int
freesasa_shrake_rupley(double *sasa,
const coord_t *xyz,
const double *r,
const freesasa_parameters *param)
{
assert(sasa);
assert(xyz);
assert(r);
if (param == NULL) param = &freesasa_default_parameters;
int n_atoms = freesasa_coord_n(xyz),
n_threads = param->n_threads,
resolution = param->shrake_rupley_n_points,
return_value = FREESASA_SUCCESS;
double probe_radius = param->probe_radius;
sr_data sr;
if (resolution <= 0)
return freesasa_fail("in %s(): n_slices_per_atom = %f is invalid, must be > 0\n",
__func__, resolution);
if (n_atoms == 0) return freesasa_warn("%s(): empty coordinates", __func__);
if (n_threads > n_atoms) {
n_threads = n_atoms;
freesasa_warn("No sense in having more threads than atoms, only using %d threads.",
n_threads);
}
if (init_sr(&sr, sasa, xyz, r, probe_radius, resolution))
return FREESASA_FAIL;
//calculate SASA
if (n_threads > 1) {
#if USE_THREADS
return_value = sr_do_threads(n_threads, &sr);
#else
return_value = freesasa_warn("%s: program compiled for single-threaded use, "
"but multiple threads were requested. Will "
"proceed in single-threaded mode.\n",
__func__);
n_threads = 1;
#endif
}
if (n_threads == 1) {
// don't want the overhead of generating threads if only one is used
for (int i = 0; i < n_atoms; ++i) {
sasa[i] = sr_atom_area(i, &sr);
}
}
release_sr(&sr);
return return_value;
}
int
init_sr(sr_data *sr,
double *sasa,
const coord_t *xyz,
const double *r,
double probe_radius,
int n_points)
{
int n_atoms = freesasa_coord_n(xyz);
coord_t *srp = test_points(n_points);
if (srp == NULL) return fail_msg("Failed to initialize test points.");
//store parameters and reference arrays
sr->n_atoms = n_atoms;
sr->n_points = n_points;
sr->probe_radius = probe_radius;
sr->xyz = xyz;
sr->srp = srp;
sr->sasa = sasa;
sr->nb = NULL;
sr->r = malloc(sizeof(double)*n_atoms);
sr->r2 = malloc(sizeof(double)*n_atoms);
if (sr->r == NULL || sr->r2 == NULL) goto cleanup;
for (int i = 0; i < n_atoms; ++i) {
double ri = r[i] + probe_radius;
sr->r[i] = ri;
sr->r2[i] = ri * ri;
}
//calculate distances
sr->nb = freesasa_nb_new(xyz, sr->r);
if (sr->nb == NULL) goto cleanup;
return FREESASA_SUCCESS;
cleanup:
release_sr(sr);
return mem_fail();
}
int
freesasa_shrake_rupley(double *sasa,
const coord_t *xyz,
const double *r,
double probe_radius,
int n_points,
int n_threads)
{
assert(sasa);
assert(xyz);
assert(r);
assert(n_threads > 0);
int n_atoms = freesasa_coord_n(xyz);
int return_value = FREESASA_SUCCESS;
sr_data sr;
if (n_atoms == 0) return freesasa_warn("%s(): empty coordinates", __func__);
if (init_sr(&sr,sasa,xyz,r,probe_radius,n_points)) return mem_fail();
//calculate SASA
if (n_threads > 1) {
#if USE_THREADS
sr_do_threads(n_threads, sr);
#else
return_value = freesasa_warn("%s: program compiled for single-threaded use, "
"but multiple threads were requested. Will "
"proceed in single-threaded mode.\n",
__func__);
n_threads = 1;
#endif
}
if (n_threads == 1) {
// don't want the overhead of generating threads if only one is used
for (int i = 0; i < n_atoms; ++i) {
sasa[i] = sr_atom_area(i,sr);
}
}
release_sr(sr);
return return_value;
}
