0,
"MY": 0.255,
"FP": 0.42,
"FQ": 0.459,
"FR": 1.0,
"FS": 0.548,
"FT": 0.499,
"FV": 0.252,
"FW": 0.207,
"FY": 0.179,
"FA": 0.508,
"FC": 0.405,
"FD": 0.977,
"FE": 0.918,
"FF": 0.0,
"FG": 0.69,
"FH": 0.663,
"FI": 0.128,
"FK": 0.903,
"FL": 0.131,
"FM": 0.169,
"FN": 0.541,
"SY": 0.615,
"SS": 0.0,
"SR": 1.0,
"SQ": 0.358,
"SP": 0.181,
"SW": 0.827,
"SV": 0.342,
"ST": 0.174,
"SK": 0.883,
"SI": 0.478,
"SH": 0.718,
"SN": 0.289,
"SM": 0.44,
"SL": 0.474,
"SC": 0.185,
"SA": 0.1,
"SG": 0.17,
"SF": 0.622,
"SE": 0.812,
"SD": 0.801,
"YI": 0.23,
"YH": 0.678,
"YK": 0.904,
"YM": 0.268,
"YL": 0.219,
"YN": 0.512,
"YA": 0.587,
"YC": 0.478,
"YE": 0.932,
"YD": 1.0,
"YG": 0.782,
"YF": 0.202,
"YY": 0.0,
"YQ": 0.404,
"YP": 0.444,
"YS": 0.612,
"YR": 0.995,
"YT": 0.557,
"YW": 0.244,
"YV": 0.328,
"LF": 0.139,
"LG": 0.596,
"LD": 0.944,
"LE": 0.892,
"LC": 0.296,
"LA": 0.405,
"LN": 0.452,
"LL": 0.0,
"LM": 0.062,
"LK": 0.893,
"LH": 0.653,
"LI": 0.013,
"LV": 0.133,
"LW": 0.341,
"LT": 0.397,
"LR": 1.0,
"LS": 0.443,
"LP": 0.309,
"LQ": 0.376,
"LY": 0.205,
"RT": 0.808,
"RV": 0.914,
"RW": 1.0,
"RP": 0.796,
"RQ": 0.668,
"RR": 0.0,
"RS": 0.86,
"RY": 0.859,
"RD": 0.305,
"RE": 0.225,
"RF": 0.977,
"RG": 0.928,
"RA": 0.919,
"RC": 0.905,
"RL": 0.92,
"RM": 0.908,
"RN": 0.69,
"RH": 0.498,
"RI": 0.929,
"RK": 0.141,
"VH": 0.649,
"VI": 0.135,
"EM": 0.83,
"EL": 0.854,
"EN": 0.599,
"EI": 0.86,
"EH": 0.406,
"EK": 0.143,
"EE": 0.0,
"ED": 0.133,
"EG": 0.779,
"EF": 0.932,
"EA": 0.79,
"EC": 0.788,
"VM": 0.12,
"EY": 0.837,
"VN": 0.38,
"ET": 0.682,
"EW": 1.0,
"EV": 0.824,
"EQ": 0.598,
"EP": 0.688,
"ES": 0.726,
"ER": 0.234,
"VP": 0.212,
"VQ": 0.339,
"VR": 1.0,
"VT": 0.305,
"VW": 0.472,
"KC": 0.871,
"KA": 0.889,
"KG": 0.9,
"KF": 0.957,
"KE": 0.149,
"KD": 0.279,
"KK": 0.0,
"KI": 0.899,
"KH": 0.438,
"KN": 0.667,
"KM": 0.871,
"KL": 0.892,
"KS": 0.825,
"KR": 0.154,
"KQ": 0.639,
"KP": 0.757,
"KW": 1.0,
"KV": 0.882,
"KT": 0.759,
"KY": 0.848,
"DN": 0.56,
"DL": 0.841,
"DM": 0.819,
"DK": 0.249,
"DH": 0.435,
"DI": 0.847,
"DF": 0.924,
"DG": 0.697,
"DD": 0.0,
"DE": 0.124,
"DC": 0.742,
"DA": 0.729,
"DY": 0.836,
"DV": 0.797,
"DW": 1.0,
"DT": 0.649,
"DR": 0.295,
"DS": 0.667,
"DP": 0.657,
"DQ": 0.584,
"QQ": 0.0,
"QP": 0.272,
"QS": 0.461,
"QR": 1.0,
"QT": 0.389,
"QW": 0.831,
"QV": 0.464,
"QY": 0.522,
"QA": 0.512,
"QC": 0.462,
"QE": 0.861,
"QD": 0.903,
"QG": 0.648,
"QF": 0.671,
"QI": 0.532,
"QH": 0.765,
"QK": 0.881,
"QM": 0.505,
"QL": 0.518,
"QN": 0.181,
"WG": 0.829,
"WF": 0.196,
"WE": 0.931,
"WD": 1.0,
"WC": 0.56,
"WA": 0.658,
"WN": 0.631,
"WM": 0.344,
