double json_number_value(const json_t *json)
{
if(json_is_integer(json))
return json_integer_value(json);
else if(json_is_real(json))
return json_real_value(json);
else
return 0.0;
}
int json_real_set(const json_t *json, double value)
{
if(!json_is_real(json))
return 0;
json_to_real(json)->value = value;
return 0;
}
Value NDKHelper::getValueFromJson(json_t *obj)
{
if (obj == NULL) {
return Value::Null;
}
if (json_is_object(obj)) {
ValueMap valueMap;
const char *key;
json_t *value;
void *iter = json_object_iter(obj);
while (iter) {
key = json_object_iter_key(iter);
value = json_object_iter_value(iter);
valueMap[key] = NDKHelper::getValueFromJson(value);
iter = json_object_iter_next(obj, iter);
}
return Value(valueMap);
} else if (json_is_array(obj)) {
ValueVector valueVector;
size_t sizeArray = json_array_size(obj);
for (unsigned int i = 0; i < sizeArray; i++) {
valueVector.push_back(NDKHelper::getValueFromJson(json_array_get(obj, i)));
}
return Value(valueVector);
} else if (json_is_boolean(obj)) {
if (json_is_true(obj)) {
return Value(true);
} else {
return Value(false);
}
} else if (json_is_integer(obj)) {
int value = (int) json_integer_value(obj);
return Value(value);
} else if (json_is_real(obj)) {
double value = json_real_value(obj);
return Value(value);
} else if (json_is_string(obj)) {
std::string value = json_string_value(obj);
return Value(value);
}
return Value::Null;
}
static void decode_int_as_real()
{
json_t *json;
json_error_t error;
#if JSON_INTEGER_IS_LONG_LONG
const char *imprecise;
json_int_t expected;
#endif
char big[311];
json = json_loads("42", JSON_DECODE_INT_AS_REAL | JSON_DECODE_ANY, &error);
if (!json || !json_is_real(json) || json_real_value(json) != 42.0)
fail("json_load decode int as real failed - int");
json_decref(json);
#if JSON_INTEGER_IS_LONG_LONG
/* This number cannot be represented exactly by a double */
imprecise = "9007199254740993";
expected = 9007199254740992ll;
json = json_loads(imprecise, JSON_DECODE_INT_AS_REAL | JSON_DECODE_ANY,
&error);
if (!json || !json_is_real(json) || expected != (json_int_t)json_real_value(json))
fail("json_load decode int as real failed - expected imprecision");
json_decref(json);
#endif
/* 1E309 overflows. Here we create 1E309 as a decimal number, i.e.
1000...(309 zeroes)...0. */
big[0] = '1';
memset(big + 1, '0', 309);
big[310] = '\0';
json = json_loads(big, JSON_DECODE_INT_AS_REAL | JSON_DECODE_ANY, &error);
if (json || strcmp(error.text, "real number overflow") != 0 ||
json_error_code(&error) != json_error_numeric_overflow)
fail("json_load decode int as real failed - expected overflow");
json_decref(json);
}
int jansson_to_val(pv_value_t* val, char** freeme, json_t* v) {
val->flags = 0;
if(json_is_object(v) || json_is_array(v)) {
const char* value = json_dumps(v, JSON_COMPACT|JSON_PRESERVE_ORDER);
*freeme = (char*)value;
val->rs.s = (char*)value;
val->rs.len = strlen(value);
val->flags = PV_VAL_STR;
}else if(json_is_string(v)) {
const char* value = json_string_value(v);
val->rs.s = (char*)value;
val->rs.len = strlen(value);
val->flags = PV_VAL_STR;
}else if(json_is_boolean(v)) {
val->ri = json_is_true(v) ? 0 : 1;
val->flags = PV_TYPE_INT|PV_VAL_INT;
}else if(json_is_real(v)) {
char* value = NULL;
if(asprintf(&value, "%.15g", json_real_value(v))<0) {
ERR("asprintf failed\n");
return -1;
}
*freeme = value;
val->rs.s = value;
val->rs.len = strlen(value);
val->flags = PV_VAL_STR;
}else if(json_is_integer(v)) {
long long value = json_integer_value(v);
if ((value > INT_MAX) || (value < INT_MIN)) {
char* svalue = NULL;
if (asprintf(&svalue, "%"JSON_INTEGER_FORMAT, value) < 0) {
ERR("asprintf failed\n");
return -1;
}
*freeme = svalue;
val->rs.s = svalue;
val->rs.len = strlen(svalue);
val->flags = PV_VAL_STR;
} else {
val->ri = (int)value;
val->flags = PV_TYPE_INT|PV_VAL_INT;
}
}else if(json_is_null(v)) {
val->flags = PV_VAL_NULL;
}else {
ERR("unrecognized json type: %d\n", json_typeof(v));
return -1;
}
return 0;
}
//## float Json.getFloat(String key);
static KMETHOD Json_getFloat(KonohaContext *kctx, KonohaStack *sfp)
{
json_t* obj = ((struct _kJson *)sfp[0].asObject)->obj;
CHECK_JSON(obj, KReturnFloatValue(0.0));
const char *key = S_text(sfp[1].asString);
json_t* ret = json_object_get(obj, key);
if(!json_is_real(ret)) {
KReturnFloatValue(0.0);
}
ret = json_incref(ret);
double val = json_real_value(ret);
KReturnFloatValue(val);
}
/* 判断janson的类型 */
int
my_json_type (json_t * value)
{
if (json_is_object (value)) {
printf ("json_is_object\n");
return JSON_OBJECT;
}
if (json_is_array (value)) {
printf ("json_is_array\n");
return JSON_ARRAY;
}
if (json_is_string (value)) {
printf ("json_is_string\n");
return JSON_STRING;
}
if (json_is_integer (value)) {
printf ("json_is_integer\n");
return JSON_INTEGER;
}
if (json_is_real (value)) {
printf ("json_is_real\n");
return JSON_REAL;
}
if (json_is_number (value)) {
printf ("json_is_number\n");
}
if (json_is_boolean (value)) {
printf ("json_is_boolean\n");
}
if (json_is_null (value)) {
printf ("json_is_null\n");
return JSON_NULL;
}
if (json_is_true (value)) {
printf ("json_boolean(1)\n");
return JSON_TRUE;
}
if (json_is_false (value)) {
printf ("json_boolean(0)\n");
return JSON_FALSE;
}
}
json_t *json_true(void)
{
static json_t the_true = {
.type = JSON_TRUE,
.refcount = (unsigned int)1
};
return &the_true;
}
json_t *json_false(void)
{
static json_t the_false = {
.type = JSON_FALSE,
.refcount = (unsigned int)1
};
return &the_false;
}
json_t *json_null(void)
{
static json_t the_null = {
.type = JSON_NULL,
.refcount = (unsigned int)1
};
return &the_null;
}
/*** deletion ***/
void json_delete(json_t *json)
{
if(json_is_object(json))
json_delete_object(json_to_object(json));
else if(json_is_array(json))
json_delete_array(json_to_array(json));
else if(json_is_string(json))
json_delete_string(json_to_string(json));
else if(json_is_integer(json))
json_delete_integer(json_to_integer(json));
else if(json_is_real(json))
json_delete_real(json_to_real(json));
/* json_delete is not called for true, false or null */
}
GratingParams parse_grating_info(const json_t * const root) {
GratingParams result;
json_t *data_json;
data_json = json_object_get(root, "reset_phase_position");
flyvr_assert(data_json != NULL);
flyvr_assert(json_is_boolean(data_json));
result.reset_phase_position = json_is_true( data_json );
data_json = json_object_get(root, "phase_position");
flyvr_assert(data_json != NULL);
flyvr_assert(json_is_real(data_json));
result.phase_position = json_real_value( data_json );
data_json = json_object_get(root, "phase_velocity");
flyvr_assert(data_json != NULL);
flyvr_assert(json_is_real(data_json));
result.phase_velocity = json_real_value( data_json );
data_json = json_object_get(root, "wavelength");
flyvr_assert(data_json != NULL);
flyvr_assert(json_is_real(data_json));
result.wavelength = json_real_value( data_json );
data_json = json_object_get(root, "contrast");
flyvr_assert(data_json != NULL);
flyvr_assert(json_is_real(data_json));
result.contrast = json_real_value( data_json );
data_json = json_object_get(root, "orientation");
flyvr_assert(data_json != NULL);
flyvr_assert(json_is_real(data_json));
