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
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/KERNEL/PDBAtom.h>
#include <BALL/KERNEL/chain.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/KERNEL/residue.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/CONCEPT/textPersistenceManager.h>
///////////////////////////
using namespace BALL;
bool testEqual(const PDBAtom& a, const PDBAtom& b)
{
return a.getElement() == b.getElement() &&
a.getName() == b.getName() &&
a.getTypeName() == b.getTypeName() &&
a.getType() == b.getType() &&
a.getPosition() == b.getPosition() &&
a.getVelocity() == b.getVelocity() &&
a.getForce() == b.getForce() &&
a.getCharge() == b.getCharge() &&
a.getRadius() == b.getRadius() &&
a.getBranchDesignator() == b.getBranchDesignator() &&
a.getRemotenessIndicator() == b.getRemotenessIndicator() &&
a.getAlternateLocationIndicator() == b.getAlternateLocationIndicator() &&
a.getOccupancy() == b.getOccupancy() &&
a.getTemperatureFactor() == b.getTemperatureFactor();
}
START_TEST(PDBAtom)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
// tests for class PDBAtom::
PDBAtom* pa = 0;
CHECK(PDBAtom() throw())
pa = new PDBAtom;
TEST_NOT_EQUAL(pa, 0)
TEST_EQUAL(pa->isValid(), true)
RESULT
CHECK(~PDBAtom() throw())
delete pa;
RESULT
Vector3 position(0.1, 1.1, 2.1);
Vector3 velocity(3.1, 4.1, 5.1);
Vector3 force(6.1, 7.1, 8.1);
String filename;
TextPersistenceManager pm;
using std::ofstream;
using std::ifstream;
using std::ios;
using namespace RTTI;
CHECK(PDBAtom(Element& element, const String& name, const String& type_name = BALL_ATOM_DEFAULT_TYPE_NAME, Atom::Type atom_type = BALL_ATOM_DEFAULT_TYPE, const Vector3& position = Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3& velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3& force = Vector3(BALL_ATOM_DEFAULT_FORCE), float charge = BALL_ATOM_DEFAULT_CHARGE, float radius = BALL_ATOM_DEFAULT_RADIUS, char branch_designator =BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, char remoteness_indicator =BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, char alternate_location_indicator = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, float occupancy = BALL_PDBATOM_DEFAULT_OCCUPANCY, float temperature_factor = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR) throw())
pa = new PDBAtom(PTE.getElement(1), "name", "type_name" , 0, position, velocity, force, 9.1, 10.1, 'a', 'b', 'c', 11.1, 12.1);
TEST_NOT_EQUAL(pa, 0)
TEST_EQUAL(pa->isValid(), true)
delete pa;
RESULT
PDBAtom pdba(PTE.getElement(13), "name", "type_name" , 0, position, velocity, force, 9.1, 10.1, 'a', 'b', 'c', 11.1, 12.1);
CHECK(PDBAtom(const PDBAtom& pdb_atom, bool deep = true) throw())
PDBAtom* p2 = new PDBAtom(pdba);
TEST_NOT_EQUAL(p2, 0)
TEST_EQUAL(testEqual(pdba, *p2), true)
delete p2;
RESULT
CHECK(bool operator == (const PDBAtom& pdb_atom) const throw())
