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1 # -*- coding: utf-8 -*-
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2 """
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3 Compute the composition, transition and distribution descriptors based on the
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4 different properties of AADs.
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5 The AADs with the same properties is marked as the same number. You can get 147
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6 descriptors for a given protein sequence.
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7 References
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8 ----------
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9 .. [1] Inna Dubchak, Ilya Muchink, Stephen R.Holbrook and Sung-Hou Kim.
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10 Prediction of protein folding class using global description of amino
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11 acid sequence. Proc.Natl. Acad.Sci.USA, 1995, 92, 8700-8704.
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12 .. [2] Inna Dubchak, Ilya Muchink, Christopher Mayor, Igor Dralyuk and Sung-Hou
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13 Kim. Recognition of a Protein Fold in the Context of the SCOP
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14 classification. Proteins: Structure, Function and
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15 Genetics, 1999, 35, 401-407.
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16 Authors: Dongsheng Cao and Yizeng Liang.
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17 Date: 2010.11.22
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18 Email: oriental-cds@163.com
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19 """
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20
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21 # Core Library
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22 import copy
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23 import math
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24 from typing import Any, Dict
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25
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26 _Hydrophobicity = {"1": "RKEDQN", "2": "GASTPHY", "3": "CLVIMFW"}
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27 # '1'stand for Polar; '2'stand for Neutral, '3' stand for Hydrophobicity
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28
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29 _NormalizedVDWV = {"1": "GASTPD", "2": "NVEQIL", "3": "MHKFRYW"}
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30 # '1'stand for (0-2.78); '2'stand for (2.95-4.0), '3' stand for (4.03-8.08)
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31
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32 _Polarity = {"1": "LIFWCMVY", "2": "CPNVEQIL", "3": "KMHFRYW"}
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33 # '1'stand for (4.9-6.2); '2'stand for (8.0-9.2), '3' stand for (10.4-13.0)
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34
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35 _Charge = {"1": "KR", "2": "ANCQGHILMFPSTWYV", "3": "DE"}
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36 # '1'stand for Positive; '2'stand for Neutral, '3' stand for Negative
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37
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38 _SecondaryStr = {"1": "EALMQKRH", "2": "VIYCWFT", "3": "GNPSD"}
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39 # '1'stand for Helix; '2'stand for Strand, '3' stand for coil
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40
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41 _SolventAccessibility = {"1": "ALFCGIVW", "2": "RKQEND", "3": "MPSTHY"}
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42 # '1'stand for Buried; '2'stand for Exposed, '3' stand for Intermediate
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43
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44 _Polarizability = {"1": "GASDT", "2": "CPNVEQIL", "3": "KMHFRYW"}
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45 # '1'stand for (0-0.108); '2'stand for (0.128-0.186), '3' stand for (0.219-0.409)
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46
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47
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48 # You can continuely add other properties of AADs to compute descriptors of
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49 # protein sequence.