result.orientation = json_real_value( data_json );
return result;
}
static kbool_t IsJsonType(struct JsonBuf *jsonbuf, KJSONTYPE type)
{
switch(type) {
case KJSON_OBJECT: return json_is_object(jsonbuf->jsonobj);
case KJSON_ARRAY: return json_is_array(jsonbuf->jsonobj);
case KJSON_STRING: return json_is_string(jsonbuf->jsonobj);
case KJSON_INT: return json_is_integer(jsonbuf->jsonobj);
case KJSON_DOUBLE: return json_is_real(jsonbuf->jsonobj);
case KJSON_BOOLEAN: return json_is_boolean(jsonbuf->jsonobj);
case KJSON_NULL: return json_is_null(jsonbuf->jsonobj);
case KJSON_INT64: return json_is_integer(jsonbuf->jsonobj);
case KJSON_LONG: return json_is_integer(jsonbuf->jsonobj);
}
return false;
}
static size_t
write_real(json_t* json, stream_t* stream)
{
uint8_t op = BSER_TAG_REAL;
assert(json_is_real(json));
double val = json_real_value(json);
size_t bytes = 0;
if (stream->write(stream, &op, SIZE_U8) == SIZE_U8) {
if (stream->write(stream, &val, SIZE_DBL) == SIZE_DBL) {
bytes = SIZE_U8 + SIZE_DBL;
}
}
return bytes;
}
static cxConstChars jsonToConstChars(json_t *v)
{
CX_RETURN(v == NULL, NULL);
cxConstChars str = NULL;
v = jsonParseRegisterValue(v);
if(json_is_string(v)){
str = json_string_value(v);
}else if(json_is_integer(v)){
str = cxConstStr("%"JSON_INTEGER_FORMAT,json_integer_value(v));
}else if(json_is_real(v)){
str = cxConstStr("%f",json_real_value(v));
}else if(json_is_boolean(v)){
str = cxConstStr("%s",json_is_true(v)?"true":"false");
}else if(json_is_object(v)){
str = jsonStrConvert(v);
}
return str;
}
int
jsonUnpackOoiRespFloat( json_t *responseObj, float **outFloat ) {
float myFloat;
if ( !json_is_real( responseObj ) ) {
rodsLog( LOG_ERROR,
"jsonUnpackOoiRespInt: responseObj type %d is not JSON_REAL",
json_typeof( responseObj ) );
return OOI_JSON_TYPE_ERR;
}
else {
myFloat = json_real_value( responseObj );
}
*outFloat = ( float * ) malloc( sizeof( float ) );
*( *outFloat ) = myFloat;
return 0;
}
//## void Json.setFloat(String key, String value);
static KMETHOD Json_setFloat(KonohaContext *kctx, KonohaStack *sfp)
{
json_t* obj = ((struct _kJson *)sfp[0].asObject)->obj;
CHECK_JSON(obj, KReturnDefaultObjectValue());
const char *key = S_text(sfp[1].asString);
float fval = sfp[2].floatValue;
json_t* val = json_real(fval);
if(!json_is_real(val)) {
DBG_P("[ERROR]: Value is not Json object.");
//KLIB KonohaRuntime_raise(kctx, 1, sfp, pline, msg);
KReturnDefaultObjectValue();
}
int ret = json_object_set(obj, key, val);
if(ret < 0) {
DBG_P("[WARNING] Json set cannnot set target object");
KReturnDefaultObjectValue();
}
KReturnVoid();
}
void json_delete(json_t *json)
{
if(json_is_object(json))
json_delete_object(json_to_object(json));
else if(json_is_array(json))
json_delete_array(json_to_array(json));
else if(json_is_string(json))
json_delete_string(json_to_string(json));
else if(json_is_integer(json))
json_delete_integer(json_to_integer(json));
else if(json_is_real(json))
json_delete_real(json_to_real(json));
/* json_delete is not called for true, false or null */
}
QMap<QString, QVariant> mapFromJSON(json_t *json, json_error_t *error)
{
QMap<QString, QVariant> dict;
void *member;
const char *key;
json_t *value;
for (member = json_object_iter(json); member; member = json_object_iter_next(json, member)) {
key = json_object_iter_key(member);
value = json_object_iter_value(member);
QString k = QString::fromUtf8(key);
QVariant v;
// json_is_object(const json_t *json)
// json_is_array(const json_t *json)
// json_is_string(const json_t *json)
// json_is_integer(const json_t *json)
// json_is_real(const json_t *json)
// json_is_true(const json_t *json)
// json_is_false(const json_t *json)
// json_is_null(const json_t *json)
if (json_is_object(value)) {
v = mapFromJSON(json, NULL);
} else if (json_is_array(value)) {
v = listFromJSON(value);
} else if (json_is_string(value)) {
v = QString::fromUtf8(json_string_value(value));
} else if (json_is_integer(value)) {
v = json_integer_value(value);
} else if (json_is_real(value)) {
v = json_real_value(value);
} else if (json_is_boolean(value)) {
v = json_is_true(value);
}
if (v.isValid()) {
dict[k] = v;
}
}
return dict;
}
int read_cfg_real(json_t *root, const char *key, double *val, bool required, double default_val)
{
json_t *node = json_object_get(root, key);
if (!node) {
if (required) {
return -__LINE__;
} else {
*val = default_val;
return 0;
}
}
if (json_is_integer(node)) {
*val = json_integer_value(node);
} else if (json_is_real(node)) {
*val = json_real_value(node);
} else {
return -__LINE__;
}
return 0;
}
static void
dump_perf(json_t *time)
{
const char *key = NULL;
bool first = true;
json_t *val = 0;
json_object_foreach(time, key, val) {
int v = 0;
if (!first)
printf(" ");
else
first = false;
if (json_is_integer(val))
v = json_integer_value(val);
else if (json_is_real(val))
v = json_real_value(val) * 1000000;
printf("%s=%d", key, v);
}
/**
* Convert JSON object to PyObject
* @param JSONObject
* @return PyObject
*/
static PyObject* convert(json_t *json) {
PyObject* object = NULL;
json_t* val;
int result = 0;
if (json_is_object(json)) {
object = PyDict_New();
char* key;
json_object_foreach(json, key, val) {
if (json_is_object(val) || json_is_array(val)) {
result = PyDict_SetItemString(object, key, convert(val));
}
else if(json_is_string(val)) {
const char *str = json_string_value(val);
result = PyDict_SetItemString(object, key,
PyString_DecodeEscape(str, str ? strlen(str) : 0, NULL, 0, NULL));
}
else if(json_is_boolean(val)) {
result = PyDict_SetItemString(object, key,
json_is_true(val) ? Py_True : Py_False);
}
else if(json_is_integer(val)) {
result = PyDict_SetItemString(object, key,
PyInt_FromLong(json_integer_value(val)));
}
else if(json_is_real(val)) {
result = PyDict_SetItemString(object, key,
PyFloat_FromDouble(json_real_value(val)));
}
else {
result = PyDict_SetItemString(object, key, Py_None);
}
if (result == -1)
goto failure;
}
}
else if (json_is_array(json)) {
static int _jsonParseInt(const char *key, json_t *value)
{
if (!value)
{
return 0;
}
if (json_is_true(value))
{
return 1;
}
if (json_is_false(value))
{
return 0;
}
if (json_is_integer(value))
{
return (int)json_integer_value(value);
}
if (json_is_real(value))
{
return (int)json_real_value(value);
}
if (json_is_string(value))
{
char *pEnd;
return strtol(json_string_value(value), &pEnd, 10);
}
lmLog(gLoomApplicationConfigLogGroup, "WARNING: unknown json int conversion in config for key %s", key);
return 0;
}
// little helpers that do conversion
static bool _jsonParseBool(const char *key, json_t *value)
{
if (!value)
{
return false;
}
if (json_is_true(value))
{
return true;
}
if (json_is_false(value))
{
return false;
}
if (json_is_integer(value))
{
return json_integer_value(value) ? true : false;
}
if (json_is_real(value))
{
return json_real_value(value) ? true : false;
}
if (json_is_string(value))
{
return !stricmp(json_string_value(value), "true") ? true : false;
}
lmLog(gLoomApplicationConfigLogGroup, "WARNING: unknown json bool conversion in config for key %s", key);
return false;
}
/* Call the simple functions not covered by other tests of the public API */
int main()
{