"WL": 0.304,
"WK": 0.892,
"WI": 0.305,
"WH": 0.678,
"WW": 0.0,
"WV": 0.418,
"WT": 0.638,
"WS": 0.689,
"WR": 0.968,
"WQ": 0.538,
"WP": 0.555,
"WY": 0.204,
"PR": 1.0,
"PS": 0.196,
"PP": 0.0,
"PQ": 0.228,
"PV": 0.244,
"PW": 0.72,
"PT": 0.161,
"PY": 0.481,
"PC": 0.179,
"PA": 0.22,
"PF": 0.515,
"PG": 0.376,
"PD": 0.852,
"PE": 0.831,
"PK": 0.875,
"PH": 0.696,
"PI": 0.363,
"PN": 0.231,
"PL": 0.357,
"PM": 0.326,
"CK": 0.887,
"CI": 0.304,
"CH": 0.66,
"CN": 0.324,
"CM": 0.277,
"CL": 0.301,
"CC": 0.0,
"CA": 0.114,
"CG": 0.32,
"CF": 0.437,
"CE": 0.838,
"CD": 0.847,
"CY": 0.457,
"CS": 0.176,
"CR": 1.0,
"CQ": 0.341,
"CP": 0.157,
"CW": 0.639,
"CV": 0.167,
"CT": 0.233,
"IY": 0.213,
"VA": 0.275,
"VC": 0.165,
"VD": 0.9,
"VE": 0.867,
"VF": 0.269,
"VG": 0.471,
"IQ": 0.383,
"IP": 0.311,
"IS": 0.443,
"IR": 1.0,
"VL": 0.134,
"IT": 0.396,
"IW": 0.339,
"IV": 0.133,
"II": 0.0,
"IH": 0.652,
"IK": 0.892,
"VS": 0.322,
"IM": 0.057,
"IL": 0.013,
"VV": 0.0,
"IN": 0.457,
"IA": 0.403,
"VY": 0.31,
"IC": 0.296,
"IE": 0.891,
"ID": 0.942,
"IG": 0.592,
"IF": 0.134,
"HY": 0.821,
"HR": 0.697,
"HS": 0.865,
"HP": 0.777,
"HQ": 0.716,
"HV": 0.831,
"HW": 0.981,
"HT": 0.834,
"HK": 0.566,
"HH": 0.0,
"HI": 0.848,
"HN": 0.754,
"HL": 0.842,
"HM": 0.825,
"HC": 0.836,
"HA": 0.896,
"HF": 0.907,
"HG": 1.0,
"HD": 0.629,
"HE": 0.547,
"NH": 0.78,
"NI": 0.615,
"NK": 0.891,
"NL": 0.603,
"NM": 0.588,
"NN": 0.0,
"NA": 0.424,
"NC": 0.425,
"ND": 0.838,
"NE": 0.835,
"NF": 0.766,
"NG": 0.512,
"NY": 0.641,
"NP": 0.266,
"NQ": 0.175,
"NR": 1.0,
"NS": 0.361,
"NT": 0.368,
"NV": 0.503,
"NW": 0.945,
"TY": 0.596,
"TV": 0.345,
"TW": 0.816,
"TT": 0.0,
"TR": 1.0,
"TS": 0.185,
"TP": 0.159,
"TQ": 0.322,
"TN": 0.315,
"TL": 0.453,
"TM": 0.403,
"TK": 0.866,
"TH": 0.737,
"TI": 0.455,
"TF": 0.604,
"TG": 0.312,
"TD": 0.83,
"TE": 0.812,
"TC": 0.261,
"TA": 0.251,
"AA": 0.0,
"AC": 0.112,
"AE": 0.827,
"AD": 0.819,
"AG": 0.208,
"AF": 0.54,
"AI": 0.407,
"AH": 0.696,
"AK": 0.891,
"AM": 0.379,
"AL": 0.406,
"AN": 0.318,
"AQ": 0.372,
"AP": 0.191,
"AS": 0.094,
"AR": 1.0,
"AT": 0.22,
"AW": 0.739,
"AV": 0.273,
"AY": 0.552,
"VK": 0.889,
}
#############################################################################################
#############################################################################################
[docs]def GetSequenceOrderCouplingNumber(ProteinSequence, d=1, distancematrix=_Distance1):
"""
###############################################################################
Computing the dth-rank sequence order coupling number for a protein.