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50
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51 _AATProperty = (
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52 _Hydrophobicity,
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53 _NormalizedVDWV,
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54 _Polarity,
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55 _Charge,
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56 _SecondaryStr,
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57 _SolventAccessibility,
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58 _Polarizability,
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59 )
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60
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61 _AATPropertyName = (
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62 "_Hydrophobicity",
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63 "_NormalizedVDWV",
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64 "_Polarity",
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65 "_Charge",
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66 "_SecondaryStr",
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67 "_SolventAccessibility",
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68 "_Polarizability",
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69 )
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70
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71
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72 def StringtoNum(ProteinSequence: str, AAProperty: Dict[Any, Any]) -> str:
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73 hardProteinSequence = copy.deepcopy(ProteinSequence)
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74 for k, m in list(AAProperty.items()):
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75 for index in m:
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76 hardProteinSequence = hardProteinSequence.replace(index, k)
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77 TProteinSequence = hardProteinSequence
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78
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79 return TProteinSequence
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80
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81
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82 def CalculateComposition(
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83 ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str) -> Dict[Any, Any]:
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84 TProteinSequence = StringtoNum(ProteinSequence, AAProperty)
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85 result = {}
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86 num = len(TProteinSequence)
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87 result[AAPName + "C" + "1"] = round(float(TProteinSequence.count("1")) / num, 3)
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88 result[AAPName + "C" + "2"] = round(float(TProteinSequence.count("2")) / num, 3)
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89 result[AAPName + "C" + "3"] = round(float(TProteinSequence.count("3")) / num, 3)
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90 return result
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91
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92
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93 def CalculateTransition(
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94 ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str
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95 ) -> Dict[Any, Any]:
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96 TProteinSequence = StringtoNum(ProteinSequence, AAProperty)
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97 Result = {}
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98 num = len(TProteinSequence)
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99 CTD = TProteinSequence
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100 Result[AAPName + "T" + "12"] = round(
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101 float(CTD.count("12") + CTD.count("21")) / (num - 1), 3
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102 )
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103 Result[AAPName + "T" + "13"] = round(
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104 float(CTD.count("13") + CTD.count("31")) / (num - 1), 3
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105 )
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106 Result[AAPName + "T" + "23"] = round(
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107 float(CTD.count("23") + CTD.count("32")) / (num - 1), 3
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108 )
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109 return Result
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110
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111
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112 def CalculateDistribution(
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113 ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str
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114 ) -> Dict[Any, Any]:
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115 TProteinSequence = StringtoNum(ProteinSequence, AAProperty)
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116 Result: Dict[str, float] = {}
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117 Num = len(TProteinSequence)
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118 for i in ("1", "2", "3"):
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119 num = TProteinSequence.count(i)
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120 ink = 1
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121 indexk = 0
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122 cds = []
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123 while ink <= num:
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124 indexk = TProteinSequence.find(i, indexk) + 1
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125 cds.append(indexk)
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126 ink = ink + 1
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127
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128 if cds == []:
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129 Result[AAPName + "D" + i + "001"] = 0
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130 Result[AAPName + "D" + i + "025"] = 0
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131 Result[AAPName + "D" + i + "050"] = 0
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132 Result[AAPName + "D" + i + "075"] = 0
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133 Result[AAPName + "D" + i + "100"] = 0
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134 else:
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135 Result[AAPName + "D" + i + "001"] = round(float(cds[0]) / Num * 100, 3)
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136 Result[AAPName + "D" + i + "025"] = round(
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137 float(cds[int(math.floor(num * 0.25)) - 1]) / Num * 100, 3
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138 )
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139 Result[AAPName + "D" + i + "050"] = round(
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140 float(cds[int(math.floor(num * 0.5)) - 1]) / Num * 100, 3
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141 )
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142 Result[AAPName + "D" + i + "075"] = round(
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143 float(cds[int(math.floor(num * 0.75)) - 1]) / Num * 100, 3
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144 )
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145 Result[AAPName + "D" + i + "100"] = round(float(cds[-1]) / Num * 100, 3)
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146