json_t *value;
value = json_integer(1);
if(json_typeof(value) != JSON_INTEGER)
fail("json_typeof failed");
if(json_is_object(value))
fail("json_is_object failed");
if(json_is_array(value))
fail("json_is_array failed");
if(json_is_string(value))
fail("json_is_string failed");
if(!json_is_integer(value))
fail("json_is_integer failed");
if(json_is_real(value))
fail("json_is_real failed");
if(!json_is_number(value))
fail("json_is_number failed");
if(json_is_true(value))
fail("json_is_true failed");
if(json_is_false(value))
fail("json_is_false failed");
if(json_is_boolean(value))
fail("json_is_boolean failed");
if(json_is_null(value))
fail("json_is_null failed");
json_decref(value);
value = json_string("foo");
if(!value)
fail("json_string failed");
if(strcmp(json_string_value(value), "foo"))
fail("invalid string value");
if(json_string_set(value, "bar"))
fail("json_string_set failed");
if(strcmp(json_string_value(value), "bar"))
fail("invalid string value");
json_decref(value);
value = json_string(NULL);
if(value)
fail("json_string(NULL) failed");
/* invalid UTF-8 */
value = json_string("a\xefz");
if(value)
fail("json_string(<invalid utf-8>) failed");
value = json_string_nocheck("foo");
if(!value)
fail("json_string_nocheck failed");
if(strcmp(json_string_value(value), "foo"))
fail("invalid string value");
if(json_string_set_nocheck(value, "bar"))
fail("json_string_set_nocheck failed");
if(strcmp(json_string_value(value), "bar"))
fail("invalid string value");
json_decref(value);
/* invalid UTF-8 */
value = json_string_nocheck("qu\xff");
if(!value)
fail("json_string_nocheck failed");
if(strcmp(json_string_value(value), "qu\xff"))
fail("invalid string value");
if(json_string_set_nocheck(value, "\xfd\xfe\xff"))
fail("json_string_set_nocheck failed");
if(strcmp(json_string_value(value), "\xfd\xfe\xff"))
fail("invalid string value");
json_decref(value);
value = json_integer(123);
if(!value)
fail("json_integer failed");
if(json_integer_value(value) != 123)
fail("invalid integer value");
if(json_number_value(value) != 123.0)
fail("invalid number value");
if(json_integer_set(value, 321))
fail("json_integer_set failed");
if(json_integer_value(value) != 321)
fail("invalid integer value");
if(json_number_value(value) != 321.0)
fail("invalid number value");
json_decref(value);
value = json_real(123.123);
if(!value)
fail("json_real failed");
if(json_real_value(value) != 123.123)
fail("invalid integer value");
if(json_number_value(value) != 123.123)
fail("invalid number value");
if(json_real_set(value, 321.321))
fail("json_real_set failed");
if(json_real_value(value) != 321.321)
fail("invalid real value");
if(json_number_value(value) != 321.321)
fail("invalid number value");
json_decref(value);
value = json_true();
if(!value)
fail("json_true failed");
json_decref(value);
value = json_false();
if(!value)
fail("json_false failed");
json_decref(value);
value = json_null();
if(!value)
fail("json_null failed");
json_decref(value);
/* Test reference counting on singletons (true, false, null) */
value = json_true();
if(value->refcount != (size_t)-1)
fail("refcounting true works incorrectly");
json_decref(value);
if(value->refcount != (size_t)-1)
fail("refcounting true works incorrectly");
json_incref(value);
if(value->refcount != (size_t)-1)
fail("refcounting true works incorrectly");
value = json_false();
if(value->refcount != (size_t)-1)
fail("refcounting false works incorrectly");
json_decref(value);
if(value->refcount != (size_t)-1)
fail("refcounting false works incorrectly");
json_incref(value);
if(value->refcount != (size_t)-1)
fail("refcounting false works incorrectly");
value = json_null();
if(value->refcount != (size_t)-1)
fail("refcounting null works incorrectly");
json_decref(value);
if(value->refcount != (size_t)-1)
fail("refcounting null works incorrectly");
json_incref(value);
if(value->refcount != (size_t)-1)
fail("refcounting null works incorrectly");
return 0;
}
void read_ff_json(const char *json_file, struct atomgrp *ag)
{
json_error_t json_file_error;
json_t *base = json_load_file(json_file, 0, &json_file_error);
if (!base) {
fprintf(stderr,
"error reading json file %s on line %d column %d: %s\n",
json_file, json_file_error.line, json_file_error.column,
json_file_error.text);
}
if (!json_is_object(base)) {
fprintf(stderr, "json file not an object %s\n", json_file);
}
json_t *atoms, *bonds, *angles, *torsions, *impropers;
atoms = json_object_get(base, "atoms");
if (!json_is_array(atoms)) {
fprintf(stderr, "json atoms are not an array %s\n", json_file);
}
size_t natoms = json_array_size(atoms);
if (natoms != (size_t) ag->natoms) {
fprintf(stderr,
"json file has a different number of atoms %zd vs. %d : %s\n",
natoms, ag->natoms, json_file);
}
ag->num_atom_types = 0;
for (size_t i = 0; i < natoms; i++) {
json_t *atom = json_array_get(atoms, i);
if (!json_is_object(atom)) {
fprintf(stderr,
"Atom %zd not an object in json file %s\n", i,
json_file);
}
json_t *ace_volume, *ftype_index, *ftype_name, *eps03;
json_t *name, *radius03, *eps;
json_t *charge, *radius, *element;
ace_volume = json_object_get(atom, "ace_volume");
if (!json_is_real(ace_volume)) {
fprintf(stderr,
"json ace volume is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].acevolume = json_real_value(ace_volume);
ftype_index = json_object_get(atom, "ftype_index");
if (!json_is_integer(ftype_index)) {
fprintf(stderr,
"json ftype index is not integer for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].atom_ftypen = json_integer_value(ftype_index);
if (ag->atoms[i].atom_ftypen > ag->num_atom_types) {
ag->num_atom_types = ag->atoms[i].atom_ftypen;
}
ftype_name = json_object_get(atom, "ftype_name");
if (!json_is_string(ftype_name)) {
fprintf(stderr,
"json ftype name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].ftype_name = strdup(json_string_value(ftype_name));
element = json_object_get(atom, "element");
if (!json_is_string(element)) {
fprintf(stderr,
"json element name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].element = strdup(json_string_value(element));
eps = json_object_get(atom, "eps");
if (!json_is_real(eps)) {
fprintf(stderr,
"json eps is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps = sqrt(-json_real_value(eps));
eps03 = json_object_get(atom, "eps03");
if (!json_is_real(eps03)) {
fprintf(stderr,
"json eps03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps03 = sqrt(-json_real_value(eps03));
radius = json_object_get(atom, "radius");
if (!json_is_real(radius)) {
fprintf(stderr,
"json radius is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh = json_real_value(radius);
radius03 = json_object_get(atom, "radius03");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json radius03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh03 = json_real_value(radius03);
charge = json_object_get(atom, "charge");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json charge is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].chrg = json_real_value(charge);
name = json_object_get(atom, "name");
if (!json_is_string(name)) {
fprintf(stderr,
"json name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].name = strdup(json_string_value(name));
