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
|
# 04_cootaneer.py
# Copyright 2007, 2008 by The University of York
# Author: Bernhard Lohkamp
# Copyright 2007, 2008 by The University of Oxford
# Author: Paul Emsley
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
import unittest
import os
import coot
import coot_utils
import begin
rnase_pir = os.path.join(begin.unittest_data_dir, "rnase.pir")
poly_ala_frag = os.path.join(begin.unittest_data_dir, "crashes_on_cootaneering-v2.pdb")
class CootaneerTestFunctions(unittest.TestCase):
def test01_0(self):
"""Assignment of new PIR sequence overwrites old assignment"""
imol = begin.unittest_pdb("tutorial-modern.pdb")
seq_1 = "ACDEFGHIKLMNPQ"
seq_2 = "ACDEFGHIKLMNPQRST"
pir_seq_1 = ">test\n\n" + seq_1 + "*"
pir_seq_2 = ">test\n\n" + seq_2 + "*"
coot.assign_pir_sequence(imol, "A", pir_seq_1)
si = coot.sequence_info(imol)
chains = [item[0] for item in si]
self.assertTrue(chains.count("A") > 0,
"""chain A not found in sequence info\n
Bad sequence assignment""")
seq = si[chains.index("A")][1]
# slightly different logic to greg test, since I cannot
# query list as dict in python
print("debug seq", seq)
self.assertTrue(seq == seq_1,
"bad sequence - not matched %s vs %s with 'assoc'"
%(seq, seq_1))
coot.assign_pir_sequence(imol, "A", pir_seq_2)
si = coot.sequence_info(imol)
chains = [item[0] for item in si]
self.assertTrue(chains.count("A") > 0,
"""chain A not found in sequence info\n
Bad sequence assignment - 2""")
seq = si[chains.index("A")][1]
self.assertTrue(seq == seq_2,
"bad sequence - not matched %s vs %s with 'assoc'"
%(seq, seq_2))
def test02_0(self):
"""Cootaneer Beta Strand"""
imol_model = coot.read_pdb(poly_ala_frag)
imol_map = coot.make_and_draw_map(begin.rnase_mtz(), "FWT", "PHWT", "", 0, 0)
self.assertTrue(coot_utils.valid_model_molecule_qm(imol_model),
"bad imol_model: %i from file %s" %(imol_model, poly_ala_frag))
self.assertTrue(os.path.isfile(rnase_pir), "missing rnase pir file")
seq_text = coot_utils.file_to_string(rnase_pir)
#assign_sequence_from_file(imol_model, rnase_pir)
coot.assign_pir_sequence(imol_model, "A", seq_text)
coot.set_rotation_centre(64.271, 7.036, 14.42)
n_atom = coot_utils.closest_atom(imol_model)
self.assertTrue(n_atom, "missing closest atom")
imol = n_atom[0]
chain_id = n_atom[1]
resno = n_atom[2]
inscode = n_atom[3]
at_name = n_atom[4]
alt_conf = n_atom[5]
print(" Cootaneering: imol %s chain-id %s resno %s inscode %s at-name %s alt-conf %s" \
%(imol, chain_id, resno, inscode, at_name, alt_conf))
coot.cootaneer(imol_map, imol, [chain_id, resno, inscode, at_name, alt_conf])
|
