aggrescan3d/aggrescan/data/freesasa-2.0.1/src/freesasa.c

/**
    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 <stdlib.h>
#include <string.h>
#include <assert.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
#ifdef 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 = {
    .alg = FREESASA_DEF_ALGORITHM,
    .probe_radius = FREESASA_DEF_PROBE_RADIUS,
    .shrake_rupley_n_points = FREESASA_DEF_SR_N,
    .lee_richards_n_slices = FREESASA_DEF_LR_N,
    .n_threads = 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)

{
    assert(c);
    assert(radii);

    freesasa_result *result = result_new(freesasa_coord_n(c));
    int ret;

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

    coord_t *coord = NULL;
    freesasa_result *result = NULL;

    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)
{
    assert(structure);

    freesasa_node *tree = NULL;
    freesasa_result *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)
{
    assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);
    int n_err = 0;
    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");
    }
    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");
    }
    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");
}