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
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/STRUCTURE/sideChainPlacementProcessor.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/SYSTEM/file.h>
#include <BALL/KERNEL/system.h>
///////////////////////////
using namespace BALL;
START_TEST(SideChainPlacementProcessor)
PRECISION(1e-5)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
SideChainPlacementProcessor* scpp;
CHECK(SideChainPlacementProcessor())
scpp = new SideChainPlacementProcessor();
TEST_NOT_EQUAL(scpp,0)
RESULT
CHECK(~SideChainPlacementProcessor())
delete scpp;
RESULT
CHECK(setDefaultOptions())
SideChainPlacementProcessor scpp;
scpp.setDefaultOptions();
TEST_EQUAL(scpp.options.get(SideChainPlacementProcessor::Option::METHOD),
SideChainPlacementProcessor::Default::METHOD)
//if no SCWRL installed, no path available!
// TEST_EQUAL(scpp.options.get(SideChainPlacementProcessor::Option::SCWRL_BINARY_PATH),
// SideChainPlacementProcessor::Default::SCWRL_BINARY_PATH)
TEST_EQUAL(scpp.options.getBool(SideChainPlacementProcessor::Option::MUTATE_SELECTED_SIDE_CHAINS),
SideChainPlacementProcessor::Default::MUTATE_SELECTED_SIDE_CHAINS)
TEST_EQUAL(scpp.options.get(SideChainPlacementProcessor::Option::SCWRL_INPUT_FILE),
SideChainPlacementProcessor::Default::SCWRL_INPUT_FILE)
TEST_EQUAL(scpp.options.get(SideChainPlacementProcessor::Option::SCWRL_SEQUENCE_FILE),
SideChainPlacementProcessor::Default::SCWRL_SEQUENCE_FILE)
TEST_EQUAL(scpp.options.get(SideChainPlacementProcessor::Option::SCWRL_OUTPUT_FILE),
SideChainPlacementProcessor::Default::SCWRL_OUTPUT_FILE)
RESULT
CHECK( setMutations() / getMutations() )
SideChainPlacementProcessor scpp;
TEST_EQUAL(scpp.getMutations(), "")
scpp.setMutations("CCHHPPTTAA");
TEST_EQUAL(scpp.getMutations(), "CCHHPPTTAA")
RESULT
CHECK( applied on empty System )
SideChainPlacementProcessor scpp;
scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_INPUT_FILE, BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_input_1.pdb));
scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_OUTPUT_FILE, BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_output_1.pdb));
System sys;
sys.apply(scpp);
RESULT
CHECK( operator() apply to a system )
SideChainPlacementProcessor scpp;
//TODO shouldn't we test the input file as well?
//scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_INPUT_FILE,
// BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_input_1.pdb));
//scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_SEQUENCE_FILE,
// BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_sequence_1.dat));
scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_OUTPUT_FILE,
BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_output_1.pdb));
System sys;
PDBFile mol(BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test.pdb), std::ios::in);
mol >> sys;
sys.apply(scpp);
// store the result in a temporary file
String temp;
File::createTemporaryFilename(temp);
PDBFile PDB_temp(temp, std::ios::out);
PDB_temp << sys;
PDB_temp.close();
// get the precomputed result
PDBFile PDB_pre( BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_output_pre_1.pdb), std::ios::out);
// compare
//////// does not work like this: TEST_EQUAL(PDB_temp==PDB_pre, true) //TODO
// remove the temp file
File::remove(temp);
RESULT
///////////////////TODO////////////////////////////
CHECK(apply to a protein)
SideChainPlacementProcessor scpp;
System sys;
PDBFile mol(BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test.pdb), std::ios::in);
mol >> sys;
Protein* prot = sys.getProtein(0);
RESULT
CHECK(apply to a chain)
SideChainPlacementProcessor scpp;
System sys;
PDBFile mol(BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test.pdb), std::ios::in);
mol >> sys;
Chain* chain3 = (sys.getProtein(0)->getChain(2));
RESULT
CHECK( apply to a selection)
SideChainPlacementProcessor scpp;
System sys;
PDBFile mol(BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test.pdb), std::ios::in);
mol >> sys;
Residue* res = (sys.getProtein(0)->getChain(1))->getResidue(0);
res->select();
Chain* chain2 = (sys.getProtein(0)->getChain(1));
chain2->select();
RESULT
CHECK(mutate)
SideChainPlacementProcessor scpp;
scpp.options.set(SideChainPlacementProcessor::Option::MUTATE_SELECTED_SIDE_CHAINS, true);
//TODO scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_OUTPUT_FILE, BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_output_mut1.pdb));
System sys;
PDBFile mol(BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test.pdb), std::ios::in);
mol >> sys;
//check if SCWRL path is set and the required file exists
try {
File file(scpp.options.get(SideChainPlacementProcessor::Option::SCWRL_BINARY_PATH));
if(file.isExecutable())
{
String mutated_seq = "arCdcCeg";
scpp.setMutations(mutated_seq);
printf("blubblubb\n");
sys.apply(scpp); //TODO Are both Cysteins set correctly?
TEST_EQUAL(sys.getProtein(0)->getChain(0)->getResidue(2)->getName(), "CYS")
TEST_EQUAL(sys.getProtein(0)->getChain(1)->getResidue(1)->getName(), "CYS")
scpp.clear();
scpp.options.set(SideChainPlacementProcessor::Option::MUTATE_SELECTED_SIDE_CHAINS, true);
scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_OUTPUT_FILE,
BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_output_mut2.pdb));
System sys2;
PDBFile mol2(BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test.pdb), std::ios::in);
mol2 >> sys2;
mutated_seq = "arCd";
scpp.setMutations(mutated_seq);
Chain* chain1 = (sys.getProtein(0)->getChain(0));
chain1->apply(scpp);
sys2.apply(scpp);
TEST_EQUAL(sys.getProtein(0)->getChain(0)->getResidue(2)->getName(), "CYS")
TEST_EQUAL(sys.getProtein(0)->getChain(1)->getResidue(1)->getName(), "GLN")
}
}
catch (...)
{
std::cout << "Could not find Scwrl binary" << std::endl;
}
RESULT
CHECK(check energy) //TODO
/* SideChainPlacementProcessor scpp;
scpp.options.set(SideChainPlacementProcessor::Option::SCWRL_OUTPUT_FILE, BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_output_AA.pdb));
System sys;
PDBFile mol(BALL_TEST_DATA_PATH(SideChainPlacementProcessor_test_AA.pdb), std::ios::in);
mol >> sys;
// energy before
AmberFF amber_ff;
amber_ff.setup(sys);
float before = amber_ff.updateEnergy();
sys.apply(scpp);
// energy after
amber_ff.setup(sys);
float after = amber_ff.updateEnergy();
TEST_REAL_EQUAL(before > after)
*/
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