Usage:
result = GetSequenceOrderCouplingNumber(protein,d)
Input: protein is a pure protein sequence.
d is the gap between two amino acids.
Output: result is numeric value.
###############################################################################
"""
NumProtein = len(ProteinSequence)
tau = 0.0
for i in range(NumProtein - d):
temp1 = ProteinSequence[i]
temp2 = ProteinSequence[i + d]
tau = tau + math.pow(distancematrix[temp1 + temp2], 2)
return round(tau, 3)
#############################################################################################
[docs]def GetSequenceOrderCouplingNumberp(ProteinSequence, maxlag=30, distancematrix={}):
"""
###############################################################################
Computing the sequence order coupling numbers from 1 to maxlag
for a given protein sequence based on the user-defined property.
Usage:
result = GetSequenceOrderCouplingNumberp(protein, maxlag,distancematrix)
Input: protein is a pure protein sequence
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 30.
distancematrix is the a dict form containing 400 distance values
Output: result is a dict form containing all sequence order coupling numbers based
on the given property
###############################################################################
"""
NumProtein = len(ProteinSequence)
Tau = {}
for i in range(maxlag):
Tau["tau" + str(i + 1)] = GetSequenceOrderCouplingNumber(
ProteinSequence, i + 1, distancematrix
)
return Tau
#############################################################################################
[docs]def GetSequenceOrderCouplingNumberSW(
ProteinSequence, maxlag=30, distancematrix=_Distance1
):
"""
###############################################################################
Computing the sequence order coupling numbers from 1 to maxlag
for a given protein sequence based on the Schneider-Wrede physicochemical
distance matrix
Usage:
result = GetSequenceOrderCouplingNumberSW(protein, maxlag,distancematrix)
Input: protein is a pure protein sequence
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 30.
distancematrix is a dict form containing Schneider-Wrede physicochemical
distance matrix. omitted!
Output: result is a dict form containing all sequence order coupling numbers based
on the Schneider-Wrede physicochemical distance matrix
###############################################################################
"""
NumProtein = len(ProteinSequence)
Tau = {}
for i in range(maxlag):
Tau["tausw" + str(i + 1)] = GetSequenceOrderCouplingNumber(
ProteinSequence, i + 1, distancematrix
)
return Tau
#############################################################################################
[docs]def GetSequenceOrderCouplingNumberGrant(
ProteinSequence, maxlag=30, distancematrix=_Distance2
):
"""
###############################################################################
Computing the sequence order coupling numbers from 1 to maxlag
for a given protein sequence based on the Grantham chemical distance
matrix.
Usage:
result = GetSequenceOrderCouplingNumberGrant(protein, maxlag,distancematrix)
Input: protein is a pure protein sequence
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 30.
distancematrix is a dict form containing Grantham chemical distance
matrix. omitted!
Output: result is a dict form containing all sequence order coupling numbers
based on the Grantham chemical distance matrix
###############################################################################
"""
NumProtein = len(ProteinSequence)
Tau = {}
for i in range(maxlag):
Tau["taugrant" + str(i + 1)] = GetSequenceOrderCouplingNumber(
ProteinSequence, i + 1, distancematrix
)
return Tau
#############################################################################################
[docs]def GetSequenceOrderCouplingNumberTotal(ProteinSequence, maxlag=30):
"""
###############################################################################
Computing the sequence order coupling numbers from 1 to maxlag
for a given protein sequence.
Usage:
result = GetSequenceOrderCouplingNumberTotal(protein, maxlag)
Input: protein is a pure protein sequence
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 30.
Output: result is a dict form containing all sequence order coupling numbers
###############################################################################
"""
Tau = {}
Tau.update(GetSequenceOrderCouplingNumberSW(ProteinSequence, maxlag=maxlag))
Tau.update(GetSequenceOrderCouplingNumberGrant(ProteinSequence, maxlag=maxlag))
return Tau
#############################################################################################
[docs]def GetAAComposition(ProteinSequence):
"""
###############################################################################
Calculate the composition of Amino acids
for a given protein sequence.
Usage:
result=CalculateAAComposition(protein)
Input: protein is a pure protein sequence.
Output: result is a dict form containing the composition of
20 amino acids.
