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#if HAVE_CONFIG_H
#include <config.h>
#endif
#include <check.h>
#include <freesasa.h>
#include <json-c/json_object.h>
#include <json-c/json_object_iterator.h>
#include "tools.h"
extern json_object *
freesasa_node2json(freesasa_node *node, int exclude_type, int options);
static int
compare_nodearea(json_object *obj, const freesasa_nodearea *ref, int is_abs)
{
struct json_object_iterator it = json_object_iter_begin(obj),
it_end = json_object_iter_end(obj);
double total, polar, apolar, bb, sc;
while (!json_object_iter_equal(&it, &it_end)) {
const char *key = json_object_iter_peek_name(&it);
json_object *val = json_object_iter_peek_value(&it);
if (!strcmp(key, "total")) {
ck_assert(json_object_is_type(val, json_type_double));
total = json_object_get_double(val);
} else if (!strcmp(key, "polar")) {
ck_assert(json_object_is_type(val, json_type_double));
polar = json_object_get_double(val);
} else if (!strcmp(key, "apolar")) {
ck_assert(json_object_is_type(val, json_type_double));
apolar = json_object_get_double(val);
} else if (!strcmp(key, "main-chain")) {
ck_assert(json_object_is_type(val, json_type_double));
bb = json_object_get_double(val);
} else if (!strcmp(key, "side-chain")) {
ck_assert(json_object_is_type(val, json_type_double));
sc = json_object_get_double(val);
} else {
ck_assert(0);
}
json_object_iter_next(&it);
}
ck_assert(total > 0);
if (is_abs) {
ck_assert(float_eq(total, polar + apolar, 1e-10));
ck_assert(float_eq(total, sc + bb, 1e-10));
ck_assert(float_eq(total, ref->total, 1e-10));
ck_assert(float_eq(polar, ref->polar, 1e-10));
ck_assert(float_eq(apolar, ref->apolar, 1e-10));
ck_assert(float_eq(sc, ref->side_chain, 1e-10));
ck_assert(float_eq(bb, ref->main_chain, 1e-10));
}
return 1;
}
int test_atom(freesasa_node *node)
{
ck_assert_ptr_ne(node, NULL);
json_object *atom = freesasa_node2json(node, FREESASA_NODE_NONE, 0);
ck_assert_ptr_ne(atom, NULL);
struct json_object_iterator it = json_object_iter_begin(atom),
it_end = json_object_iter_end(atom);
while (!json_object_iter_equal(&it, &it_end)) {
const char *key = json_object_iter_peek_name(&it);
json_object *val = json_object_iter_peek_value(&it);
if (!strcmp(key, "name")) {
ck_assert(json_object_is_type(val, json_type_string));
ck_assert_str_eq(json_object_get_string(val), "N");
} else if (!strcmp(key, "area")) {
ck_assert(json_object_is_type(val, json_type_double));
ck_assert(json_object_get_double(val) > 0);
} else if (!strcmp(key, "is-polar")) {
ck_assert(json_object_is_type(val, json_type_boolean));
ck_assert(json_object_get_boolean(val));
} else if (!strcmp(key, "is-main-chain")) {
ck_assert(json_object_is_type(val, json_type_boolean));
ck_assert(json_object_get_boolean(val));
} else if (!strcmp(key, "radius")) {
ck_assert(json_object_is_type(val, json_type_double));
ck_assert(json_object_get_double(val) > 0);
} else {
ck_assert(0);
}
json_object_iter_next(&it);
}
json_object_put(atom);
return 1;
}
int test_residue(freesasa_node *node)
{
ck_assert_ptr_ne(node, NULL);
json_object *residue = freesasa_node2json(node, FREESASA_NODE_NONE, 0);
ck_assert_ptr_ne(residue, NULL);
const freesasa_nodearea *resarea = freesasa_node_area(node);
struct json_object_iterator it = json_object_iter_begin(residue),
it_end = json_object_iter_end(residue);
while (!json_object_iter_equal(&it, &it_end)) {
const char *key = json_object_iter_peek_name(&it);
json_object *val = json_object_iter_peek_value(&it);
if (!strcmp(key, "name")) {
ck_assert(json_object_is_type(val, json_type_string));
ck_assert_str_eq(json_object_get_string(val), "MET");
} else if (!strcmp(key, "number")) {
ck_assert(json_object_is_type(val, json_type_string));
ck_assert_str_eq(json_object_get_string(val), "1");
} else if (!strcmp(key, "n-atoms")) {
ck_assert(json_object_is_type(val, json_type_int));
ck_assert_int_eq(json_object_get_int(val), 8);
} else if (!strcmp(key, "atoms")) {
ck_assert(json_object_is_type(val, json_type_array));
//this is checked further by test_atom
