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
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
|
#include <check.h>
#include <freesasa_internal.h>
#include <math.h>
#include <selection.h>
#include <stdio.h>
#include <string.h>
#include "tools.h"
#define N 11
freesasa_structure *structure;
freesasa_result *result;
// clang-format off
double radii[N] = { 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8, 2, 2.2, 2.4, 2.6};
const char *name[N] = { " CA ", " CA ", " CA ", " O ", " N ", " SD ", " CB ", " OXT", "SE ", " P ", " O5'"};
const char *resn[N] = { "ALA", "ALA", "ALA", "ALA", "ARG", "MET", "VAL", "GLU", "SEC", " DC", " DA"};
const char *resi[N] = { " -2", " -1", " 1", " 1", " 2", " 3", " 4", " 1", " 2", " 4", " 5"};
const char chain[N] = { 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'B', 'B', 'B', 'B'};
const int symb_O[N] = { 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1};
const int symb_C[N] = { 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0};
const int symb_N[N] = { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0};
const int symb_S[N] = { 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0};
const int symb_SE[N]= { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0};
const int symb_P[N] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0};
const int resn_A[N] = { 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0};
const int resn_R[N] = { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0};
const int resn_M[N] = { 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0};
const int resn_V[N] = { 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0};
const int resn_Q[N] = { 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0};
const int resn_U[N] = { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0};
const int resn_DC[N]= { 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0};
const int name_CA[N]= { 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0};
const int name_O[N] = { 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0};
const int name_OXT[N]={ 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0};
const int name_O5p[N]={ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1};
const int resi_1r4[N]={ 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0};
const int resi_1[N] = { 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0};
const int resi_2r4[N]={ 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0};
const int resi_m2r1[N]={ 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0};
const int resi_m2rm1[N]={ 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0};
const int chain_A[N]= { 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0};
const int chain_B[N]= { 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1};
const int all[N]= { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
// clang-format on
char selection_name[100][FREESASA_MAX_SELECTION_NAME + 1];
double value[100];
static void
test_select(const char **command, int n_commands)
{
freesasa_selection *sel;
for (int i = 0; i < n_commands; ++i) {
ck_assert_int_eq(freesasa_select_area(command[i], selection_name[i], value + i, structure, result),
FREESASA_SUCCESS);
sel = freesasa_selection_new(command[i], structure, result);
ck_assert_ptr_ne(sel, NULL);
ck_assert_str_eq(freesasa_selection_command(sel), command[i]);
ck_assert_str_eq(freesasa_selection_name(sel), selection_name[i]);
ck_assert(float_eq(freesasa_selection_area(sel), value[i], 1e-10));
freesasa_selection_free(sel);
}
}
static void setup(void)
{
structure = freesasa_structure_new();
for (int i = 0; i < N; ++i) {
freesasa_structure_add_atom(structure, name[i], resn[i], resi[i], chain[i], i * 10, 0, 0);
}
result = freesasa_calc_structure(structure, NULL);
}
static void teardown(void)
{
freesasa_structure_free(structure);
freesasa_result_free(result);
}
static double addup(const int *sel, const freesasa_result *res)
{
double sum = 0;
for (int i = 0; i < res->n_atoms; ++i)
sum += sel[i] * res->sasa[i];
