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#include <check.h>
#include <math.h>
#include <pdb.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "tools.h"
START_TEST(test_pdb_empty_lines)
{
char buf[80];
double x[3];
// check string parsing
ck_assert_int_eq(freesasa_pdb_get_atom_name(buf, ""), FREESASA_FAIL);
ck_assert_str_eq(buf, "");
ck_assert_int_eq(freesasa_pdb_get_res_name(buf, ""), FREESASA_FAIL);
ck_assert_str_eq(buf, "");
ck_assert_int_eq(freesasa_pdb_get_res_number(buf, ""), FREESASA_FAIL);
ck_assert_str_eq(buf, "");
ck_assert_int_eq(freesasa_pdb_get_symbol(buf, ""), FREESASA_FAIL);
ck_assert_str_eq(buf, "");
// check coordinate parsing
ck_assert_int_eq(freesasa_pdb_get_coord(x, ""), FREESASA_FAIL);
// check label parsing
ck_assert_int_eq(freesasa_pdb_get_chain_label(""), '\0');
ck_assert_int_eq(freesasa_pdb_get_alt_coord_label(""), '\0');
// check element parsing
ck_assert_int_eq(freesasa_pdb_ishydrogen(""), FREESASA_FAIL);
}
END_TEST
START_TEST(test_pdb_lines)
{
char buf[80];
double x[3], v;
const char *lines[] = {
"ATOM 585 C ARG A 74 41.765 34.829 30.944 0.45 36.22 C",
"ATOM 573 NH1AARG A 72 34.110 28.437 27.768 1.00 35.02 N ",
"HETATM 610 O HOH A 83 27.707 15.908 4.653 1.00 20.30 O ",
"ATOM 573 H ARG A 72 34.110 28.437 27.768 1.00 35.02 H ",
"ATOM 585 C ARG A 74 41.765 34.829 0.45 36.22 C",
"HETATM 7673 CD CD A1978 30.426 14.804 -3.685 1.00 39.42 CD",
"ATOM 573 H ARG A 72 34.110 28.437 27.768 1.00 35.02 ",
"ATOM 573 D ARG A 72 34.110 28.437 27.768 1.00 35.02 D",
"ATOM 573 D ARG A 72 34.110 28.437 27.768 1.00 35.02 ",
};
//Atom-name
freesasa_pdb_get_atom_name(buf, lines[0]);
ck_assert_str_eq(buf, " C ");
freesasa_pdb_get_atom_name(buf, lines[1]);
ck_assert_str_eq(buf, " NH1");
freesasa_pdb_get_atom_name(buf, lines[2]);
ck_assert_str_eq(buf, " O ");
//Res-name
freesasa_pdb_get_res_name(buf, lines[0]);
ck_assert_str_eq(buf, "ARG");
freesasa_pdb_get_res_name(buf, lines[2]);
ck_assert_str_eq(buf, "HOH");
//Res-number
freesasa_pdb_get_res_number(buf, lines[0]);
ck_assert_str_eq(buf, " 74 ");
freesasa_pdb_get_res_number(buf, lines[1]);
ck_assert_str_eq(buf, " 72 ");
freesasa_pdb_get_res_number(buf, lines[2]);
ck_assert_str_eq(buf, " 83 ");
//coordinates
freesasa_pdb_get_coord(x, lines[0]);
ck_assert(float_eq(x[0], 41.765, 1e-6) &&
float_eq(x[1], 34.829, 1e-6) &&
float_eq(x[2], 30.944, 1e-6));
freesasa_set_verbosity(FREESASA_V_SILENT);
ck_assert_int_eq(freesasa_pdb_get_coord(x, lines[4]), FREESASA_FAIL);
freesasa_set_verbosity(FREESASA_V_NORMAL);
//chain label
ck_assert_int_eq(freesasa_pdb_get_chain_label(lines[0]), 'A');
// alt coord labels
ck_assert_int_eq(freesasa_pdb_get_alt_coord_label(lines[0]), ' ');
ck_assert_int_eq(freesasa_pdb_get_alt_coord_label(lines[1]), 'A');
// is hydrogen
ck_assert(!freesasa_pdb_ishydrogen(lines[0]));
ck_assert(freesasa_pdb_ishydrogen(lines[3]));
ck_assert(!freesasa_pdb_ishydrogen(lines[5]));
ck_assert(freesasa_pdb_ishydrogen(lines[6]));
ck_assert(freesasa_pdb_ishydrogen(lines[7]));
ck_assert(freesasa_pdb_ishydrogen(lines[8]));
// symbol