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147 return Result
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148
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149
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150 def CalculateCompositionHydrophobicity(ProteinSequence: str):
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151 return CalculateComposition(ProteinSequence, _Hydrophobicity, "_Hydrophobicity")
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152
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153
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154 def CalculateCompositionNormalizedVDWV(ProteinSequence: str):
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155 return CalculateComposition(ProteinSequence, _NormalizedVDWV, "_NormalizedVDWV")
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156
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157
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158 def CalculateCompositionPolarity(ProteinSequence: str):
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159 return CalculateComposition(ProteinSequence, _Polarity, "_Polarity")
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160
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161
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162 def CalculateCompositionCharge(ProteinSequence: str) -> Dict[Any, Any]:
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163 return CalculateComposition(ProteinSequence, _Charge, "_Charge")
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164
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165
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166 def CalculateCompositionSecondaryStr(ProteinSequence: str) -> Dict[Any, Any]:
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167 return CalculateComposition(ProteinSequence, _SecondaryStr, "_SecondaryStr")
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168
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169
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170 def CalculateCompositionSolventAccessibility(ProteinSequence: str) -> Dict[Any, Any]:
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171 return CalculateComposition(
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172 ProteinSequence, _SolventAccessibility, "_SolventAccessibility"
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173 )
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174
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175
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176 def CalculateCompositionPolarizability(ProteinSequence: str) -> Dict[Any, Any]:
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177 return CalculateComposition(ProteinSequence, _Polarizability, "_Polarizability")
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178
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179
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180 def CalculateTransitionHydrophobicity(ProteinSequence: str) -> Dict[Any, Any]:
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181 result = CalculateTransition(ProteinSequence, _Hydrophobicity, "_Hydrophobicity")
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182 return result
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183
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184
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185 def CalculateTransitionNormalizedVDWV(ProteinSequence: str) -> Dict[Any, Any]:
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186 result = CalculateTransition(ProteinSequence, _NormalizedVDWV, "_NormalizedVDWV")
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187 return result
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188
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189
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190 def CalculateTransitionPolarity(ProteinSequence: str) -> Dict[Any, Any]:
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191 result = CalculateTransition(ProteinSequence, _Polarity, "_Polarity")
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192 return result
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193
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194
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195 def CalculateTransitionCharge(ProteinSequence: str) -> Dict[Any, Any]:
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196 result = CalculateTransition(ProteinSequence, _Charge, "_Charge")
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197 return result
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198
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199
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200 def CalculateTransitionSecondaryStr(ProteinSequence: str) -> Dict[Any, Any]:
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201 result = CalculateTransition(ProteinSequence, _SecondaryStr, "_SecondaryStr")
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202 return result
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203
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204
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205 def CalculateTransitionSolventAccessibility(ProteinSequence: str) -> Dict[Any, Any]:
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206 result = CalculateTransition(
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207 ProteinSequence, _SolventAccessibility, "_SolventAccessibility"
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208 )
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209 return result
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210
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211
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212 def CalculateTransitionPolarizability(ProteinSequence: str) -> Dict[Any, Any]:
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213 result = CalculateTransition(ProteinSequence, _Polarizability, "_Polarizability")
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214 return result
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215
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216
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217 def CalculateDistributionHydrophobicity(ProteinSequence: str) -> Dict[Any, Any]:
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218 result = CalculateDistribution(ProteinSequence, _Hydrophobicity, "_Hydrophobicity")
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219 return result
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220
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221
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222 def CalculateDistributionNormalizedVDWV(ProteinSequence: str) -> Dict[Any, Any]:
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223 result = CalculateDistribution(ProteinSequence, _NormalizedVDWV, "_NormalizedVDWV")
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224 return result
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225
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226
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227 def CalculateDistributionPolarity(ProteinSequence: str) -> Dict[Any, Any]:
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228 result = CalculateDistribution(ProteinSequence, _Polarity, "_Polarity")
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229 return result
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230
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231
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232 def CalculateDistributionCharge(ProteinSequence: str) -> Dict[Any, Any]:
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233 result = CalculateDistribution(ProteinSequence, _Charge, "_Charge")
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234 return result
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235
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236
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237 def CalculateDistributionSecondaryStr(ProteinSequence: str) -> Dict[Any, Any]:
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238 result = CalculateDistribution(ProteinSequence, _SecondaryStr, "_SecondaryStr")
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239 return result
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240
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241
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242 def CalculateDistributionSolventAccessibility(ProteinSequence: str) -> Dict[Any, Any]:
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243 result = CalculateDistribution(
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244 ProteinSequence, _SolventAccessibility, "_SolventAccessibility"
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245 )
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246 return result
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247
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248
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249 def CalculateDistributionPolarizability(ProteinSequence: str) -> Dict[Any, Any]:
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250 result = CalculateDistribution(ProteinSequence, _Polarizability, "_Polarizability")
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251 return result
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252
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253
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254 def CalculateC(ProteinSequence: str) -> Dict[Any, Any]:
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255 result: Dict[Any, Any] = {}
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256 result.update(CalculateCompositionPolarizability(ProteinSequence))
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257 result.update(CalculateCompositionSolventAccessibility(ProteinSequence))
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258 result.update(CalculateCompositionSecondaryStr(ProteinSequence))
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259 result.update(CalculateCompositionCharge(ProteinSequence))
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260 result.update(CalculateCompositionPolarity(ProteinSequence))
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261 result.update(CalculateCompositionNormalizedVDWV(ProteinSequence))
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262 result.update(CalculateCompositionHydrophobicity(ProteinSequence))
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263 return result
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264
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265
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266 def CalculateT(ProteinSequence: str) -> Dict[Any, Any]:
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267 result: Dict[Any, Any] = {}
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268 result.update(CalculateTransitionPolarizability(ProteinSequence))
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269 result.update(CalculateTransitionSolventAccessibility(ProteinSequence))
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270 result.update(CalculateTransitionSecondaryStr(ProteinSequence))
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271 result.update(CalculateTransitionCharge(ProteinSequence))
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272 result.update(CalculateTransitionPolarity(ProteinSequence))
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273 result.update(CalculateTransitionNormalizedVDWV(ProteinSequence))
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274 result.update(CalculateTransitionHydrophobicity(ProteinSequence))
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275 return result
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276
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277
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278 def CalculateD(ProteinSequence: str) -> Dict[Any, Any]:
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279 result: Dict[Any, Any] = {}
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280 result.update(CalculateDistributionPolarizability(ProteinSequence))
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281 result.update(CalculateDistributionSolventAccessibility(ProteinSequence))
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282 result.update(CalculateDistributionSecondaryStr(ProteinSequence))
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283 result.update(CalculateDistributionCharge(ProteinSequence))
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284 result.update(CalculateDistributionPolarity(ProteinSequence))
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285 result.update(CalculateDistributionNormalizedVDWV(ProteinSequence))
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286 result.update(CalculateDistributionHydrophobicity(ProteinSequence))
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287 return result
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288
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289
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290 def CalculateCTD(ProteinSequence: str) -> Dict[Any, Any]:
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291 result: Dict[Any, Any] = {}
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292 result.update(CalculateCompositionPolarizability(ProteinSequence))
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293 result.update(CalculateCompositionSolventAccessibility(ProteinSequence))
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294 result.update(CalculateCompositionSecondaryStr(ProteinSequence))
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295 result.update(CalculateCompositionCharge(ProteinSequence))
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296 result.update(CalculateCompositionPolarity(ProteinSequence))
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297 result.update(CalculateCompositionNormalizedVDWV(ProteinSequence))
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298 result.update(CalculateCompositionHydrophobicity(ProteinSequence))
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299 result.update(CalculateTransitionPolarizability(ProteinSequence))
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300 result.update(CalculateTransitionSolventAccessibility(ProteinSequence))
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301 result.update(CalculateTransitionSecondaryStr(ProteinSequence))
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302 result.update(CalculateTransitionCharge(ProteinSequence))
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303 result.update(CalculateTransitionPolarity(ProteinSequence))
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304 result.update(CalculateTransitionNormalizedVDWV(ProteinSequence))
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305 result.update(CalculateTransitionHydrophobicity(ProteinSequence))
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306 result.update(CalculateDistributionPolarizability(ProteinSequence))
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307 result.update(CalculateDistributionSolventAccessibility(ProteinSequence))
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308 result.update(CalculateDistributionSecondaryStr(ProteinSequence))
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309 result.update(CalculateDistributionCharge(ProteinSequence))
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310 result.update(CalculateDistributionPolarity(ProteinSequence))
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311 result.update(CalculateDistributionNormalizedVDWV(ProteinSequence))
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312 result.update(CalculateDistributionHydrophobicity(ProteinSequence))
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313 return result
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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