return sum;
}
START_TEST(test_selection_name)
{
freesasa_select_area("c, name ca", selection_name[0], value, structure, result);
ck_assert_str_eq(selection_name[0], "c");
freesasa_select_area("1, name ca", selection_name[0], value, structure, result);
ck_assert_str_eq(selection_name[0], "1");
freesasa_select_area("c1, name ca", selection_name[0], value, structure, result);
ck_assert_str_eq(selection_name[0], "c1");
freesasa_select_area("1c, name ca", selection_name[0], value, structure, result);
ck_assert_str_eq(selection_name[0], "1c");
freesasa_select_area("-1, name ca", selection_name[0], value, structure, result);
ck_assert_str_eq(selection_name[0], "-1");
freesasa_select_area("-1+2_abc, name ca", selection_name[0], value, structure, result);
ck_assert_str_eq(selection_name[0], "-1+2_abc");
}
END_TEST
START_TEST(test_name)
{
const char *commands[] = {"c1, name ca+o",
"c2, name ca",
"c3, name oxt",
"c4, name ca AND name o",
"c5, name ca OR name o",
"c6, name ca+o+oxt",
"c7, name o5'",
"c8, name o5'+ca"};
test_select(commands, 7);
ck_assert(value[0] > 5); // check that it's non-zero
ck_assert(float_eq(value[0], addup(name_CA, result) + addup(name_O, result), 1e-10));
ck_assert(float_eq(value[0], value[4], 1e-10));
ck_assert(float_eq(value[1], addup(name_CA, result), 1e-10));
ck_assert(float_eq(value[2], addup(name_OXT, result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[5],
addup(name_CA, result) + addup(name_O, result) + addup(name_OXT, result),
1e-10));
ck_assert(float_eq(value[6], addup(name_O5p, result), 1e-10));
freesasa_set_verbosity(FREESASA_V_SILENT);
ck_assert_int_eq(freesasa_select_area("c1, name ABCDE", selection_name[0], value, structure, result),
FREESASA_WARN);
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
START_TEST(test_symbol)
{
const char *commands[] = {"c1, symbol o+c",
"c2, symbol O",
"c3, symbol C",
"c4, symbol O AND symbol C",
"c5, symbol O OR symbol C",
"c6, symbol O+C+SE",
"c7, symbol SE",
"c8, symbol O+C+SE and not symbol se"};
test_select(commands, 8);
ck_assert_str_eq(selection_name[0], "c1");
ck_assert_str_eq(selection_name[1], "c2");
ck_assert_str_eq(selection_name[2], "c3");
ck_assert(value[0] > 5); //just to check that it's non-zero
ck_assert(float_eq(value[0], addup(symb_O, result) + addup(symb_C, result), 1e-10));
ck_assert(float_eq(value[1], addup(symb_O, result), 1e-10));
ck_assert(float_eq(value[2], addup(symb_C, result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[4], value[0], 1e-10));
ck_assert(float_eq(value[5],
addup(symb_O, result) + addup(symb_C, result) + addup(symb_SE, result),
1e-10));
ck_assert(float_eq(value[6], addup(symb_SE, result), 1e-10));
ck_assert(float_eq(value[7], value[0], 1e-10));
freesasa_set_verbosity(FREESASA_V_SILENT);
ck_assert_int_eq(freesasa_select_area("c1, symbol ABC", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, symbol 1", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, symbol &%", selection_name[0], value, structure, result),
FREESASA_FAIL);
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
START_TEST(test_resn)
{
const char *commands[] = {"c1, resn ala+arg",
"c2, resn ala",
"c3, resn arg",
"c4, resn ala AND resn arg",
"c5, resn ala OR resn arg",
"c6, resn ala+arg AND NOT resn arg"};
test_select(commands, 6);
ck_assert(value[0] > 5);
ck_assert(float_eq(value[0], addup(resn_A, result) + addup(resn_R, result), 1e-10));
ck_assert(float_eq(value[1], addup(resn_A, result), 1e-10));
ck_assert(float_eq(value[2], addup(resn_R, result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[4], value[0], 1e-10));
ck_assert(float_eq(value[5], value[1], 1e-10));
freesasa_set_verbosity(FREESASA_V_SILENT);
ck_assert_int_eq(freesasa_select_area("c1, resn ABCD", selection_name[0], value, structure, result),
FREESASA_WARN);
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
START_TEST(test_resi)
{
const char *commands[] = {
"c1, resi \\-2-5",
"c2, resi 2-4",
"c3, resi 1",
"c4, resi \\-2 AND resi \\-1-5",
"c5, resi \\-2 OR resi \\-1-5",