###############################################################################
"""
LengthSequence = len(ProteinSequence)
Result = {}
for i in AALetter:
Result[i] = round(float(ProteinSequence.count(i)) / LengthSequence, 3)
return Result
#############################################################################################
[docs]def GetQuasiSequenceOrder1(ProteinSequence, maxlag=30, weight=0.1, distancematrix={}):
"""
###############################################################################
Computing the first 20 quasi-sequence-order descriptors for
a given protein sequence.
Usage:
result = GetQuasiSequenceOrder1(protein,maxlag,weigt)
see method GetQuasiSequenceOrder for the choice of parameters.
###############################################################################
"""
rightpart = 0.0
for i in range(maxlag):
rightpart = rightpart + GetSequenceOrderCouplingNumber(
ProteinSequence, i + 1, distancematrix
)
AAC = GetAAComposition(ProteinSequence)
result = {}
temp = 1 + weight * rightpart
for index, i in enumerate(AALetter):
result["QSO" + str(index + 1)] = round(AAC[i] / temp, 6)
return result
#############################################################################################
[docs]def GetQuasiSequenceOrder2(ProteinSequence, maxlag=30, weight=0.1, distancematrix={}):
"""
###############################################################################
Computing the last maxlag quasi-sequence-order descriptors for
a given protein sequence.
Usage:
result = GetQuasiSequenceOrder2(protein,maxlag,weigt)
see method GetQuasiSequenceOrder for the choice of parameters.
###############################################################################
"""
rightpart = []
for i in range(maxlag):
rightpart.append(
GetSequenceOrderCouplingNumber(ProteinSequence, i + 1, distancematrix)
)
AAC = GetAAComposition(ProteinSequence)
result = {}
temp = 1 + weight * sum(rightpart)
for index in range(20, 20 + maxlag):
result["QSO" + str(index + 1)] = round(weight * rightpart[index - 20] / temp, 6)
return result
#############################################################################################
[docs]def GetQuasiSequenceOrder1SW(
ProteinSequence, maxlag=30, weight=0.1, distancematrix=_Distance1
):
"""
###############################################################################
Computing the first 20 quasi-sequence-order descriptors for
a given protein sequence.
Usage:
result = GetQuasiSequenceOrder1SW(protein,maxlag,weigt)
see method GetQuasiSequenceOrder for the choice of parameters.
###############################################################################
"""
rightpart = 0.0
for i in range(maxlag):
rightpart = rightpart + GetSequenceOrderCouplingNumber(
ProteinSequence, i + 1, distancematrix
)
AAC = GetAAComposition(ProteinSequence)
result = {}
temp = 1 + weight * rightpart
for index, i in enumerate(AALetter):
result["QSOSW" + str(index + 1)] = round(AAC[i] / temp, 6)
return result
#############################################################################################
[docs]def GetQuasiSequenceOrder2SW(
ProteinSequence, maxlag=30, weight=0.1, distancematrix=_Distance1
):
"""
###############################################################################
Computing the last maxlag quasi-sequence-order descriptors for
a given protein sequence.
Usage:
result = GetQuasiSequenceOrder2SW(protein,maxlag,weigt)
see method GetQuasiSequenceOrder for the choice of parameters.
###############################################################################
"""
rightpart = []
for i in range(maxlag):
rightpart.append(
GetSequenceOrderCouplingNumber(ProteinSequence, i + 1, distancematrix)
)
AAC = GetAAComposition(ProteinSequence)
result = {}
temp = 1 + weight * sum(rightpart)
for index in range(20, 20 + maxlag):
result["QSOSW" + str(index + 1)] = round(
weight * rightpart[index - 20] / temp, 6
)
return result
#############################################################################################
[docs]def GetQuasiSequenceOrder1Grant(
ProteinSequence, maxlag=30, weight=0.1, distancematrix=_Distance2
):
"""
###############################################################################
Computing the first 20 quasi-sequence-order descriptors for
a given protein sequence.
Usage:
result = GetQuasiSequenceOrder1Grant(protein,maxlag,weigt)
see method GetQuasiSequenceOrder for the choice of parameters.
###############################################################################
"""
rightpart = 0.0
for i in range(maxlag):
rightpart = rightpart + GetSequenceOrderCouplingNumber(
ProteinSequence, i + 1, distancematrix
)
AAC = GetAAComposition(ProteinSequence)
result = {}
temp = 1 + weight * rightpart
for index, i in enumerate(AALetter):
result["QSOgrant" + str(index + 1)] = round(AAC[i] / temp, 6)
return result
#############################################################################################
[docs]def GetQuasiSequenceOrder2Grant(
ProteinSequence, maxlag=30, weight=0.1, distancematrix=_Distance2
):
"""
###############################################################################
Computing the last maxlag quasi-sequence-order descriptors for
a given protein sequence.