ag->atoms[i].nbonds = 0;
ag->atoms[i].nangs = 0;
ag->atoms[i].ntors = 0;
ag->atoms[i].nimps = 0;
ag->atoms[i].fixed = 0;
}
bonds = json_object_get(base, "bonds");
if (!json_is_array(bonds)) {
fprintf(stderr, "json bonds are not an array %s\n", json_file);
}
size_t nbonds = json_array_size(bonds);
ag->nbonds = nbonds;
ag->bonds = _mol_calloc(nbonds, sizeof(struct atombond));
for (size_t i = 0; i < nbonds; i++) {
json_t *bond = json_array_get(bonds, i);
if (!json_is_object(bond)) {
fprintf(stderr,
"Bond %zd not an object in json file %s\n", i,
json_file);
}
json_t *length, *atom1, *atom2, *spring_constant, *sdf_type;
atom1 = json_object_get(bond, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->bonds[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nbonds)++;
atom2 = json_object_get(bond, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->bonds[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nbonds)++;
length = json_object_get(bond, "length");
if (!json_is_real(length)) {
fprintf(stderr,
"json length is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].l0 = json_real_value(length);
spring_constant = json_object_get(bond, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].k = json_real_value(spring_constant);
sdf_type = json_object_get(bond, "sdf_type");
if (!json_is_integer(sdf_type)) {
fprintf(stderr,
"json sdf_type is not integer for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].sdf_type = json_integer_value(sdf_type);
}
angles = json_object_get(base, "angles");
if (!json_is_array(angles)) {
fprintf(stderr, "json angles are not an array %s\n", json_file);
}
size_t nangles = json_array_size(angles);
ag->nangs = nangles;
ag->angs = _mol_calloc(nangles, sizeof(struct atomangle));
for (size_t i = 0; i < nangles; i++) {
json_t *angle = json_array_get(angles, i);
if (!json_is_object(angle)) {
fprintf(stderr,
"Angle %zd not an object in json file %s\n", i,
json_file);
}
json_t *theta, *atom1, *atom2, *atom3, *spring_constant;
atom1 = json_object_get(angle, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->angs[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nangs)++;
atom2 = json_object_get(angle, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->angs[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nangs)++;
atom3 = json_object_get(angle, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->angs[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nangs)++;
theta = json_object_get(angle, "theta");
if (!json_is_real(theta)) {
fprintf(stderr,
"json theta is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].th0 = json_real_value(theta);
spring_constant = json_object_get(angle, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].k = json_real_value(spring_constant);
}
torsions = json_object_get(base, "torsions");
if (!json_is_array(torsions)) {
fprintf(stderr, "json torsions are not an array %s\n",
json_file);
}
size_t ntorsions = json_array_size(torsions);
ag->ntors = ntorsions;
ag->tors = _mol_calloc(ntorsions, sizeof(struct atomtorsion));
for (size_t i = 0; i < ntorsions; i++) {
json_t *torsion = json_array_get(torsions, i);
if (!json_is_object(torsion)) {
fprintf(stderr,
"Torsion %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *minima, *delta_constant,
*spring_constant;
atom1 = json_object_get(torsion, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->tors[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].ntors)++;
atom2 = json_object_get(torsion, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->tors[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].ntors)++;
atom3 = json_object_get(torsion, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->tors[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].ntors)++;
atom4 = json_object_get(torsion, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->tors[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].ntors)++;
minima = json_object_get(torsion, "minima");
if (!json_is_integer(minima)) {
fprintf(stderr,
"json minima is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].n = json_integer_value(minima);
delta_constant = json_object_get(torsion, "delta_constant");
if (!json_is_real(delta_constant)) {
fprintf(stderr,
"json delta_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].d = json_real_value(delta_constant);
spring_constant = json_object_get(torsion, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].k = json_real_value(spring_constant);
}
impropers = json_object_get(base, "impropers");
if (!json_is_array(impropers)) {
fprintf(stderr, "json impropers are not an array %s\n",
json_file);
}
size_t nimpropers = json_array_size(impropers);
ag->nimps = nimpropers;
ag->imps = _mol_calloc(nimpropers, sizeof(struct atomimproper));
for (size_t i = 0; i < nimpropers; i++) {
json_t *improper = json_array_get(impropers, i);
if (!json_is_object(improper)) {
fprintf(stderr,
"Improper %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *phi, *spring_constant;
atom1 = json_object_get(improper, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->imps[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nimps)++;
atom2 = json_object_get(improper, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->imps[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nimps)++;
atom3 = json_object_get(improper, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->imps[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nimps)++;
atom4 = json_object_get(improper, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->imps[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].nimps)++;
phi = json_object_get(improper, "phi");
if (!json_is_real(phi)) {
fprintf(stderr,
"json phi is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].psi0 = json_real_value(phi);
spring_constant = json_object_get(improper, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].k = json_real_value(spring_constant);
}
json_decref(base);
//allocate atom arrays of pointers to parameters
for (size_t i = 0; i < natoms; i++) {
int i1 = ag->atoms[i].nbonds;
ag->atoms[i].bonds = _mol_calloc(i1, sizeof(struct atombond *));
ag->atoms[i].nbonds = 0;
i1 = ag->atoms[i].nangs;
ag->atoms[i].angs = _mol_calloc(i1, sizeof(struct atomangle *));
ag->atoms[i].nangs = 0;
i1 = ag->atoms[i].ntors;
ag->atoms[i].tors =
_mol_calloc(i1, sizeof(struct atomtorsion *));
ag->atoms[i].ntors = 0;
i1 = ag->atoms[i].nimps;
ag->atoms[i].imps =
_mol_calloc(i1, sizeof(struct atomimproper *));
ag->atoms[i].nimps = 0;
}
struct atom *atm;
//fill bonds
for (int i = 0; i < ag->nbonds; i++) {
atm = ag->bonds[i].a0;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
atm = ag->bonds[i].a1;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
}
//fill angles
for (int i = 0; i < ag->nangs; i++) {
atm = ag->angs[i].a0;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a1;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a2;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
}
//fill torsions
for (int i = 0; i < ag->ntors; i++) {