PDBAtom p2;
TEST_EQUAL(pdba == p2, false)
TEST_EQUAL(p2 == p2, true)
RESULT
CHECK(bool operator != (const PDBAtom& pdb_atom) const throw())
PDBAtom p2;
TEST_EQUAL(pdba != p2, true)
TEST_EQUAL(p2 != p2, false)
RESULT
CHECK(void persistentWrite(PersistenceManager& pm, const char* name = 0) const)
NEW_TMP_FILE(filename)
ofstream ofile(filename.c_str(), std::ios::out);
pm.setOstream(ofile);
pm.registerClass(getStreamName<PDBAtom>(), PDBAtom::createDefault);
pdba >> pm;
ofile.close();
RESULT
CHECK(void persistentRead(PersistenceManager& pm))
ifstream ifile(filename.c_str());
pm.setIstream(ifile);
PersistentObject* ptr;
ptr = pm.readObject();
ifile.close();
TEST_NOT_EQUAL(ptr, 0)
if (ptr != 0)
{
TEST_EQUAL(isKindOf<PDBAtom>(ptr), true)
if (isKindOf<PDBAtom>(ptr))
{
PDBAtom* p2 = castTo<PDBAtom>(*ptr);
TEST_EQUAL(testEqual(*p2, pdba), true)
}
delete ptr;
}
RESULT
CHECK(void set(const PDBAtom& pdb_atom, bool deep = true) throw())
PDBAtom p2;
p2.set(pdba);
TEST_EQUAL(testEqual(pdba, p2), true)
RESULT
CHECK(void get(PDBAtom& pdb_atom, bool deep = true) const throw())
PDBAtom p2;
pdba.get(p2);
TEST_EQUAL(testEqual(pdba, p2), true)
RESULT
CHECK(PDBAtom& operator = (const PDBAtom& pdb_atom) throw())
PDBAtom p2;
p2 = pdba;
TEST_EQUAL(testEqual(pdba, p2), true)
RESULT
CHECK(void swap(PDBAtom& pdb_atom) throw())
PDBAtom p2(pdba);
p2.setTemperatureFactor((float)99.9);
pdba.swap(p2);
TEST_REAL_EQUAL(p2.getTemperatureFactor(), (float) 12.1)
TEST_REAL_EQUAL(pdba.getTemperatureFactor(), (float) 99.9)
p2.swap(pdba);
TEST_REAL_EQUAL(p2.getTemperatureFactor(), (float) 99.9)
TEST_REAL_EQUAL(pdba.getTemperatureFactor(), (float) 12.1)
RESULT
Protein p;
Chain c;
Residue r;
CHECK(Protein* getProtein() throw())
TEST_EQUAL(pdba.getProtein(), 0)
p.insert(pdba);
pdba.getProtein()->setName("protein");
TEST_EQUAL(pdba.getProtein(), &p)
TEST_EQUAL(p.getName(), "protein")
p.remove(pdba);
RESULT
CHECK(const Protein* getProtein() const throw())
const PDBAtom& p2(pdba);
TEST_EQUAL(p2.getProtein(), 0)
p.insert(pdba);
TEST_EQUAL(pdba.getProtein(), &p)
TEST_EQUAL(p.getName(), "protein")
p.remove(pdba);
RESULT
c.insert(r);
CHECK(Chain* getChain() throw())
TEST_EQUAL(pdba.getChain(), 0)
r.insert(pdba);
pdba.getChain()->setName("protein");
TEST_EQUAL(pdba.getChain(), &c)
TEST_EQUAL(c.getName(), "protein")
r.remove(pdba);
RESULT
CHECK(const Chain* getChain() const throw())
const PDBAtom& p2(pdba);
TEST_EQUAL(p2.getChain(), 0)
r.insert(pdba);
TEST_EQUAL(pdba.getChain(), &c)
TEST_EQUAL(c.getName(), "protein")
r.remove(pdba);
RESULT
CHECK(Residue* getResidue() throw())
TEST_EQUAL(pdba.getResidue(), 0)
r.insert(pdba);
pdba.getResidue()->setName("protein");
TEST_EQUAL(pdba.getResidue(), &r)
TEST_EQUAL(c.getName(), "protein")
r.remove(pdba);
RESULT
CHECK(const Residue* getResidue() const throw())
const PDBAtom& p2(pdba);
