#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;
}