atm = ag->tors[i].a0;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a1;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a2;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a3;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
}
//fill impropers
for (int i = 0; i < ag->nimps; i++) {
atm = ag->imps[i].a0;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a1;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a2;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a3;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
}
//atom indices in the group
fill_ingrp(ag);
ag->is_psf_read = true;
// copy vals from deprecated to new data structures
int atomsi;
for (atomsi = 0; atomsi < ag->natoms; atomsi++) {
_mol_atom_create_bond_indices(&ag->atoms[atomsi],
ag->atoms[atomsi].nbonds);
}
_mol_atom_group_copy_from_deprecated(ag);
}
struct atomgrp *read_json_ag(const char *json_file)
{
struct atomgrp *ag =
(struct atomgrp *)_mol_calloc(1, sizeof(struct atomgrp));
json_error_t json_file_error;
json_t *base = json_load_file(json_file, 0, &json_file_error);
if (!base) {
fprintf(stderr,
"error reading json file %s on line %d column %d: %s\n",
json_file, json_file_error.line, json_file_error.column,
json_file_error.text);
}
if (!json_is_object(base)) {
fprintf(stderr, "json file not an object %s\n", json_file);
}
json_t *atoms, *bonds, *angles, *torsions, *impropers;
atoms = json_object_get(base, "atoms");
if (!json_is_array(atoms)) {
fprintf(stderr, "json atoms are not an array %s\n", json_file);
}
size_t natoms = json_array_size(atoms);
ag->natoms = natoms;
ag->atoms = (struct atom *)_mol_calloc(ag->natoms, sizeof(struct atom));
ag->num_atom_types = 0;
char *prev_segment = _mol_calloc(1, sizeof(char));
char *prev_residue = _mol_calloc(1, sizeof(char));
int prev_residue_seq = -107;
ag->nres = 0;
int alloc_res = 250;
ag->iares = _mol_malloc(alloc_res*sizeof(int));
for (size_t i = 0; i < natoms; i++) {
json_t *atom = json_array_get(atoms, i);
if (!json_is_object(atom)) {
fprintf(stderr,
"Atom %zd not an object in json file %s\n", i,
json_file);
}
json_t *ace_volume, *ftype_index, *ftype_name, *eps03;
json_t *name, *radius03, *eps, *acp_type, *residue_name;
json_t *charge, *radius, *element;
json_t *x, *y, *z;
json_t *yeti_type, *sybyl_type;
json_t *backbone, *hb_acceptor, *hb_donor, *hb_weight;
json_t *segment, *residue;
segment = json_object_get(atom, "segment");
residue = json_object_get(atom, "residue");
if ((segment != NULL) && (residue != NULL)) {
if (!json_is_string(segment)) {
fprintf(stderr,
"json segment is not string for atom %zd in json_file %s\n",
i, json_file);
}
if (!json_is_string(residue)) {
fprintf(stderr,
"json residue is not string for atom %zd in json_file %s\n",
i, json_file);
}
const char *cur_segment = json_string_value(segment);
const char *cur_residue = json_string_value(residue);
if (strcmp(cur_segment, prev_segment) != 0) {
prev_residue_seq += 100;
free(prev_segment);
prev_segment = strdup(cur_segment);
}
if (strcmp(cur_residue, prev_residue) != 0) {
int cur_residue_int = atoi(cur_residue);
int prev_residue_int = atoi(prev_residue);
if ((cur_residue_int - prev_residue_int) > 1) {
prev_residue_seq +=
(cur_residue_int -
prev_residue_int);
} else {
prev_residue_seq += 1;
}
free(prev_residue);
prev_residue = strdup(cur_residue);
if (ag->nres +1 == alloc_res) {
alloc_res *= 2;
ag->iares = _mol_realloc(ag->iares, alloc_res * i);
}
ag->iares[ag->nres] = i;
ag->nres++;
}
ag->atoms[i].comb_res_seq = prev_residue_seq;
} else {
ag->atoms[i].comb_res_seq = prev_residue_seq;
}
ace_volume = json_object_get(atom, "ace_volume");
if (!json_is_real(ace_volume)) {
fprintf(stderr,
"json ace volume is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].acevolume = json_real_value(ace_volume);
ftype_index = json_object_get(atom, "ftype_index");
if (!json_is_integer(ftype_index)) {
fprintf(stderr,
"json ftype index is not integer for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].atom_ftypen = json_integer_value(ftype_index);
if (ag->atoms[i].atom_ftypen > ag->num_atom_types) {
ag->num_atom_types = ag->atoms[i].atom_ftypen;
}
ftype_name = json_object_get(atom, "ftype_name");
if (!json_is_string(ftype_name)) {
fprintf(stderr,
"json ftype name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].ftype_name = strdup(json_string_value(ftype_name));
element = json_object_get(atom, "element");
if (!json_is_string(element)) {
fprintf(stderr,
"json element name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].element = strdup(json_string_value(element));
eps = json_object_get(atom, "eps");
if (!json_is_real(eps)) {
fprintf(stderr,
"json eps is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps = sqrt(-json_real_value(eps));
eps03 = json_object_get(atom, "eps03");
if (!json_is_real(eps03)) {
fprintf(stderr,
"json eps03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps03 = sqrt(-json_real_value(eps03));
radius = json_object_get(atom, "radius");
if (!json_is_real(radius)) {
fprintf(stderr,
"json radius is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh = json_real_value(radius);
radius03 = json_object_get(atom, "radius03");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json radius03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh03 = json_real_value(radius03);
charge = json_object_get(atom, "charge");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json charge is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].chrg = json_real_value(charge);
name = json_object_get(atom, "name");
if (!json_is_string(name)) {
fprintf(stderr,
"json name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].name = strdup(json_string_value(name));
residue_name = json_object_get(atom, "residue_name");
if (residue_name != NULL) {
if (!json_is_string(residue_name)) {
fprintf(stderr,
"json residue_name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].residue_name =
strdup(json_string_value(residue_name));
} else {
ag->atoms[i].residue_name = NULL;
}
x = json_object_get(atom, "x");
if (!json_is_real(x)) {
fprintf(stderr,
"json coordinate x is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].X = json_real_value(x);
y = json_object_get(atom, "y");
if (!json_is_real(y)) {
fprintf(stderr,
"json coordinate y is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].Y = json_real_value(y);
z = json_object_get(atom, "z");
if (!json_is_real(z)) {
fprintf(stderr,
"json coordinate z is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].Z = json_real_value(z);
acp_type = json_object_get(atom, "acp_type");
if (acp_type != NULL) {
if (!json_is_integer(acp_type)) {
fprintf(stderr,
"json acp_type index is not integer for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].acp_type = json_integer_value(acp_type);
} else {
ag->atoms[i].acp_type = -1;
}
yeti_type = json_object_get(atom, "yeti_type");
if (yeti_type != NULL) {
const char *yeti_type_string;
if (!json_is_string(yeti_type)) {
fprintf(stderr,
"json yeti_type is not string for atom %zd in json_file %s\n",
i, json_file);
}
yeti_type_string = json_string_value(yeti_type);
if (strcmp("carbonyl", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_CARBONYL;
