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#if HAVE_CONFIG_H
#include <config.h>
#endif
#include <json-c/json_object.h>
#include <assert.h>
#include <errno.h>
#include <string.h>
#include "freesasa.h"
#include "freesasa_internal.h"
#include "classifier.h"
/** The functions in JSON-C does not seem to have any documented error
return values. Therefore these errors are not caught. */
json_object *
freesasa_json_atom(freesasa_node *node,
int options)
{
assert(node);
json_object *atom = json_object_new_object();
const freesasa_nodearea *area = freesasa_node_area(node);
const char *name = freesasa_node_name(node);
int n_len = strlen(name);
char trim_name[n_len+1];
sscanf(name, "%s", trim_name);
json_object_object_add(atom, "name", json_object_new_string(trim_name));
json_object_object_add(atom, "area", json_object_new_double(area->total));
json_object_object_add(atom, "is-polar",
json_object_new_boolean(freesasa_node_atom_is_polar(node)));
json_object_object_add(atom, "is-main-chain",
json_object_new_boolean(freesasa_atom_is_backbone(name)));
json_object_object_add(atom, "radius",
json_object_new_double(freesasa_node_atom_radius(node)));
return atom;
}
static json_object *
freesasa_json_nodearea(const freesasa_nodearea *area)
{
json_object *obj = json_object_new_object();
json_object_object_add(obj, "total",
json_object_new_double(area->total));
json_object_object_add(obj, "polar",
json_object_new_double(area->polar));
json_object_object_add(obj, "apolar",
json_object_new_double(area->apolar));
json_object_object_add(obj, "main-chain",
json_object_new_double(area->main_chain));
json_object_object_add(obj, "side-chain",
json_object_new_double(area->side_chain));
return obj;
}
json_object *
freesasa_json_residue(freesasa_node *node,
int options)
{
assert(node);
assert(freesasa_node_type(node) == FREESASA_NODE_RESIDUE);
json_object *obj = json_object_new_object();
const char *name = freesasa_node_name(node), *number;
const freesasa_nodearea *abs = freesasa_node_area(node),
*reference = freesasa_node_residue_reference(node);
freesasa_nodearea rel;
number = freesasa_node_residue_number(node);
int n_len = strlen(number);
char trim_number[n_len+1];
sscanf(number, "%s", trim_number);
json_object_object_add(obj, "name", json_object_new_string(name));
json_object_object_add(obj, "number", json_object_new_string(trim_number));
json_object_object_add(obj, "area", freesasa_json_nodearea(abs));
if ((reference != NULL) && !(options & FREESASA_OUTPUT_SKIP_REL)) {
freesasa_residue_rel_nodearea(&rel, abs, reference);
json_object_object_add(obj, "relative-area", freesasa_json_nodearea(&rel));
}
json_object_object_add(obj, "n-atoms",
json_object_new_int(freesasa_node_residue_n_atoms(node)));
return obj;
}
json_object *
freesasa_json_chain(freesasa_node *node,
int options)
{
json_object *obj = json_object_new_object();
const char *name = freesasa_node_name(node);
json_object_object_add(obj, "label", json_object_new_string(name));
json_object_object_add(obj, "n-residues", json_object_new_int(freesasa_node_chain_n_residues(node)));
json_object_object_add(obj, "area",
freesasa_json_nodearea(freesasa_node_area(node)));
return obj;
}
json_object *
freesasa_json_selection(const freesasa_selection **selections)
{
assert(selections);
json_object *obj = json_object_new_array();
while (*selections) {
json_object *json_selection = json_object_new_object();
json_object_object_add(json_selection, "name", json_object_new_string(freesasa_selection_name(*selections)));
json_object_object_add(json_selection, "area", json_object_new_double(freesasa_selection_area(*selections)));
json_object_array_add(obj, json_selection);
++selections;
};
return obj;
}
json_object *
freesasa_json_structure(freesasa_node *node,
int options)
{
json_object *obj = json_object_new_object();
const freesasa_selection **selections = freesasa_node_structure_selections(node);
