-
Notifications
You must be signed in to change notification settings - Fork 0
/
test_viz.py
80 lines (60 loc) · 2.08 KB
/
test_viz.py
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
import viz
testPDBfile = '''HEADER EXTRACELLULAR MATRIX 22-JAN-98 1A3I
TITLE X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE
TITLE 2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)
EXPDTA X-RAY DIFFRACTION
AUTHOR R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA,
AUTHOR 2 B.BRODSKY,A.ZAGARI,H.M.BERMAN
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
SEQRES 1 A 9 PRO PRO GLY PRO PRO GLY PRO PRO GLY
SEQRES 1 B 6 PRO PRO GLY PRO PRO GLY
SEQRES 1 C 6 PRO PRO GLY PRO PRO GLY
ATOM 1 N PRO A 1 8.316 21.206 21.530 1.00 17.44 N
ATOM 2 CA PRO A 1 7.608 20.729 20.336 1.00 17.44 C
ATOM 3 C PRO A 1 8.487 20.707 19.092 1.00 17.44 C
ATOM 4 O PRO A 1 9.466 21.457 19.005 1.00 17.44 O
ATOM 5 CB PRO A 1 6.460 21.723 20.211 1.00 22.26 C
HETATM 130 C ACY 401 3.682 22.541 11.236 1.00 21.19 C
HETATM 131 O ACY 401 2.807 23.097 10.553 1.00 21.19 O
HETATM 132 OXT ACY 401 4.306 23.101 12.291 1.00 21.19 O
'''
def test_create_distance_matrix():
pass
def test_get_translation_table():
pass
def test_naive_backtranslate():
pass
def test_get_peptide_index():
pass
def test_demo_dna_features_viewer():
pass
def test_ngrams():
pass
def test_make_trigrams():
pass
def test_nucleotide_distribution():
pass
def test_get_peptide_toplot():
pass
def test_peptide_distribution():
pass
def test_plot_ABI():
pass
def test_get_genbank_sequence():
pass
def test_get_fasta_sequence():
pass
def test_iter_calc_sequence_similarity():
pass
def test_calc_sequence_similarity():
pass
def test_multiprocess_similarity():
result = viz.multiprocess_similarity
print(result)
def test_make_parser():
pass
def test_main():
pass