} else if (strcmp("hydroxyl", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_HYDROXYL;
} else if (strcmp("sulfonamide", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_SULFONAMIDE;
} else if (strcmp("N5_aromatic", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_N5_AROMATIC;
} else if (strcmp("N6_aromatic", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_N6_AROMATIC;
} else {
fprintf(stderr,
"unknown json yeti_type %s for atom %zd in json_file %s\n",
yeti_type_string, i, json_file);
ag->atoms[i].yeti_type = MOL_YETI_NONE;
}
} else {
ag->atoms[i].yeti_type = MOL_YETI_NONE;
}
sybyl_type = json_object_get(atom, "sybyl_type");
if (sybyl_type != NULL) {
const char *sybyl_type_string;
if (!json_is_string(sybyl_type)) {
fprintf(stderr,
"json sybyl_type is not string for atom %zd in json_file %s\n",
i, json_file);
}
sybyl_type_string = json_string_value(sybyl_type);
ag->atoms[i].hybridization =
mol_hydridization_from_sybyl(sybyl_type_string);
} else {
ag->atoms[i].hybridization = UNKNOWN_HYBRID;
}
backbone = json_object_get(atom, "backbone");
if (backbone != NULL) {
if (!json_is_boolean(backbone)) {
fprintf(stderr,
"json backbone is not boolean for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].backbone = json_is_true(backbone);
} else {
ag->atoms[i].backbone = false;
}
ag->atoms[i].hprop = 0;
hb_acceptor = json_object_get(atom, "hb_acceptor");
if (hb_acceptor != NULL) {
if (!json_is_boolean(hb_acceptor)) {
fprintf(stderr,
"json hb_acceptor is not boolean for atom %zd in json_file %s\n",
i, json_file);
}
if (json_is_true(hb_acceptor)) {
ag->atoms[i].hprop |= HBOND_ACCEPTOR;
}
}
hb_donor = json_object_get(atom, "hb_donor");
if (hb_donor != NULL) {
if (!json_is_boolean(hb_donor)) {
fprintf(stderr,
"json hb_donor is not boolean for atom %zd in json_file %s\n",
i, json_file);
}
if (json_is_true(hb_donor)) {
ag->atoms[i].hprop |= DONATABLE_HYDROGEN;
}
}
ag->atoms[i].hbond_weight = 1.0;
hb_weight = json_object_get(atom, "hb_weight");
if (hb_weight != NULL) {
if (!json_is_real(hb_weight)) {
fprintf(stderr,
"json hb_weight is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].hbond_weight = json_real_value(hb_weight);
}
ag->atoms[i].nbonds = 0;
ag->atoms[i].nangs = 0;
ag->atoms[i].ntors = 0;
ag->atoms[i].nimps = 0;
ag->atoms[i].fixed = 0;
ag->atoms[i].sa = -1;
ag->atoms[i].base = -1;
ag->atoms[i].base2 = -1;
}
ag->iares[ag->nres] = ag->natoms;
ag->iares = _mol_realloc(ag->iares, (ag->nres+1) * sizeof(int));
free(prev_segment);
free(prev_residue);
bonds = json_object_get(base, "bonds");
if (!json_is_array(bonds)) {
fprintf(stderr, "json bonds are not an array %s\n", json_file);
}
size_t nbonds = json_array_size(bonds);
ag->nbonds = nbonds;
ag->bonds = _mol_calloc(nbonds, sizeof(struct atombond));
for (size_t i = 0; i < nbonds; i++) {
json_t *bond = json_array_get(bonds, i);
if (!json_is_object(bond)) {
fprintf(stderr,
"Bond %zd not an object in json file %s\n", i,
json_file);
}
json_t *length, *atom1, *atom2, *spring_constant, *sdf_type;
atom1 = json_object_get(bond, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->bonds[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nbonds)++;
atom2 = json_object_get(bond, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->bonds[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nbonds)++;
length = json_object_get(bond, "length");
if (!json_is_real(length)) {
fprintf(stderr,
"json length is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].l0 = json_real_value(length);
spring_constant = json_object_get(bond, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].k = json_real_value(spring_constant);
sdf_type = json_object_get(bond, "sdf_type");
if (sdf_type != NULL) {
if (!json_is_integer(sdf_type)) {
fprintf(stderr,
"json sdf_type is not integer for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].sdf_type = json_integer_value(sdf_type);
} else {
ag->bonds[i].sdf_type = 0;
}
}
angles = json_object_get(base, "angles");
if (!json_is_array(angles)) {
fprintf(stderr, "json angles are not an array %s\n", json_file);
}
size_t nangles = json_array_size(angles);
ag->nangs = nangles;
ag->angs = _mol_calloc(nangles, sizeof(struct atomangle));
for (size_t i = 0; i < nangles; i++) {
json_t *angle = json_array_get(angles, i);
if (!json_is_object(angle)) {
fprintf(stderr,
"Angle %zd not an object in json file %s\n", i,
json_file);
}
json_t *theta, *atom1, *atom2, *atom3, *spring_constant;
atom1 = json_object_get(angle, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->angs[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nangs)++;
atom2 = json_object_get(angle, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->angs[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nangs)++;
atom3 = json_object_get(angle, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->angs[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nangs)++;
theta = json_object_get(angle, "theta");
if (!json_is_real(theta)) {
fprintf(stderr,
"json theta is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].th0 = json_real_value(theta);
spring_constant = json_object_get(angle, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].k = json_real_value(spring_constant);
}
torsions = json_object_get(base, "torsions");
if (!json_is_array(torsions)) {
fprintf(stderr, "json torsions are not an array %s\n",
json_file);
}
size_t ntorsions = json_array_size(torsions);
ag->ntors = ntorsions;
ag->tors = _mol_calloc(ntorsions, sizeof(struct atomtorsion));
for (size_t i = 0; i < ntorsions; i++) {
json_t *torsion = json_array_get(torsions, i);
if (!json_is_object(torsion)) {
fprintf(stderr,
"Torsion %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *minima, *delta_constant,
*spring_constant;
atom1 = json_object_get(torsion, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->tors[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].ntors)++;
atom2 = json_object_get(torsion, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->tors[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].ntors)++;
atom3 = json_object_get(torsion, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->tors[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].ntors)++;
atom4 = json_object_get(torsion, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->tors[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].ntors)++;
minima = json_object_get(torsion, "minima");
if (!json_is_integer(minima)) {
fprintf(stderr,
"json minima is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].n = json_integer_value(minima);
delta_constant = json_object_get(torsion, "delta_constant");
if (!json_is_real(delta_constant)) {
fprintf(stderr,
"json delta_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].d = json_real_value(delta_constant);
spring_constant = json_object_get(torsion, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].k = json_real_value(spring_constant);
}
impropers = json_object_get(base, "impropers");
if (!json_is_array(impropers)) {
fprintf(stderr, "json impropers are not an array %s\n",
json_file);
}
size_t nimpropers = json_array_size(impropers);
ag->nimps = nimpropers;
