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
|
# 06_ssm.py
# Copyright 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 coot_testing_utils
ssm_ref_1_file = os.path.join(coot_testing_utils.unittest_data_dir, "2qd9.pdb")
ssm_ref_2_file = os.path.join(coot_testing_utils.unittest_data_dir, "2gtn.pdb")
class TestSSMFunctions(unittest.TestCase):
def test01_0(self):
"""SSM - Frank von Delft's Example"""
imol_a = coot.handle_read_draw_molecule_with_recentre(os.path.join(coot_testing_utils.unittest_data_dir, "1wly.pdb"), 0)
imol_b = coot.handle_read_draw_molecule_with_recentre(os.path.join(coot_testing_utils.unittest_data_dir, "1yb5.pdb"), 1)
self.assertTrue(coot_utils.valid_model_molecule_qm(imol_a) and coot_utils.valid_model_molecule_qm(imol_b))
coot.graphics_to_ca_plus_ligands_representation(imol_a)
coot.superpose_with_atom_selection(imol_a, imol_b, "A/2-111", "A/6-115", 0)
coot.set_rotation_centre(65.65, -3, -4)
view_number = coot_utils.add_view([49.7269, 7.69693, 3.93221],
[-0.772277, 0.277494, 0.292497, 0.490948],
98.9608, "SSM View")
coot.go_to_view_number(view_number, 1)
# coot.rotate_y_scene(coot.rotate_n_frames(100), 0.1)
coot.set_mol_displayed(imol_a, 0)
coot.set_mol_displayed(imol_b, 0)
# didnt crash....
def test02_0(self):
"""SSM - Alice Dawson's Example"""
imol_s = coot.handle_read_draw_molecule_with_recentre(os.path.join(coot_testing_utils.unittest_data_dir, "1pyd.pdb"), 0)
coot.graphics_to_ca_plus_ligands_representation(imol_s)
coot.set_graphics_window_size(678, 452)
coot_utils.print_molecule_names()
coot.superpose_with_atom_selection(imol_s, imol_s, "A/100-400", "B/50-450", 1)
imol_copy = coot.graphics_n_molecules() - 1
coot.graphics_to_ca_plus_ligands_representation(imol_copy)
# coot.rotate_y_scene(coot.rotate_n_frames(100), 0.1)
# didnt crash...
def test03_0(self):
"""SSM by atom selection [JED Example]"""
imol_1 = coot.read_pdb(ssm_ref_1_file)
imol_2 = coot.read_pdb(ssm_ref_2_file)
coot.superpose_with_atom_selection(imol_1, imol_2,"//A/140-160", "//A/140-160", 0)
# didn't crash?
# testing for something else?!
|