TEST_EQUAL(p2.getResidue(), 0)
r.insert(pdba);
TEST_EQUAL(pdba.getResidue(), &r)
TEST_EQUAL(c.getName(), "protein")
r.remove(pdba);
RESULT
CHECK(void setBranchDesignator(char branch_designator) throw())
PDBAtom p2;
p2.setBranchDesignator('A');
TEST_EQUAL(p2.getBranchDesignator(), 'A')
RESULT
CHECK(char getBranchDesignator() const throw())
PDBAtom p;
TEST_EQUAL(p.getBranchDesignator(), ' ')
RESULT
CHECK(void setRemotenessIndicator(char remoteness_indicator) throw())
PDBAtom p2;
p2.setRemotenessIndicator('B');
TEST_EQUAL(p2.getRemotenessIndicator(), 'B')
RESULT
CHECK(char getRemotenessIndicator() const throw())
PDBAtom p;
TEST_EQUAL(p.getRemotenessIndicator(), ' ')
RESULT
CHECK(void setAlternateLocationIndicator(char alternate_location_indicator) throw())
PDBAtom p2;
p2.setAlternateLocationIndicator('B');
TEST_EQUAL(p2.getAlternateLocationIndicator(), 'B')
RESULT
CHECK(char getAlternateLocationIndicator() const throw())
PDBAtom p;
TEST_EQUAL(p.getAlternateLocationIndicator(), ' ')
RESULT
CHECK(void setOccupancy(float occupancy) throw())
PDBAtom p2;
p2.setOccupancy(12.23);
TEST_REAL_EQUAL(p2.getOccupancy(), (float) 12.23)
RESULT
CHECK(float getOccupancy() const throw())
PDBAtom p;
TEST_REAL_EQUAL(p.getOccupancy(), 1)
RESULT
CHECK(void setTemperatureFactor(float temperature_factor) throw())
PDBAtom p2;
p2.setTemperatureFactor(23.34);
TEST_REAL_EQUAL(p2.getTemperatureFactor(), (float) 23.34)
RESULT
CHECK(float getTemperatureFactor() const throw())
PDBAtom p;
TEST_REAL_EQUAL(p.getTemperatureFactor(), 0)
RESULT
CHECK(void dump(std::ostream& s = std::cout, Size depth = 0) const throw())
NEW_TMP_FILE(filename)
std::ofstream outfile(filename.c_str(), std::ios::out);
pdba.dump(outfile);
outfile.close();
TEST_FILE_REGEXP(filename.c_str(), BALL_TEST_DATA_PATH(PDBAtom_test_dump.txt))
RESULT
CHECK(BALL_CREATE_DEEP(PDBAtom))
PDBAtom empty;
PDBAtom p(PTE.getElement(1), "name", "type_name" , 0, position, velocity, force, 9.1, 10.1, 'a', 'b', 'c', 11.1, 12.1);
PDBAtom* test;
test = (PDBAtom*) p.create(false, true);
TEST_EQUAL(testEqual(*test, empty), true)
delete test;
test = (PDBAtom*) p.create(true, false);
TEST_EQUAL(testEqual(*test, p), true)
delete test;
RESULT
CHECK(PDBAtom(const String& name) throw())
PDBAtom p("pdbatom1");
TEST_EQUAL(p.getName(), "pdbatom1")
p.setName("");
PDBAtom empty;
TEST_EQUAL(testEqual(empty, p), true)
RESULT
CHECK(void clear() throw())
PDBAtom empty;
PDBAtom p(PTE.getElement(1), "name", "type_name" , 0, position, velocity, force, 9.1, 10.1, 'a', 'b', 'c', 11.1, 12.1);
p.clear();
TEST_EQUAL(testEqual(empty, p), true)
RESULT
CHECK(void destroy() throw())
PDBAtom empty;
PDBAtom p(PTE.getElement(1), "name", "type_name" , 0, position, velocity, force, 9.1, 10.1, 'a', 'b', 'c', 11.1, 12.1);
p.destroy();
TEST_EQUAL(testEqual(empty, p), true)
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