json_object_object_add(obj, "chains", json_object_new_string(freesasa_node_structure_chain_labels(node)));
json_object_object_add(obj, "model", json_object_new_int(freesasa_node_structure_model(node)));
json_object_object_add(obj, "area",
freesasa_json_nodearea(freesasa_node_area(node)));
if (selections != NULL) {
json_object_object_add(obj, "selections",
freesasa_json_selection(selections));
}
return obj;
}
json_object *
freesasa_node2json(freesasa_node *node,
int exclude_type,
int options)
{
json_object *obj, *array = NULL;
int lowest = 0;
int type = freesasa_node_type(node);
freesasa_node *child = freesasa_node_children(node);
if (child) {
if (freesasa_node_type(child) == exclude_type) lowest = 1;
if (!lowest) array = json_object_new_array();
}
switch (type) {
case FREESASA_NODE_RESULT:
obj = array;
break;
case FREESASA_NODE_STRUCTURE:
obj = freesasa_json_structure(node, options);
if (!lowest) json_object_object_add(obj, "chains", array);
break;
case FREESASA_NODE_CHAIN:
obj = freesasa_json_chain(node, options);
if (!lowest) json_object_object_add(obj, "residues", array);
break;
case FREESASA_NODE_RESIDUE:
obj = freesasa_json_residue(node, options);
if (!lowest) json_object_object_add(obj, "atoms", array);
break;
case FREESASA_NODE_ATOM:
obj = freesasa_json_atom(node, options);
break;
case FREESASA_NODE_ROOT:
default:
assert(0 && "Tree illegal");
}
if (!lowest) {
while (child) {
json_object_array_add(array, freesasa_node2json(child, exclude_type, options));
child = freesasa_node_next(child);
}
}
return obj;
}
static json_object *
parameters2json(const freesasa_parameters *p)
{
json_object *obj = json_object_new_object(), *res;
json_object_object_add(obj, "algorithm", json_object_new_string(freesasa_alg_name(p->alg)));
json_object_object_add(obj, "probe-radius", json_object_new_double(p->probe_radius));
switch(p->alg) {
case FREESASA_SHRAKE_RUPLEY:
res = json_object_new_int(p->shrake_rupley_n_points);
break;
case FREESASA_LEE_RICHARDS:
res = json_object_new_int(p->lee_richards_n_slices);
break;
default:
assert(0);
break;
}
json_object_object_add(obj, "resolution", res);
return obj;
}
static json_object *
json_result(freesasa_node *result,
int options)
{
json_object *obj = json_object_new_object();
freesasa_nodetype exclude_type = FREESASA_NODE_NONE;
const freesasa_parameters *parameters = freesasa_node_result_parameters(result);
if (options & FREESASA_OUTPUT_STRUCTURE) exclude_type = FREESASA_NODE_CHAIN;
if (options & FREESASA_OUTPUT_CHAIN) exclude_type = FREESASA_NODE_RESIDUE;
if (options & FREESASA_OUTPUT_RESIDUE) exclude_type = FREESASA_NODE_ATOM;
json_object_object_add(obj, "input", json_object_new_string(freesasa_node_name(result)));
json_object_object_add(obj, "classifier", json_object_new_string(freesasa_node_classified_by(result)));
json_object_object_add(obj, "parameters", parameters2json(parameters));
json_object_object_add(obj, "structure", freesasa_node2json(result, exclude_type, options));
return obj;
}
int
freesasa_write_json(FILE *output,
freesasa_node *root,
int options)
{
assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);
json_object *results = json_object_new_array(),
*json_root = json_object_new_object();
freesasa_node *child = freesasa_node_children(root);
json_object_object_add(json_root, "source", json_object_new_string(freesasa_string));
json_object_object_add(json_root, "length-unit", json_object_new_string("Ångström"));
json_object_object_add(json_root, "results", results);
while (child) {
json_object_array_add(results, json_result(child, options));
child = freesasa_node_next(child);
}
fputs(json_object_to_json_string_ext(json_root, JSON_C_TO_STRING_PRETTY), output);
json_object_put(json_root);
fflush(output);
if (ferror(output)) {
return fail_msg(strerror(errno));
}
return FREESASA_SUCCESS;
}
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