"c6, resi \\-2-2+2-5",
"c7, resi \\-1+\\-2-4+5",
"c8, resi \\-2-2+7+9+3-5+100",
"c9, resi 1-4 AND NOT resi 2-4",
"c10,resi \\-2-",
"c11,resi -5",
"c12,resi \\-2-2+2-5",
"c13,resi -5 AND NOT resi \\-2+\\-1+1+5",
"c14,resi 1-2+3- AND NOT resi 5",
"c15,resi 2- AND NOT resi 5",
};
freesasa_set_verbosity(FREESASA_V_SILENT);
test_select(commands, 15);
freesasa_set_verbosity(FREESASA_V_NORMAL);
ck_assert(value[0] > 5);
ck_assert(float_eq(value[0], addup(all, result), 1e-10));
ck_assert(float_eq(value[1], addup(resi_2r4, result), 1e-10));
ck_assert(float_eq(value[2], addup(resi_1, result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[4], value[0], 1e-10));
ck_assert(float_eq(value[5], value[0], 1e-10));
ck_assert(float_eq(value[6], value[0], 1e-10));
ck_assert(float_eq(value[7], value[0], 1e-10));
ck_assert(float_eq(value[8], value[2], 1e-10));
ck_assert(float_eq(value[9], value[0], 1e-10));
ck_assert(float_eq(value[10], value[0], 1e-10));
ck_assert(float_eq(value[11], value[0], 1e-10));
ck_assert(float_eq(value[12], value[1], 1e-10));
ck_assert(float_eq(value[13], value[1] + value[2], 1e-10));
ck_assert(float_eq(value[14], value[1], 1e-10));
freesasa_set_verbosity(FREESASA_V_SILENT);
ck_assert_int_eq(freesasa_select_area("c1, resi 1A", selection_name[0], value, structure, result),
FREESASA_SUCCESS);
ck_assert_int_eq(freesasa_select_area("c1, resi 1a", selection_name[0], value, structure, result),
FREESASA_SUCCESS);
ck_assert_int_eq(freesasa_select_area("c1, resi A", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, resi A1", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, resi 1AA", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, resi 1aa", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, resi 1-A", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, resi 1A-2", selection_name[0], value, structure, result),
FREESASA_WARN);
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
START_TEST(test_chain)
{
const char *commands[] = {"c1, chain A+B",
"c2, chain A",
"c3, chain B",
"c4, chain A AND chain B",
"c5, chain A OR chain B",
"c6, chain A-B",
"c7, chain A-B AND NOT chain A"};
test_select(commands, 7);
ck_assert(value[0] > 5);
ck_assert(float_eq(value[0], addup(chain_A, result) + addup(chain_B, result), 1e-10));
ck_assert(float_eq(value[0], value[4], 1e-10));
ck_assert(float_eq(value[0], value[5], 1e-10));
ck_assert(float_eq(value[1], addup(chain_A, result), 1e-10));
ck_assert(float_eq(value[2], addup(chain_B, result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[6], addup(chain_B, result), 1e-10));
freesasa_set_verbosity(FREESASA_V_SILENT);
ck_assert_int_eq(freesasa_select_area("c1, chain AA", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, chain A-1", selection_name[0], value, structure, result),
FREESASA_WARN);
ck_assert_int_eq(freesasa_select_area("c1, chain &", selection_name[0], value, structure, result),
FREESASA_FAIL);
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
START_TEST(test_syntax_error)
{
double a;
int i;
char s[FREESASA_MAX_SELECTION_NAME + 1];
char s2[2 * FREESASA_MAX_SELECTION_NAME + 1], c = 'a';
const char *err[] = {
"",
"a",
"a,",
"a,b",
// no selection arg
"a,resi",
"a,resn",
"a,name",
"a,symbol",
"a,chain",
// no name of selection
",resn ala",
",resi 1",
",name ca",
", symbol c",
",chain a",
"resn ala",
"resi 1",
"name ca",
"symbol c",
"chain a",
// comma wrong place, no name
"resn, ala",
"resi, 1",
"name, ca",
"symbol, c",
"chain, a",
// ranges (-) used where not allowed
"a, resn ala-arg",
"a, name ca-cb",
"a, symbol c-o",
// illegal range syntax
"a, resi 1-2-3",
"a, resi -1-2",
"a, resi 1-2-",
"a, chain A-",
// trailing +
"a, resn ala+",
"a, resn ala+arg+",
"a, resi 1-2+",
"a, resi 1+2-5+",
// boolean operators
"a, (resn ala) AND",
"a,(resn ala) OR",
"a,(resn ala) OR NOT",
"a, (resn ala) AND arg",
"a,(resn ala) OR arg",
"a, (resn ala) OR NOT arg",
"a, ala OR resn arg",
};
int n = sizeof(err) / sizeof(char *);
freesasa_set_verbosity(FREESASA_V_SILENT);
