freesasa-sys 0.1.12

/**
 * This source file contains everything that is in freesasa.h
 * interface and does not have a natural home in any of the other
 * source files.
 */

#if HAVE_CONFIG_H
#include <config.h>
#endif
#include <assert.h>
#include <stdlib.h>
#include <string.h>

#include "freesasa_internal.h"

#ifdef PACKAGE_VERSION
const char *freesasa_version = PACKAGE_VERSION;
#else
const char *freesasa_version = "";
#endif

#ifdef PACKAGE_STRING
const char *freesasa_string = PACKAGE_STRING;
#else
const char *freesasa_string = "FreeSASA";
#endif

/* Allows compilation with different defaults
   depending on USE_THREADS. but still exposing the value in a header
   that doesn't depend on USE_THREADS */
#if USE_THREADS
#define DEF_NUMBER_THREADS 2
#else
#define DEF_NUMBER_THREADS 1
#endif
const int FREESASA_DEF_NUMBER_THREADS = DEF_NUMBER_THREADS;

const freesasa_parameters freesasa_default_parameters = {
    FREESASA_DEF_ALGORITHM,
    FREESASA_DEF_PROBE_RADIUS,
    FREESASA_DEF_SR_N,
    FREESASA_DEF_LR_N,
    DEF_NUMBER_THREADS};

static freesasa_result *
result_new(int n)
{
    freesasa_result *result = malloc(sizeof(freesasa_result));

    if (result == NULL) {
        mem_fail();
        return NULL;
    }

    result->sasa = malloc(sizeof(double) * n);

    if (result->sasa == NULL) {
        mem_fail();
        freesasa_result_free(result);
        return NULL;
    }

    result->n_atoms = n;

    return result;
}

void freesasa_result_free(freesasa_result *r)
{
    if (r) {
        free(r->sasa);
        free(r);
    }
}

freesasa_result *
freesasa_calc(const coord_t *c,
              const double *radii,
              const freesasa_parameters *parameters)

{
    freesasa_result *result;
    int ret = FREESASA_SUCCESS, i;

    assert(c);
    assert(radii);

    result = result_new(freesasa_coord_n(c));

    if (result == NULL) {
        fail_msg("");
        return NULL;
    }

    if (parameters == NULL) parameters = &freesasa_default_parameters;

    switch (parameters->alg) {
    case FREESASA_SHRAKE_RUPLEY:
        ret = freesasa_shrake_rupley(result->sasa, c, radii, parameters);
        break;
    case FREESASA_LEE_RICHARDS:
        ret = freesasa_lee_richards(result->sasa, c, radii, parameters);
        break;
    default:
        assert(0); /* should never get here */
        break;
    }
    if (ret == FREESASA_FAIL) {
        freesasa_result_free(result);
        return NULL;
    }

    result->total = 0;
    for (i = 0; i < freesasa_coord_n(c); ++i) {
        result->total += result->sasa[i];
    }
    result->parameters = *parameters;

    return result;
}

freesasa_result *
freesasa_calc_coord(const double *xyz,
                    const double *radii,
                    int n,
                    const freesasa_parameters *parameters)
{
    coord_t *coord = NULL;
    freesasa_result *result = NULL;

    assert(xyz);
    assert(radii);
    assert(n > 0);

    coord = freesasa_coord_new_linked(xyz, n);
    if (coord != NULL) result = freesasa_calc(coord, radii, parameters);
    if (result == NULL) fail_msg("");

    freesasa_coord_free(coord);

    return result;
}

freesasa_result *
freesasa_calc_structure(const freesasa_structure *structure,
                        const freesasa_parameters *parameters)
{
    assert(structure);

    return freesasa_calc(freesasa_structure_xyz(structure),
                         freesasa_structure_radius(structure),
                         parameters);
}

freesasa_node *
freesasa_calc_tree(const freesasa_structure *structure,
                   const freesasa_parameters *parameters,
                   const char *name)
{
    freesasa_node *tree = NULL;
    freesasa_result *result;

    assert(structure);

    result = freesasa_calc(freesasa_structure_xyz(structure),
                           freesasa_structure_radius(structure),
                           parameters);

    if (result != NULL) {
        tree = freesasa_tree_init(result, structure, name);
    } else {
        fail_msg("");
    }

    if (tree == NULL) {
        fail_msg("");
    }

    freesasa_result_free(result);

    return tree;
}

static inline void
count_err(int return_value, int *n_err)
{
    if (return_value == FREESASA_FAIL) {
        (*n_err)++;
    }
}

int freesasa_tree_export(FILE *file,
                         freesasa_node *root,
                         int options)
{
    int n_err = 0;

    assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);

    if (options & FREESASA_LOG) {
        count_err(freesasa_write_log(file, root), &n_err);
    }
    if (options & FREESASA_RES) {
        count_err(freesasa_write_res(file, root), &n_err);
    }
    if (options & FREESASA_SEQ) {
        count_err(freesasa_write_seq(file, root), &n_err);
    }
    if (options & FREESASA_PDB) {
        count_err(freesasa_write_pdb(file, root), &n_err);
    }
    if (options & FREESASA_RSA) {
        count_err(freesasa_write_rsa(file, root, options), &n_err);
    }
    if (options & FREESASA_JSON) {
#if USE_JSON
        count_err(freesasa_write_json(file, root, options), &n_err);
#else
        return fail_msg("library was built without support for JSON output");
#endif
    }
    if (options & FREESASA_XML) {
#if USE_XML
        count_err(freesasa_write_xml(file, root, options), &n_err);
#else
        return fail_msg("library was built without support for XML output");
#endif
    }
    if (n_err > 0) {
        return fail_msg("there were errors when writing output");
    }
    return FREESASA_SUCCESS;
}

freesasa_result *
freesasa_result_clone(const freesasa_result *result)
{
    freesasa_result *clone = result_new(result->n_atoms);

    if (clone == NULL) {
        fail_msg("");
        return NULL;
    }

    clone->n_atoms = result->n_atoms;
    clone->total = result->total;
    clone->parameters = result->parameters;
    memcpy(clone->sasa, result->sasa, sizeof(double) * clone->n_atoms);

    return clone;
}

const char *
freesasa_alg_name(freesasa_algorithm alg)
{
    switch (alg) {
    case FREESASA_SHRAKE_RUPLEY:
        return "Shrake & Rupley";
    case FREESASA_LEE_RICHARDS:
        return "Lee & Richards";
    }
    assert(0 && "Illegal algorithm");
}