ck_assert_int_eq(freesasa_pdb_get_symbol(buf, lines[0]), FREESASA_SUCCESS);
ck_assert_str_eq(buf, " C");
ck_assert_int_eq(freesasa_pdb_get_symbol(buf, lines[1]), FREESASA_SUCCESS);
ck_assert_str_eq(buf, " N");
// B-factor
ck_assert_int_eq(freesasa_pdb_get_bfactor(&v, lines[0]), FREESASA_SUCCESS);
ck_assert(float_eq(v, 36.22, 1e-4));
// Occupancy
ck_assert_int_eq(freesasa_pdb_get_occupancy(&v, lines[0]), FREESASA_SUCCESS);
ck_assert(float_eq(v, 0.45, 1e-4));
}
END_TEST
START_TEST(test_get_models)
{
// FILE without models
FILE *pdb = fopen(DATADIR "1ubq.pdb", "r");
struct file_range *it;
int n = freesasa_pdb_get_models(pdb, &it);
ck_assert_int_eq(n, 0);
ck_assert(it == NULL);
fclose(pdb);
pdb = fopen(DATADIR "model_mismatch.pdb", "r");
freesasa_set_verbosity(FREESASA_V_SILENT);
ck_assert_int_eq(freesasa_pdb_get_models(pdb, &it), FREESASA_FAIL);
freesasa_set_verbosity(FREESASA_V_NORMAL);
fclose(pdb);
// this file has models
pdb = fopen(DATADIR "2jo4.pdb", "r");
n = freesasa_pdb_get_models(pdb, &it);
ck_assert_int_eq(n, 10);
for (int i = 0; i < n; ++i) {
char *line = NULL;
size_t len;
ck_assert_int_gt(it[i].end, it[i].begin);
fseek(pdb, it[i].begin, 0);
ck_assert(getline(&line, &len, pdb) > 0);
// each segment should begin with MODEL
ck_assert(strncmp(line, "MODEL", 5) == 0);
while (1) {
ck_assert(getline(&line, &len, pdb) > 0);
// there should be only one MODEL per model
ck_assert(strncmp(line, "MODEL", 5) != 0);
if (ftell(pdb) >= it[i].end) break;
}
// the last line of the segment should be ENDMDL
ck_assert(strncmp(line, "ENDMDL", 6) == 0);
free(line);
}
free(it);
fclose(pdb);
}
END_TEST
START_TEST(test_get_chains)
{
// Test a non PDB file
FILE *pdb = fopen(DATADIR "err.config", "r");
struct file_range whole_file = freesasa_whole_file(pdb), *it = NULL;
int nc = freesasa_pdb_get_chains(pdb, whole_file, &it, 0);
fclose(pdb);
ck_assert_int_eq(nc, 0);
ck_assert_ptr_eq(it, NULL);
// This file only has one chain
pdb = fopen(DATADIR "1ubq.pdb", "r");
whole_file = freesasa_whole_file(pdb);
nc = freesasa_pdb_get_chains(pdb, whole_file, &it, 0);
fclose(pdb);
ck_assert_int_eq(nc, 1);
ck_assert_ptr_ne(it, NULL);
free(it);
// This file has 4 chains
pdb = fopen(DATADIR "2jo4.pdb", "r");
int nm = freesasa_pdb_get_models(pdb, &it);
ck_assert_int_eq(nm, 10);
ck_assert_ptr_ne(it, NULL);
for (int i = 0; i < nm; ++i) {
struct file_range *jt = NULL;
nc = freesasa_pdb_get_chains(pdb, it[i], &jt, 0);
ck_assert_int_eq(nc, 4);
ck_assert_ptr_ne(jt, NULL);
for (int j = 1; j < nc; ++j) {
ck_assert_int_ge(jt[j].begin, jt[j - 1].end);
}
free(jt);
}
free(it);
}
END_TEST
extern TCase *test_pdb_static();
Suite *pdb_suite()
{
Suite *s = suite_create("PDB-parser");
TCase *tc_core = tcase_create("Core");
tcase_add_test(tc_core, test_pdb_empty_lines);
tcase_add_test(tc_core, test_pdb_lines);
tcase_add_test(tc_core, test_get_models);
tcase_add_test(tc_core, test_get_chains);
TCase *tc_static = test_pdb_static();
suite_add_tcase(s, tc_core);
suite_add_tcase(s, tc_static);
return s;
}
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