} else if (!strcmp(key, "area")) {
ck_assert(compare_nodearea(val, resarea, 1));
} else if (!strcmp(key, "relative-area")) {
ck_assert(compare_nodearea(val, resarea, 0));
} else {
ck_assert_str_eq(key, "unknown-key");
}
json_object_iter_next(&it);
}
json_object_put(residue);
return 1;
}
int test_chain(freesasa_node *node, const freesasa_result *result)
{
ck_assert_ptr_ne(node, NULL);
json_object *chain = freesasa_node2json(node, FREESASA_NODE_NONE, 0);
const freesasa_nodearea *chain_area = freesasa_node_area(node);
ck_assert_ptr_ne(chain, NULL);
ck_assert(float_eq(chain_area->total, result->total, 1e-10));
struct json_object_iterator it = json_object_iter_begin(chain),
it_end = json_object_iter_end(chain);
while (!json_object_iter_equal(&it, &it_end)) {
const char *key = json_object_iter_peek_name(&it);
json_object *val = json_object_iter_peek_value(&it);
if (!strcmp(key, "label")) {
ck_assert(json_object_is_type(val, json_type_string));
ck_assert_str_eq(json_object_get_string(val), "A");
} else if (!strcmp(key, "n-residues")) {
ck_assert(json_object_is_type(val, json_type_int));
ck_assert_int_eq(json_object_get_int(val), 76);
} else if (!strcmp(key, "area")) {
ck_assert(compare_nodearea(val, chain_area, 1));
} else if (!strcmp(key, "residues")) {
ck_assert(json_object_is_type(val, json_type_array));
// the rest is checked in test_residue
} else {
ck_assert_str_eq(key, "unknown-key");
}
json_object_iter_next(&it);
}
json_object_put(chain);
return 1;
}
int test_structure(freesasa_node *node)
{
ck_assert_ptr_ne(node, NULL);
freesasa_nodearea structure_area = {
.name = "1ubq",
.total = 4804.0556411417447,
.polar = 2504.2173023011442,
.apolar = 2299.838338840601,
.side_chain = 3689.8982162353718,
.main_chain = 1114.157424906374};
json_object *jstruct = freesasa_node2json(node, FREESASA_NODE_NONE, 0);
ck_assert_ptr_ne(jstruct, NULL);
struct json_object_iterator it = json_object_iter_begin(jstruct),
it_end = json_object_iter_end(jstruct);
while (!json_object_iter_equal(&it, &it_end)) {
const char *key = json_object_iter_peek_name(&it);
json_object *val = json_object_iter_peek_value(&it);
if (!strcmp(key, "input")) {
ck_assert(json_object_is_type(val, json_type_string));
ck_assert_str_eq(json_object_get_string(val), "test");
} else if (!strcmp(key, "chain-labels")) {
ck_assert(json_object_is_type(val, json_type_string));
ck_assert_str_eq(json_object_get_string(val), "A");
} else if (!strcmp(key, "area")) {
compare_nodearea(val, &structure_area, 1);
} else if (!strcmp(key, "model")) {
ck_assert(json_object_is_type(val, json_type_int));
// ck_assert_str_eq(json_object_get_string(val), "1");
// these components are tested in test_chains
} else if (!strcmp(key, "chains")) {
ck_assert(json_object_is_type(val, json_type_array));
// these components are tested in test_chains
} else {
ck_assert_str_eq(key, "unknown-key");
}
json_object_iter_next(&it);
}
json_object_put(jstruct);
return 1;
}
START_TEST(test_json)
{
FILE *pdb = fopen(DATADIR "1ubq.pdb", "r");
freesasa_structure *ubq =
freesasa_structure_from_pdb(pdb, &freesasa_default_classifier, 0);
fclose(pdb);
freesasa_result *result = freesasa_calc_structure(ubq, NULL);
freesasa_node *tree = freesasa_tree_new();
freesasa_tree_add_result(tree, result, ubq, "test");
freesasa_node *result_node = freesasa_node_children(tree);
freesasa_node *structures = freesasa_node_children(result_node);
freesasa_node *chains = freesasa_node_children(structures);
freesasa_node *residues = freesasa_node_children(chains);
freesasa_node *atoms = freesasa_node_children(residues);
ck_assert(test_atom(atoms));
ck_assert(test_residue(residues));
ck_assert(test_chain(chains, result));
ck_assert(test_structure(structures));
freesasa_structure_free(ubq);
freesasa_result_free(result);
freesasa_node_free(tree);
}
END_TEST
Suite *json_suite()
{
Suite *s = suite_create("JSON");
TCase *tc_core = tcase_create("Core");
tcase_add_test(tc_core, test_json);
suite_add_tcase(s, tc_core);
return s;
}
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