ag->imps = _mol_calloc(nimpropers, sizeof(struct atomimproper));
for (size_t i = 0; i < nimpropers; i++) {
json_t *improper = json_array_get(impropers, i);
if (!json_is_object(improper)) {
fprintf(stderr,
"Improper %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *phi, *spring_constant;
atom1 = json_object_get(improper, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->imps[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nimps)++;
atom2 = json_object_get(improper, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->imps[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nimps)++;
atom3 = json_object_get(improper, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->imps[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nimps)++;
atom4 = json_object_get(improper, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->imps[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].nimps)++;
phi = json_object_get(improper, "phi");
if (!json_is_real(phi)) {
fprintf(stderr,
"json phi is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].psi0 = json_real_value(phi);
spring_constant = json_object_get(improper, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].k = json_real_value(spring_constant);
}
json_decref(base);
//allocate atom arrays of pointers to parameters
for (size_t i = 0; i < natoms; i++) {
int i1 = ag->atoms[i].nbonds;
ag->atoms[i].bonds = _mol_calloc(i1, sizeof(struct atombond *));
ag->atoms[i].nbonds = 0;
i1 = ag->atoms[i].nangs;
ag->atoms[i].angs = _mol_calloc(i1, sizeof(struct atomangle *));
ag->atoms[i].nangs = 0;
i1 = ag->atoms[i].ntors;
ag->atoms[i].tors =
_mol_calloc(i1, sizeof(struct atomtorsion *));
ag->atoms[i].ntors = 0;
i1 = ag->atoms[i].nimps;
ag->atoms[i].imps =
_mol_calloc(i1, sizeof(struct atomimproper *));
ag->atoms[i].nimps = 0;
}
struct atom *atm;
//fill bonds
for (int i = 0; i < ag->nbonds; i++) {
atm = ag->bonds[i].a0;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
atm = ag->bonds[i].a1;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
}
//fill angles
for (int i = 0; i < ag->nangs; i++) {
atm = ag->angs[i].a0;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a1;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a2;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
}
//fill torsions
for (int i = 0; i < ag->ntors; i++) {
atm = ag->tors[i].a0;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a1;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a2;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a3;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
}
//fill impropers
for (int i = 0; i < ag->nimps; i++) {
atm = ag->imps[i].a0;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a1;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a2;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a3;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
}
//atom indices in the group
fill_ingrp(ag);
ag->is_psf_read = true;
// copy vals from deprecated to new data structures
int atomsi;
for (atomsi = 0; atomsi < ag->natoms; atomsi++) {
_mol_atom_create_bond_indices(&ag->atoms[atomsi],
ag->atoms[atomsi].nbonds);
}
_mol_atom_group_copy_from_deprecated(ag);
return ag;
}
CCObject* NDKHelper::GetCCObjectFromJson(json_t *obj)
{
if (obj == NULL)
return NULL;
if (json_is_object(obj))
{
CCDictionary *dictionary = new CCDictionary();
//CCDictionary::create();
const char *key;
json_t *value;
void *iter = json_object_iter(obj);
while(iter)
{
key = json_object_iter_key(iter);
value = json_object_iter_value(iter);
dictionary->setObject(NDKHelper::GetCCObjectFromJson(value)->autorelease(), string(key));
iter = json_object_iter_next(obj, iter);
}
return dictionary;
}
else if (json_is_array(obj))
{
size_t sizeArray = json_array_size(obj);
CCArray *array = new CCArray();
//CCArray::createWithCapacity(sizeArray);
for (unsigned int i = 0; i < sizeArray; i++)
{
array->addObject(NDKHelper::GetCCObjectFromJson(json_array_get(obj, i))->autorelease());
}
return array;
}
else if (json_is_boolean(obj))
{
stringstream str;
if (json_is_true(obj))
str << true;
else if (json_is_false(obj))
str << false;
CCString *ccString = new CCString(str.str());
//CCString::create(str.str());
return ccString;
}
else if (json_is_integer(obj))
{
stringstream str;
str << json_integer_value(obj);
CCString *ccString = new CCString(str.str());
//CCString::create(str.str());
return ccString;
}
else if (json_is_real(obj))
{
stringstream str;
str << json_real_value(obj);
CCString *ccString = new CCString(str.str());
//CCString::create(str.str());
return ccString;
}
else if (json_is_string(obj))
{
stringstream str;
str << json_string_value(obj);
CCString *ccString = new CCString(str.str());
//CCString::create(str.str());
return ccString;
}
else if (json_is_null(obj))
{
return new CCString("null");
}
return NULL;
}
static qeo_retcode_t array_to_data(json_t *elemtype, json_t *json_data, qeocore_data_t *data)
{
qeo_retcode_t result = QEO_EINVAL;
json_t *type = json_object_get(elemtype, KEY_QEO_TYPE_CODE); // Mandatory
if ((NULL == type) || (!json_is_integer(type))) {
return result;
}
qeo_sequence_t seq = { 0 };
if (QEO_OK != qeocore_data_sequence_new(data, &seq, json_array_size(json_data))) {
result = QEO_EFAIL;
return result;
}
qeocore_typecode_t qeoTypeCode = (qeocore_typecode_t) json_integer_value(type);
result = QEO_OK;
int i;
int numOfElem = json_array_size(json_data);
for (i = 0; i < numOfElem; ++i) {
json_t *elem = json_array_get(json_data, i);
if (NULL == elem) {
result = QEO_EFAIL;
break;
}
result = QEO_EFAIL;
switch (qeoTypeCode) {
case QEOCORE_TYPECODE_BOOLEAN:
{
if (json_is_boolean(elem)) {
((qeo_boolean_t *)DDS_SEQ_DATA(seq))[i] = json_is_true(elem);
result = QEO_OK;
}
}
break;
case QEOCORE_TYPECODE_INT8:
{
if (json_is_integer(elem)) {
json_int_t json_value = json_integer_value(elem);
if ((-128LL <= json_value) && (json_value <= 127LL)) {
((int8_t *)DDS_SEQ_DATA(seq))[i] = (int8_t) json_value;
result = QEO_OK;
}
}
}
break;
case QEOCORE_TYPECODE_INT16:
{
if (json_is_integer(elem)) {
json_int_t json_value = json_integer_value(elem);
if ((-32768LL <= json_value) && (json_value <= 32767LL)) {
((int16_t *)DDS_SEQ_DATA(seq))[i] = (int16_t) json_value;
result = QEO_OK;
}
}
}
break;
case QEOCORE_TYPECODE_INT32:
{
if (json_is_integer(elem)) {
json_int_t json_value = json_integer_value(elem);
if ((-2147483648LL <= json_value) && (json_value <= 2147483647LL)) {
((int32_t *)DDS_SEQ_DATA(seq))[i] = (int32_t) json_value;
result = QEO_OK;
}
}
}
break;
case QEOCORE_TYPECODE_INT64:
{
if (json_is_integer(elem)) {
((int64_t *)DDS_SEQ_DATA(seq))[i] = (int64_t) json_integer_value(elem);
result = QEO_OK;
}
if (json_is_string(elem)) {
const char *qeo_value = json_string_value(elem);
intmax_t num = strtoimax(qeo_value, NULL, 10);
((int64_t *)DDS_SEQ_DATA(seq))[i] = (int64_t) num;
result = QEO_OK;
}
}
break;
case QEOCORE_TYPECODE_FLOAT32:
{
/*
*Also allow integer values, when float:0.0 is written in a webview then JSON.stringify can result into float:0
*meaning that the float 0.0 is transformed in an integer like 0, that's why we also need to allow integers, to be
*able to handle these rounding issues.
