1 # Copyright Yair Benita Y.Benita@pharm.uu.nl
2 # Biopython (http://biopython.org) license applies
5 import ProtParamData, IsoelectricPoint
6 from ProtParamData import kd # Added by Iddo to enable the gravy method
7 from Bio.Seq import Seq
8 from Bio.Alphabet import IUPAC
9 from Bio.Data import IUPACData
10 #from BioModule import
12 class ProteinAnalysis:
14 This class contains methods for protein analysis. The class init method takes
15 only one argument, the protein sequence as a string and build a sequence
16 object using the Bio.Seq module. This is done just to make sure the sequence
17 is a protein sequence and not anything else.
23 Simply counts the number times an amino acid is repeated in the protein
24 sequence. Returns a dictionary {AminoAcid:Number} and also stores the
25 dictionary in self.amino_acids_content.
27 get_amino_acids_percent:
29 The same as count_amino_acids only returns the Number in percentage of entire
30 sequence. Returns a dictionary and stores the dictionary in
31 self.amino_acids_content_percent.
34 Calculates the molecular weight of a protein.
38 Calculates the aromaticity value of a protein according to Lobry, 1994. It is
39 simply the relative frequency of Phe+Trp+Tyr.
44 Implementation of the method of Guruprasad et al. (Protein Engineering
45 4:155-161,1990). This method tests a protein for stability. Any value above 40
46 means the protein is unstable (=has a short half life).
49 Implementation of the flexibility method of Vihinen et al. (Proteins. 1994 Jun;19(2):141-9).
52 This method uses the module IsoelectricPoint to calculate the pI of a protein.
54 secondary_structure_fraction:
55 This methods returns a list of the fraction of amino acids which tend to be in Helix, Turn or Sheet.
56 Amino acids in helix: V, I, Y, F, W, L.
57 Amino acids in Turn: N, P, G, S.
58 Amino acids in sheet: E, M, A, L.
59 The list contains 3 values: [Helix, Turn, Sheet].
62 protein_scale(Scale, WindwonSize, Edge):
64 An amino acid scale is defined by a numerical value assigned to each type of
65 amino acid. The most frequently used scales are the hydrophobicity or
66 hydrophilicity scales and the secondary structure conformational parameters
67 scales, but many other scales exist which are based on different chemical and
68 physical properties of the amino acids. You can set several parameters that
69 control the computation of a scale profile, such as the window size and the
70 window edge relative weight value. WindowSize: The window size is the length
71 of the interval to use for the profile computation. For a window size n, we
72 use the i- ( n-1)/2 neighboring residues on each side of residue it compute
73 the score for residue i. The score for residue is the sum of the scale values
74 for these amino acids, optionally weighted according to their position in the
75 window. Edge: The central amino acid of the window always has a weight of 1.
76 By default, the amino acids at the remaining window positions have the same
77 weight, but you can make the residue at the center of the window have a
78 larger weight than the others by setting the edge value for the residues at
79 the beginning and end of the interval to a value between 0 and 1. For
80 instance, for Edge=0.4 and a window size of 5 the weights will be: 0.4, 0.7,
81 1.0, 0.7, 0.4. The method returns a list of values which can be plotted to
82 view the change along a protein sequence. Many scales exist. Just add your
83 favorites to the ProtParamData modules.
85 def __init__(self, ProtSequence):
86 if ProtSequence.islower():
87 self.sequence = Seq(ProtSequence.upper(), IUPAC.protein)
89 self.sequence = Seq(ProtSequence, IUPAC.protein)
90 self.amino_acids_content = None
91 self.amino_acids_percent = None
92 self.length = len(self.sequence)
94 def count_amino_acids(self):
95 ProtDic = dict([ (k, 0) for k in IUPACData.protein_letters])
96 for i in ProtDic.keys():
97 ProtDic[i]=self.sequence.count(i)
98 self.amino_acids_content = ProtDic
101 """Calculate the amino acid content in percents.
102 input is the dictionary from CountAA.
103 output is a dictionary with AA as keys."""
104 def get_amino_acids_percent(self):
105 if not self.amino_acids_content:
106 self.count_amino_acids()
109 for i in self.amino_acids_content.keys():
110 if self.amino_acids_content[i] > 0:
111 PercentAA[i]=self.amino_acids_content[i]/float(self.length)
114 self.amino_acids_percent = PercentAA
117 # Calculate MW from Protein sequence
118 # Calculate MW from Protein sequence
119 def molecular_weight (self):
120 # make local dictionary for speed
122 # remove a molecule of water from the amino acid weight.
123 for i in IUPACData.protein_weights.keys():
124 MwDict[i] = IUPACData.protein_weights[i] - 18.02
125 MW = 18.02 # add just one water molecule for the whole sequence.
126 for i in self.sequence:
130 # calculate the aromaticity according to Lobry, 1994.
