File: molecular_weight.py

package info (click to toggle)
python-cogent 1.9-14
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 19,752 kB
  • sloc: python: 137,485; makefile: 149; sh: 64
file content (72 lines) | stat: -rw-r--r-- 1,875 bytes parent folder | download | duplicates (2)
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
#!/usr/bin/python
"""Data for molecular weight calculations on proteins and nucleotides."""

__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"

ProteinWeights = {
    'A': 71.09,
    'C': 103.16,
    'D': 115.10,
    'E': 129.13,
    'F': 147.19,
    'G': 57.07,
    'H': 137.16,
    'I': 113.18,
    'K': 128.19,
    'L': 113.18,
    'M': 131.21,
    'N': 114.12,
    'P': 97.13,
    'Q': 128.15,
    'R': 156.20,
    'S': 87.09,
    'T': 101.12,
    'V': 99.15,
    'W': 186.23,
    'Y': 163.19,
    'U': 150.06,
}

RnaWeights = {
    'A': 313.21,
    'U': 290.17,
    'C': 289.19,
    'G': 329.21,
}

DnaWeights = {
    'A': 297.21,
    'T': 274.17,
    'C': 273.19,
    'G': 313.21,
}

ProteinWeightCorrection = 18.0          #terminal residues not dehydrated
DnaWeightCorrection = 61.96             #assumes 5' monophosphate, 3' OH
RnaWeightCorrection = DnaWeightCorrection

class WeightCalculator(object):
    """Calculates molecular weight of a non-degenerate sequence."""
    def __init__(self, Weights, Correction):
        """Returns a new WeightCalculator object (class, so serializable)."""
        self.Weights = Weights
        self.Correction = Correction
    def __call__(self, seq, correction=None):
        """Returns the molecular weight of a specified sequence."""
        if not seq:
            return 0
        if correction is None:
            correction = self.Correction
        get_mw = self.Weights.get
        return sum([get_mw(i, 0) for i in seq]) + correction

DnaMW = WeightCalculator(DnaWeights, DnaWeightCorrection)
RnaMW = WeightCalculator(RnaWeights, DnaWeightCorrection)
ProteinMW = WeightCalculator(ProteinWeights, ProteinWeightCorrection)