Usage:
result = GetQuasiSequenceOrder2Grant(protein,maxlag,weigt)
see method GetQuasiSequenceOrder for the choice of parameters.
###############################################################################
"""
rightpart = []
for i in range(maxlag):
rightpart.append(
GetSequenceOrderCouplingNumber(ProteinSequence, i + 1, distancematrix)
)
AAC = GetAAComposition(ProteinSequence)
result = {}
temp = 1 + weight * sum(rightpart)
for index in range(20, 20 + maxlag):
result["QSOgrant" + str(index + 1)] = round(
weight * rightpart[index - 20] / temp, 6
)
return result
#############################################################################################
[docs]def GetQuasiSequenceOrder(ProteinSequence, maxlag=30, weight=0.1):
"""
###############################################################################
Computing quasi-sequence-order descriptors for a given protein.
[1]:Kuo-Chen Chou. Prediction of Protein Subcellar Locations by
Incorporating Quasi-Sequence-Order Effect. Biochemical and Biophysical
Research Communications 2000, 278, 477-483.
Usage:
result = GetQuasiSequenceOrder(protein,maxlag,weight)
Input: protein is a pure protein sequence
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 30.
weight is a weight factor. please see reference 1 for its choice. default is 0.1.
Output: result is a dict form containing all quasi-sequence-order descriptors
###############################################################################
"""
result = dict()
result.update(GetQuasiSequenceOrder1SW(ProteinSequence, maxlag, weight, _Distance1))
result.update(GetQuasiSequenceOrder2SW(ProteinSequence, maxlag, weight, _Distance1))
result.update(
GetQuasiSequenceOrder1Grant(ProteinSequence, maxlag, weight, _Distance2)
)
result.update(
GetQuasiSequenceOrder2Grant(ProteinSequence, maxlag, weight, _Distance2)
)
return result
#############################################################################################
[docs]def GetQuasiSequenceOrderp(ProteinSequence, maxlag=30, weight=0.1, distancematrix={}):
"""
###############################################################################
Computing quasi-sequence-order descriptors for a given protein.
[1]:Kuo-Chen Chou. Prediction of Protein Subcellar Locations by
Incorporating Quasi-Sequence-Order Effect. Biochemical and Biophysical
Research Communications 2000, 278, 477-483.
Usage:
result = GetQuasiSequenceOrderp(protein,maxlag,weight,distancematrix)
Input: protein is a pure protein sequence
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 30.
weight is a weight factor. please see reference 1 for its choice. default is 0.1.
distancematrix is a dict form containing 400 distance values
Output: result is a dict form containing all quasi-sequence-order descriptors
###############################################################################
"""
result = dict()
result.update(
GetQuasiSequenceOrder1(ProteinSequence, maxlag, weight, distancematrix)
)
result.update(
GetQuasiSequenceOrder2(ProteinSequence, maxlag, weight, distancematrix)
)
return result
#############################################################################################
if __name__ == "__main__":
protein = "ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT\
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC\
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK\
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK\
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF\
APTEVRRYTGGHERQKRVPFVVQSQHLLAGILQQQKNLLAAVEAQQQMLKLTIWGVK"
print(len(protein))
SCN = GetSequenceOrderCouplingNumberTotal(protein, maxlag=30)
print(len(SCN))
for i in SCN:
print(i, SCN[i])
QSO1 = GetQuasiSequenceOrder1(
protein, maxlag=30, weight=0.1, distancematrix=_Distance1
)
print(QSO1)
for i in QSO1:
print(i, QSO1[i])
QSO2 = GetQuasiSequenceOrder2(
protein, maxlag=30, weight=0.1, distancematrix=_Distance1
)
print(QSO2)
for i in QSO2:
print(i, QSO2[i])
QSO = GetQuasiSequenceOrder(protein, maxlag=30, weight=0.1)
print(len(QSO))
for i in QSO:
print(i, QSO[i])
SCN = GetSequenceOrderCouplingNumberp(protein, maxlag=30, distancematrix=_Distance1)
print(len(SCN))
for i in SCN:
print(i, SCN[i])
QSO = GetQuasiSequenceOrderp(protein, maxlag=30, distancematrix=_Distance1)
print(len(QSO))
for i in QSO:
print(i, QSO[i])
