Spaces:
No application file
No application file
File size: 13,021 Bytes
b7731cd |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 |
# Copyright 2003 Yair Benita. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Simple protein analysis.
Examples
--------
>>> from Bio.SeqUtils.ProtParam import ProteinAnalysis
>>> X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGT"
... "RDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEEC"
... "LFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILF"
... "LPLPV")
>>> print(X.count_amino_acids()['A'])
6
>>> print(X.count_amino_acids()['E'])
12
>>> print("%0.2f" % X.get_amino_acids_percent()['A'])
0.04
>>> print("%0.2f" % X.get_amino_acids_percent()['L'])
0.12
>>> print("%0.2f" % X.molecular_weight())
17103.16
>>> print("%0.2f" % X.aromaticity())
0.10
>>> print("%0.2f" % X.instability_index())
41.98
>>> print("%0.2f" % X.isoelectric_point())
7.72
>>> sec_struc = X.secondary_structure_fraction() # [helix, turn, sheet]
>>> print("%0.2f" % sec_struc[0]) # helix
0.28
>>> epsilon_prot = X.molar_extinction_coefficient() # [reduced, oxidized]
>>> print(epsilon_prot[0]) # with reduced cysteines
17420
>>> print(epsilon_prot[1]) # with disulfid bridges
17545
Other public methods are:
- gravy
- protein_scale
- flexibility
- charge_at_pH
"""
import sys
from Bio.SeqUtils import ProtParamData # Local
from Bio.SeqUtils import IsoelectricPoint # Local
from Bio.Seq import Seq
from Bio.Data import IUPACData
from Bio.SeqUtils import molecular_weight
class ProteinAnalysis:
"""Class containing methods for protein analysis.
The constructor takes two arguments.
The first is the protein sequence as a string or a Seq object.
The second argument is optional. If set to True, the weight of the amino
acids will be calculated using their monoisotopic mass (the weight of the
most abundant isotopes for each element), instead of the average molecular
mass (the averaged weight of all stable isotopes for each element).
If set to false (the default value) or left out, the IUPAC average
molecular mass will be used for the calculation.
"""
def __init__(self, prot_sequence, monoisotopic=False):
"""Initialize the class."""
self.sequence = prot_sequence.upper()
self.amino_acids_content = None
self.amino_acids_percent = None
self.length = len(self.sequence)
self.monoisotopic = monoisotopic
def count_amino_acids(self):
"""Count standard amino acids, return a dict.
Counts the number times each amino acid is in the protein
sequence. Returns a dictionary {AminoAcid:Number}.
The return value is cached in self.amino_acids_content.
It is not recalculated upon subsequent calls.
"""
if self.amino_acids_content is None:
prot_dic = {k: 0 for k in IUPACData.protein_letters}
for aa in prot_dic:
prot_dic[aa] = self.sequence.count(aa)
self.amino_acids_content = prot_dic
return self.amino_acids_content
def get_amino_acids_percent(self):
"""Calculate the amino acid content in percentages.
The same as count_amino_acids only returns the Number in percentage of
entire sequence. Returns a dictionary of {AminoAcid:percentage}.
The return value is cached in self.amino_acids_percent.
input is the dictionary self.amino_acids_content.
output is a dictionary with amino acids as keys.
"""
if self.amino_acids_percent is None:
aa_counts = self.count_amino_acids()
percentages = {aa: count / self.length for aa, count in aa_counts.items()}
self.amino_acids_percent = percentages
return self.amino_acids_percent
def molecular_weight(self):
"""Calculate MW from Protein sequence."""
return molecular_weight(
self.sequence, seq_type="protein", monoisotopic=self.monoisotopic
)
def aromaticity(self):
"""Calculate the aromaticity according to Lobry, 1994.
Calculates the aromaticity value of a protein according to Lobry, 1994.
It is simply the relative frequency of Phe+Trp+Tyr.
"""
aromatic_aas = "YWF"
aa_percentages = self.get_amino_acids_percent()
aromaticity = sum(aa_percentages[aa] for aa in aromatic_aas)
return aromaticity
def instability_index(self):
"""Calculate the instability index according to Guruprasad et al 1990.
Implementation of the method of Guruprasad et al. 1990 to test a
protein for stability. Any value above 40 means the protein is unstable
(has a short half life).
See: Guruprasad K., Reddy B.V.B., Pandit M.W.
Protein Engineering 4:155-161(1990).
"""
index = ProtParamData.DIWV
score = 0.0
for i in range(self.length - 1):
this, next = self.sequence[i : i + 2]
dipeptide_value = index[this][next]
score += dipeptide_value
return (10.0 / self.length) * score
def flexibility(self):
"""Calculate the flexibility according to Vihinen, 1994.
No argument to change window size because parameters are specific for
a window=9. The parameters used are optimized for determining the
flexibility.
"""
flexibilities = ProtParamData.Flex
window_size = 9
weights = [0.25, 0.4375, 0.625, 0.8125, 1]
scores = []
for i in range(self.length - window_size):
subsequence = self.sequence[i : i + window_size]
score = 0.0
for j in range(window_size // 2):
front = subsequence[j]
back = subsequence[window_size - j - 1]
score += (flexibilities[front] + flexibilities[back]) * weights[j]
middle = subsequence[window_size // 2 + 1]
score += flexibilities[middle]
scores.append(score / 5.25)
return scores
def gravy(self, scale="KyteDoolitle"):
"""Calculate the GRAVY (Grand Average of Hydropathy) according to Kyte and Doolitle, 1982.