for (i = 0; i < n; ++i) {
ck_assert_int_eq(freesasa_select_area(err[i], s, &a, structure, result), FREESASA_FAIL);
}
// check that really long strings are truncated properly
for (i = 0; i < FREESASA_MAX_SELECTION_NAME + 5; ++i) {
s2[i] = c + (i % 25);
}
strcpy(s2 + i, ", resn ala");
ck_assert_int_eq(freesasa_select_area(s2, s, &a, structure, result), FREESASA_SUCCESS);
ck_assert_int_eq(strlen(s), FREESASA_MAX_SELECTION_NAME);
ck_assert(strncmp(s2, s, strlen(s)) == 0);
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
// check that some complex constructs don't cause errors, but no checks for valid selection
START_TEST(test_complex_syntax)
{
double a;
char s[FREESASA_MAX_SELECTION_NAME + 1];
const char *stmt[] = {"a, (resn ala AND resi 1-3) OR (NOT chain A+B AND (symbol C OR symbol O))",
"a, NOT symbol SE+C AND NOT resi 5-7+1+\\-6-\\-2+100+200+10-11"};
int n = sizeof(stmt) / sizeof(char *);
freesasa_set_verbosity(FREESASA_V_SILENT);
for (int i = 0; i < n; ++i) {
ck_assert_int_eq(freesasa_select_area(stmt[i], s, &a, structure, result), FREESASA_SUCCESS);
}
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
extern void *freesasa_selection_dummy_ptr;
extern int
freesasa_wrap_select_atoms(void *selection,
const expression *expr,
const freesasa_structure *structure);
extern freesasa_selection *
freesasa_selection_alloc(const char *name, const char *command);
START_TEST(test_memerr)
{
void *ptr1, *ptr2, *ptr3, *ptr4;
freesasa_set_verbosity(FREESASA_V_SILENT);
set_fail_after(1);
ptr1 = freesasa_selection_atom(E_SYMBOL, "C");
ptr2 = freesasa_selection_create(NULL, "bla");
ptr3 = freesasa_selection_selector(E_SYMBOL, NULL);
ptr4 = freesasa_selection_operation(E_AND, NULL, NULL);
set_fail_after(0);
ck_assert_ptr_eq(ptr1, NULL);
ck_assert_ptr_eq(ptr2, NULL);
ck_assert_ptr_eq(ptr3, NULL);
ck_assert_ptr_eq(ptr4, NULL);
set_fail_after(2);
ptr1 = freesasa_selection_atom(E_SYMBOL, "C");
set_fail_after(2);
ptr2 = freesasa_selection_create(NULL, "bla");
set_fail_after(2);
ptr3 = freesasa_selection_atom(E_NEGNUM, "-1");
set_fail_after(0);
ck_assert_ptr_eq(ptr1, NULL);
ck_assert_ptr_eq(ptr2, NULL);
ck_assert_ptr_eq(ptr3, NULL);
expression e = {.left = NULL, .right = NULL, .type = E_OR, .value = NULL};
for (int i = 1; i < 5; ++i) {
set_fail_after(i);
int ret = freesasa_wrap_select_atoms(freesasa_selection_dummy_ptr, &e, structure);
set_fail_after(0);
ck_assert_int_eq(ret, FREESASA_FAIL);
}
freesasa_selection *sel, *sel2;
// the following lines fail with some compilers (at least gcc-5.4 on Ubuntu 16.04)
// todo: figure out why and fix it
// can't go deeper here, because our malloc mocking doesn't work with flex/bison.
// set_fail_after(1);
// sel = freesasa_selection_new("a, atom 1", structure, result);
// set_fail_after(0);
// ck_assert_ptr_eq(sel, NULL);
for (int i = 1; i < 4; ++i) {
set_fail_after(i);
sel = freesasa_selection_alloc("bla", "bla");
set_fail_after(0);
ck_assert_ptr_eq(sel, NULL);
// this one should be valid
sel = freesasa_selection_alloc("bla", "bla");
set_fail_after(i);
sel2 = freesasa_selection_clone(sel);
set_fail_after(0);
ck_assert_ptr_eq(sel2, NULL);
}
freesasa_set_verbosity(FREESASA_V_NORMAL);
}
END_TEST
extern TCase *test_selection_static();
Suite *selector_suite()
{
Suite *s = suite_create("Selector");
TCase *tc_core = tcase_create("Core");
tcase_add_checked_fixture(tc_core, setup, teardown);
tcase_add_test(tc_core, test_selection_name);
tcase_add_test(tc_core, test_name);
tcase_add_test(tc_core, test_symbol);
tcase_add_test(tc_core, test_resn);
tcase_add_test(tc_core, test_resi);
tcase_add_test(tc_core, test_chain);
tcase_add_test(tc_core, test_memerr);
TCase *tc_static = test_selection_static();
TCase *tc_syntax = tcase_create("Syntax");
// just to avoid passing NULL pointers
tcase_add_checked_fixture(tc_syntax, setup, teardown);
tcase_add_test(tc_syntax, test_syntax_error);
tcase_add_test(tc_syntax, test_complex_syntax);
suite_add_tcase(s, tc_core);
suite_add_tcase(s, tc_syntax);
suite_add_tcase(s, tc_static);
return s;
}
|
