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
|
'''
unit tests for pymol.wizard.nucmutagenesis
'''
import os
import sys
import tempfile
import unittest
from pymol import cmd, testing
@testing.requires_version('2.2')
class TestNucMutagenesis(testing.PyMOLTestCase):
def test_CanGetSourceSequence(self):
cmd.load(self.datafile("1rna.cif"))
seq = cmd.get_fastastr('/1rna/A/A').splitlines()[1]
self.assertEqual(seq, "UUAUAUAUAUAUAA")
def test_CanGetFragment(self):
cmd.fragment("gtp")
numAtoms = cmd.count_atoms("gtp")
self.assertEqual(numAtoms, 48)
def test_CanInit(self):
cmd.wizard("nucmutagenesis")
self.assertTrue(cmd.get_wizard() != None)
def test_CorrectChiDihedral(self):
cmd.load(self.datafile("1rna.cif"))
src_dihedral = cmd.get_dihedral("/1rna/A/A/14 & name O4'",
"/1rna/A/A/14 & name C1'",
"/1rna/A/A/14 & name N9",
"/1rna/A/A/14 & name C4'")
cmd.wizard("nucmutagenesis")
cmd.select("/1rna/A/A/14")
cmd.get_wizard().mode = "Guanine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
des_dihedral = cmd.get_dihedral("/1rna/A/A/14 & name O4'",
"/1rna/A/A/14 & name C1'",
"/1rna/A/A/14 & name N9",
"/1rna/A/A/14 & name C4'")
self.assertAlmostEqual(src_dihedral, des_dihedral, delta = 2.0)
def test_CanGetNewRNASequence(self):
cmd.load(self.datafile("1rna.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1rna/A/A/14")
cmd.get_wizard().mode = "Guanine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1rna/A/A").splitlines()[1]
self.assertEqual(seq, "UUAUAUAUAUAUAG")
def test_CanGetNewDNASequence(self):
cmd.load(self.datafile("1bna.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1bna/A/A/1")
cmd.get_wizard().mode = "Adenine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1bna/A/A").splitlines()[1]
self.assertEqual(seq, "AGCGAATTCGCG")
def test_CanMutateNonCanonicalNucleo(self):
cmd.load(self.datafile("1k5e.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1k5e/A/A/6")
cmd.get_wizard().mode = "Adenine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1k5e/A/A").splitlines()[1]
self.assertEqual(seq, "CGGACAAGAAG")
|