Utilizes the given Hydrophobicity scale, by default uses the original
proposed by Kyte and Doolittle (KyteDoolitle). Other options are:
Aboderin, AbrahamLeo, Argos, BlackMould, BullBreese, Casari, Cid,
Cowan3.4, Cowan7.5, Eisenberg, Engelman, Fasman, Fauchere, GoldSack,
Guy, Jones, Juretic, Kidera, Miyazawa, Parker,Ponnuswamy, Rose,
Roseman, Sweet, Tanford, Wilson and Zimmerman.
New scales can be added in ProtParamData.
"""
selected_scale = ProtParamData.gravy_scales.get(scale, -1)
if selected_scale == -1:
raise ValueError(f"scale: {scale} not known")
total_gravy = sum(selected_scale[aa] for aa in self.sequence)
return total_gravy / self.length
def _weight_list(self, window, edge):
"""Make list of relative weight of window edges (PRIVATE).
The relative weight of window edges are compared to the window
center. The weights are linear. It actually generates half a list.
For a window of size 9 and edge 0.4 you get a list of
[0.4, 0.55, 0.7, 0.85].
"""
unit = 2 * (1.0 - edge) / (window - 1)
weights = [0.0] * (window // 2)
for i in range(window // 2):
weights[i] = edge + unit * i
return weights
def protein_scale(self, param_dict, window, edge=1.0):
"""Compute a profile by any amino acid scale.
An amino acid scale is defined by a numerical value assigned to each
type of amino acid. The most frequently used scales are the
hydrophobicity or hydrophilicity scales and the secondary structure
conformational parameters scales, but many other scales exist which
are based on different chemical and physical properties of the
amino acids. You can set several parameters that control the
computation of a scale profile, such as the window size and the window
edge relative weight value.
WindowSize: The window size is the length of the interval to use for
the profile computation. For a window size n, we use the i-(n-1)/2
neighboring residues on each side to compute the score for residue i.
The score for residue i is the sum of the scaled values for these
amino acids, optionally weighted according to their position in the
window.
Edge: The central amino acid of the window always has a weight of 1.
By default, the amino acids at the remaining window positions have the
same weight, but you can make the residue at the center of the window
have a larger weight than the others by setting the edge value for the
residues at the beginning and end of the interval to a value between
0 and 1. For instance, for Edge=0.4 and a window size of 5 the weights
will be: 0.4, 0.7, 1.0, 0.7, 0.4.
The method returns a list of values which can be plotted to view the
change along a protein sequence. Many scales exist. Just add your
favorites to the ProtParamData modules.
Similar to expasy's ProtScale:
http://www.expasy.org/cgi-bin/protscale.pl
"""
# generate the weights
# _weight_list returns only one tail. If the list should be
# [0.4,0.7,1.0,0.7,0.4] what you actually get from _weights_list
# is [0.4,0.7]. The correct calculation is done in the loop.
weights = self._weight_list(window, edge)
scores = []
# the score in each Window is divided by the sum of weights
# (* 2 + 1) since the weight list is one sided:
sum_of_weights = sum(weights) * 2 + 1
for i in range(self.length - window + 1):
subsequence = self.sequence[i : i + window]
score = 0.0
for j in range(window // 2):
# walk from the outside of the Window towards the middle.
# Iddo: try/except clauses added to avoid raising an exception
# on a non-standard amino acid
try:
front = param_dict[subsequence[j]]
back = param_dict[subsequence[window - j - 1]]
score += weights[j] * front + weights[j] * back
except KeyError:
sys.stderr.write(
"warning: %s or %s is not a standard "
"amino acid.\n" % (subsequence[j], subsequence[window - j - 1])
)
# Now add the middle value, which always has a weight of 1.
middle = subsequence[window // 2]
if middle in param_dict:
score += param_dict[middle]
else:
sys.stderr.write(f"warning: {middle} is not a standard amino acid.\n")
scores.append(score / sum_of_weights)
return scores
def isoelectric_point(self):
"""Calculate the isoelectric point.
Uses the module IsoelectricPoint to calculate the pI of a protein.
"""
aa_content = self.count_amino_acids()
ie_point = IsoelectricPoint.IsoelectricPoint(self.sequence, aa_content)
return ie_point.pi()
def charge_at_pH(self, pH):
"""Calculate the charge of a protein at given pH."""
aa_content = self.count_amino_acids()
charge = IsoelectricPoint.IsoelectricPoint(self.sequence, aa_content)
return charge.charge_at_pH(pH)
def secondary_structure_fraction(self):
"""Calculate fraction of helix, turn and sheet.
Returns a list of the fraction of amino acids which tend
to be in Helix, Turn or Sheet.
Amino acids in helix: V, I, Y, F, W, L.
Amino acids in Turn: N, P, G, S.
Amino acids in sheet: E, M, A, L.
Returns a tuple of three floats (Helix, Turn, Sheet).
"""
aa_percentages = self.get_amino_acids_percent()
helix = sum(aa_percentages[r] for r in "VIYFWL")
turn = sum(aa_percentages[r] for r in "NPGS")
sheet = sum(aa_percentages[r] for r in "EMAL")
return helix, turn, sheet
def molar_extinction_coefficient(self):
"""Calculate the molar extinction coefficient.
Calculates the molar extinction coefficient assuming cysteines
(reduced) and cystines residues (Cys-Cys-bond)
"""
num_aa = self.count_amino_acids()
mec_reduced = num_aa["W"] * 5500 + num_aa["Y"] * 1490
mec_cystines = mec_reduced + (num_aa["C"] // 2) * 125
return (mec_reduced, mec_cystines)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
|