*/
if (json_is_real(json_data) || json_is_integer(json_data)) {
((float *)DDS_SEQ_DATA(seq))[i] = (float) json_real_value(elem);
result = QEO_OK;
}
}
break;
case QEOCORE_TYPECODE_STRING:
{
if (json_is_string(elem)) {
((char **)DDS_SEQ_DATA(seq))[i] = strdup(json_string_value(elem));
result = QEO_OK;
}
}
break;
case QEOCORE_TYPECODE_STRUCT:
{
if (json_is_object(elem)) {
json_t *item = json_object_get(elemtype, KEY_ITEM);
if ((NULL != item) && json_is_object(item)) {
qeocore_data_t *qeo_value = ((qeocore_data_t **)DDS_SEQ_DATA(seq))[i];
result = object_to_data(item, elem, qeo_value);
}
}
}
break;
case QEOCORE_TYPECODE_SEQUENCE:
{
if (json_is_array(elem)) {
json_t *items = json_object_get(elemtype, KEY_ITEMS);
if ((NULL != items) && json_is_object(items)) {
qeocore_data_t *qeo_value = ((qeocore_data_t **)DDS_SEQ_DATA(seq))[i];
result = array_to_data(items, elem, qeo_value);
}
}
}
break;
case QEOCORE_TYPECODE_ENUM:
{
if (!json_is_integer(json_data)){
qeo_log_e("Enum should be integer");
break;
}
qeo_enum_value_t enum_val = (qeo_enum_value_t) json_integer_value(json_data);
if (is_valid_enum_value(elemtype, enum_val) == false){
qeo_log_e("Could not convert json to enum");
break;
}
((qeo_enum_value_t *)DDS_SEQ_DATA(seq))[i] = enum_val;
}
break;
}
if (QEO_OK != result) {
break;
}
}
if (QEO_OK == result) {
result = qeocore_data_sequence_set(data, &seq, 0);
}
return result;
}
static qeo_retcode_t member_to_data(json_t *member, json_t *json_data, qeocore_data_t *data)
{
qeo_retcode_t result = QEO_EINVAL;
json_t *id = json_object_get(member, KEY_ID); // Mandatory
json_t *type = json_object_get(member, KEY_QEO_TYPE_CODE); // Mandatory
if ((NULL == id) || (!json_is_integer(id)) ||
(NULL == type) || (!json_is_integer(type))) {
return result;
}
result = QEO_EFAIL;
qeocore_member_id_t qeo_member_id = (qeocore_member_id_t) json_integer_value(id);
qeocore_typecode_t qeoTypeCode = (qeocore_typecode_t) json_integer_value(type);
/*
bool isKey = false;
json_t *key_value = json_object_get(member, KEY_KEY);
if ((NULL != key_value) && (json_is_true(key_value))) {
isKey = true;
}
*/
switch (qeoTypeCode) {
case QEOCORE_TYPECODE_BOOLEAN:
{
if (json_is_boolean(json_data)) {
qeo_boolean_t qeo_value = (qeo_boolean_t) json_is_true(json_data);
result = qeocore_data_set_member(data, qeo_member_id, &qeo_value);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed");
}
}
}
break;
case QEOCORE_TYPECODE_INT8:
{
if (json_is_integer(json_data)) {
json_int_t json_value = json_integer_value(json_data);
if ((-128LL <= json_value) && (json_value <= 127LL)) {
int8_t qeo_value = (int8_t)json_value;
result = qeocore_data_set_member(data, qeo_member_id, &qeo_value);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed");
}
}
}
}
break;
case QEOCORE_TYPECODE_INT16:
{
if (json_is_integer(json_data)) {
json_int_t json_value = json_integer_value(json_data);
if ((-32768LL <= json_value) && (json_value <= 32767LL)) {
int16_t qeo_value = (int16_t)json_value;
result = qeocore_data_set_member(data, qeo_member_id, &qeo_value);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed");
}
}
}
}
break;
case QEOCORE_TYPECODE_INT32:
{
if (json_is_integer(json_data)) {
json_int_t json_value = json_integer_value(json_data);
if ((-2147483648LL <= json_value) && (json_value <= 2147483647LL)) {
int32_t qeo_value = (int32_t)json_value;
result = qeocore_data_set_member(data, qeo_member_id, &qeo_value);
}
}
}
break;
case QEOCORE_TYPECODE_INT64:
{
if (json_is_integer(json_data)) {
int64_t qeo_value = (int64_t) json_integer_value(json_data);
result = qeocore_data_set_member(data, qeo_member_id, &qeo_value);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed");
}
}
if (json_is_string(json_data)) {
const char *qeo_value = json_string_value(json_data);
intmax_t num = strtoimax(qeo_value, NULL, 10);
result = qeocore_data_set_member(data, qeo_member_id, (int64_t *) &num);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed");
}
}
}
break;
case QEOCORE_TYPECODE_FLOAT32:
{
/*
*Also allow integer values, when float:0.0 is written in a webview then JSON.stringify can result into float:0
*meaning that the float 0.0 is transformed in an integer like 0, that's why we also need to allow integers, to be
*able to handle these rounding issues.
*/
if (json_is_real(json_data) || json_is_integer(json_data)) {
float qeo_value = (float) json_real_value(json_data);
result = qeocore_data_set_member(data, qeo_member_id, &qeo_value);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed");
}
}
}
break;
case QEOCORE_TYPECODE_STRING:
{
if (json_is_string(json_data)) {
const char *qeo_value = json_string_value(json_data);
result = qeocore_data_set_member(data, qeo_member_id, &qeo_value);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed");
}
}
}
break;
case QEOCORE_TYPECODE_STRUCT:
{
if (json_is_object(json_data)) {
qeocore_data_t *qeo_data = NULL;
do {
if (QEO_OK != qeocore_data_get_member(data, qeo_member_id, &qeo_data)) {
qeo_log_e("qeocore_data_get_member failed");
break;
}
if (NULL == qeo_data) {
qeo_log_e("NULL == qeo_data");
break;
}
json_t *item = json_object_get(member, KEY_ITEM);
if (NULL == item) {
qeo_log_e("NULL == item");
break;
}
if (!json_is_object(item)) {
qeo_log_e("item is not an object");
break;
}
result = object_to_data(item, json_data, qeo_data);
if (QEO_OK != result) {
qeo_log_e("object_to_data failed");
break;
}
result = qeocore_data_set_member(data, qeo_member_id, &qeo_data);
if (QEO_OK != result) {
qeo_log_e("qeocore_data_set_member failed: member_id:%u", qeo_member_id);
break;
}
} while (0);
if (NULL != qeo_data) {
qeocore_data_free(qeo_data);
}
}
}
break;
case QEOCORE_TYPECODE_SEQUENCE:
{
if (json_is_array(json_data)) {
qeocore_data_t *qeo_data = NULL;
if ((QEO_OK == qeocore_data_get_member(data, qeo_member_id, &qeo_data)) && (NULL != qeo_data)) {
json_t *items = json_object_get(member, KEY_ITEMS);
if ((NULL != items) && json_is_object(items)) {
if (QEO_OK == array_to_data(items, json_data, qeo_data)) {
result = qeocore_data_set_member(data, qeo_member_id, &qeo_data);
}
}
}
qeocore_data_free(qeo_data);
}
}
break;
case QEOCORE_TYPECODE_ENUM:
{
if (!json_is_integer(json_data)){
qeo_log_e("Enum should be integer");
break;
}
qeo_enum_value_t enum_val = (qeo_enum_value_t) json_integer_value(json_data);
if (is_valid_enum_value(member, enum_val) == false){
qeo_log_e("Could not convert json to enum");
break;
}
result = qeocore_data_set_member(data, qeo_member_id, &enum_val);
}
break;
}
return result;
}
double JsonReader::_readDouble(const string& name){
auto val = json_object_get(getCurrentObject(), name.c_str());
if (!json_is_real(val))
throwBadType(name, "real");
return json_real_value(val);
}
// Parse pools array in json config
bool parse_pool_array(json_t *obj)
{
size_t idx;
json_t *p, *val;
if (!json_is_array(obj))
return false;
// array of objects [ {}, {} ]
json_array_foreach(obj, idx, p)
{
if (!json_is_object(p))
continue;
for (int i = 0; i < ARRAY_SIZE(cfg_array_keys); i++)
{
int opt = -1;
char *s = NULL;
if (cfg_array_keys[i].cat != CFG_POOL)
continue;
val = json_object_get(p, cfg_array_keys[i].name);
if (!val)
continue;
for (int k = 0; k < options_count(); k++)
{
const char *alias = cfg_array_keys[i].longname;
if (alias && !strcasecmp(options[k].name, alias)) {
opt = k;
break;
}
if (!alias && !strcasecmp(options[k].name, cfg_array_keys[i].name)) {
opt = k;
break;
}
}
if (opt == -1)
continue;
if (json_is_string(val)) {
s = strdup(json_string_value(val));
if (!s)
continue;
// applog(LOG_DEBUG, "pool key %s '%s'", options[opt].name, s);
parse_arg(options[opt].val, s);
free(s);
} else {
// numeric or bool
char buf[32] = { 0 };
double d = 0.;
if (json_is_true(val)) d = 1.;
else if (json_is_integer(val))
d = 1.0 * json_integer_value(val);
else if (json_is_real(val))
d = json_real_value(val);
snprintf(buf, sizeof(buf)-1, "%f", d);
// applog(LOG_DEBUG, "pool key %s '%f'", options[opt].name, d);
parse_arg(options[opt].val, buf);
}
}
}
return true;
}
bool Json::isReal() const {
return json_is_real(m_json) > 0;
}