131 # Arom=sum of relative frequency of Phe+Trp+Tyr
132 def aromaticity(self):
133 if not self.amino_acids_percent:
134 self.get_amino_acids_percent()
136 Arom= self.amino_acids_percent['Y']+self.amino_acids_percent['W']+self.amino_acids_percent['F']
139 # a function to calculate the instability index according to:
140 # Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).
141 def instability_index(self):
142 #make the dictionary local for speed.
143 DIWV=ProtParamData.DIWV.copy()
145 for i in range(self.length - 1):
146 DiPeptide=DIWV[self.sequence[i]][self.sequence[i+1]]
148 return (10.0/self.length) * score
150 # Calculate the flexibility according to Vihinen, 1994.
151 # No argument to change window size because parameters are specific for a window=9.
152 # the parameters used are optimized for determining the flexibility.
153 def flexibility(self):
154 Flex = ProtParamData.Flex.copy()
156 Weights=[0.25,0.4375,0.625,0.8125,1]
158 for i in range(self.length - Window):
159 SubSeq=self.sequence[i:i+Window]
161 for j in range(Window/2):
162 score += (Flex[SubSeq[j]]+Flex[SubSeq[Window-j-1]]) * Weights[j]
163 score += Flex[SubSeq[Window/2+1]]
164 List.append(score/5.25)
167 # calculate the gravy according to kyte and doolittle.
170 for i in self.sequence:
173 return ProtGravy/self.length
175 # this method is used to make a list of relative weight of the
176 # window edges compared to the window center. The weights are linear.
177 # it actually generates half a list. For a window of size 9 and edge 0.4
178 # you get a list of [0.4, 0.55, 0.7, 0.85].
179 def _weight_list(self, window, edge):
180 unit = ((1.0-edge)/(window-1))*2
181 list = [0.0]*(window/2)
182 for i in range(window/2):
183 list[i] = edge + unit * i
186 # this method allows you to compute and represent the profile produced
187 # by any amino acid scale on a selected protein.
188 # Similar to expasy's ProtScale: http://www.expasy.org/cgi-bin/protscale.pl
189 # The weight list returns only one tail. If the list should be [0.4,0.7,1.0,0.7,0.4]
190 # what you actually get from _weights_list is [0.4,0.7]. The correct calculation is done
192 def protein_scale(self, ParamDict, Window, Edge=1.0):
193 # generate the weights
194 weight = self._weight_list(Window,Edge)
196 # the score in each Window is divided by the sum of weights
198 for i in weight: sum_of_weights += i
199 # since the weight list is one sided:
200 sum_of_weights = sum_of_weights*2+1
202 for i in range(self.length-Window+1):
203 subsequence = self.sequence[i:i+Window]
205 for j in range(Window/2):
206 # walk from the outside of the Window towards the middle.
207 # Iddo: try/except clauses added to avoid raising an exception on a non-standad amino acid
209 score += weight[j] * ParamDict[subsequence[j]] + weight[j] * ParamDict[subsequence[Window-j-1]]
211 sys.stderr.write('warning: %s or %s is not a standard amino acid.\n' %
212 (subsequence[j],subsequence[Window-j-1]))
214 # Now add the middle value, which always has a weight of 1.
215 if subsequence[Window/2] in ParamDict:
216 score += ParamDict[subsequence[Window/2]]
218 sys.stderr.write('warning: %s is not a standard amino acid.\n' % (subsequence[Window/2]))
220 list.append(score/sum_of_weights)
223 # calculate the isoelectric point.
224 def isoelectric_point(self):
225 if not self.amino_acids_content:
226 self.count_amino_acids()
227 X = IsoelectricPoint.IsoelectricPoint(self.sequence, self.amino_acids_content)
230 # calculate fraction of helix, turn and sheet
231 def secondary_structure_fraction (self):
232 if not self.amino_acids_percent:
233 self.get_amino_acids_percent()
234 Helix = self.amino_acids_percent['V'] + self.amino_acids_percent['I'] + self.amino_acids_percent['Y'] + self.amino_acids_percent['F'] + self.amino_acids_percent['W'] + self.amino_acids_percent['L']
235 Turn = self.amino_acids_percent['N'] + self.amino_acids_percent['P'] + self.amino_acids_percent['G'] + self.amino_acids_percent['S']
236 Sheet = self.amino_acids_percent['E'] + self.amino_acids_percent['M'] + self.amino_acids_percent['A'] + self.amino_acids_percent['L']
237 return Helix, Turn, Sheet
239 #---------------------------------------------------------#
241 X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
242 print X.count_amino_acids()
243 print X.get_amino_acids_percent()
244 print X.molecular_weight()
245 print X.aromaticity()
246 print X.instability_index()
247 print X.flexibility()
249 print X.secondary_structure_fraction()
250 print X.protein_scale(ProtParamData.kd, 9, 0.4)