static int ks_assign_hydrogens(const float* xyz, const int* nco_indices, const int n_residues, float *hcoords, int* skip)
/* Assign hydrogen atom coordinates
*/
{
int ri, pc_index, po_index;
__m128 pc, po, r_co, r_h, r_n, norm_r_co;
__m128 tenth = _mm_set1_ps(0.1f);
r_n = load_float3(xyz + 3*nco_indices[0]);
store_float3(hcoords, r_n);
hcoords += 3;
for (ri = 1; ri < n_residues; ri++) {
if (!skip[ri]) {
pc_index = nco_indices[3*(ri-1) + 1];
po_index = nco_indices[3*(ri-1) + 2];
pc = load_float3(xyz + 3*pc_index);
po = load_float3(xyz + 3*po_index);
r_co = _mm_sub_ps(pc, po);
r_n = load_float3(xyz + 3*nco_indices[3*ri + 0]);
norm_r_co = _mm_mul_ps(r_co, _mm_rsqrt_ps(_mm_dp_ps2(r_co, r_co, 0xFF)));
r_h = _mm_add_ps(r_n, _mm_mul_ps(tenth, norm_r_co));
store_float3(hcoords, r_h);
}
hcoords += 3;
}
return 1;
}
static void asa_frame(const float* frame, const int n_atoms, const float* atom_radii,
const float* sphere_points, const int n_sphere_points,
int* neighbor_indices, float* centered_sphere_points, float* areas)
{
/*// Calculate the accessible surface area of each atom in a single snapshot
//
// Parameters
// ----------
// frame : 2d array, shape=[n_atoms, 3]
// The coordinates of the nuclei
// n_atoms : int
// the major axis length of frame
// atom_radii : 1d array, shape=[n_atoms]
// the van der waals radii of the atoms PLUS the probe radius
// sphere_points : 2d array, shape=[n_sphere_points, 3]
// a bunch of uniformly distributed points on a sphere
// n_sphere_points : int
// the number of sphere points
// centered_sphere_points : WORK BUFFER 2d array, shape=[n_sphere_points, 3]
// empty memory that intermediate calculations can be stored in
// neighbor_indices : WORK BUFFER 2d array, shape=[n_atoms]
// empty memory that intermediate calculations can be stored in
// NOTE: the point of these work buffers is that if we want to call
// this function repreatedly, its more efficient not to keep re-mallocing
// these work buffers, but instead just reuse them.
// areas : 1d array, shape=[n_atoms]
// the output buffer to place the results in -- the surface area of each
// atom
*/
int i, j, k, k_prime;
__m128 r, r_i, r_j, r_ij, atom_radius_i, atom_radius_j, radius_cutoff;
__m128 radius_cutoff2, sp, r_jk, r2;
int n_neighbor_indices, is_accessible, k_closest_neighbor;
float constant = 4.0 * M_PI / n_sphere_points;
for (i = 0; i < n_atoms; i++) {
atom_radius_i = _mm_set1_ps(atom_radii[i]);
r_i = load_float3(frame+i*3);
/* Get all the atoms close to atom `i` */
n_neighbor_indices = 0;
for (j = 0; j < n_atoms; j++) {
if (i == j) {
continue;
}
r_j = load_float3(frame+j*3);
r_ij = _mm_sub_ps(r_i, r_j);
atom_radius_j = _mm_set1_ps(atom_radii[j]);
/* Look for atoms `j` that are nearby atom `i` */
radius_cutoff = _mm_add_ps(atom_radius_i, atom_radius_j);
radius_cutoff2 = _mm_mul_ps(radius_cutoff, radius_cutoff);
r2 = _mm_dp_ps(r_ij, r_ij, 0x7F);
if (_mm_extract_epi16(CAST__M128I(_mm_cmplt_ps(r2, radius_cutoff2)), 0)) {
neighbor_indices[n_neighbor_indices] = j;
n_neighbor_indices++;
}
if (_mm_extract_epi16(CAST__M128I(_mm_cmplt_ps(r2, _mm_set1_ps(1e-10))), 0)) {
printf("ERROR: THIS CODE IS KNOWN TO FAIL WHEN ATOMS ARE VIRTUALLY");
printf("ON TOP OF ONE ANOTHER. YOU SUPPLIED TWO ATOMS %f", _mm_cvtss_f32(r));
printf("APART. QUITTING NOW");
exit(1);
}
}
/* Center the sphere points on atom i */
for (j = 0; j < n_sphere_points; j++) {
sp = _mm_add_ps(r_i, _mm_mul_ps(atom_radius_i, load_float3(sphere_points + 3*j)));
store_float3(centered_sphere_points + 3*j, sp);
}
/* Check if each of these points is accessible */
k_closest_neighbor = 0;
for (j = 0; j < n_sphere_points; j++) {
is_accessible = 1;
r_j = load_float3(centered_sphere_points + 3*j);
/* iterate through the sphere points by cycling through them */
/* in a circle, starting with k_closest_neighbor and then wrapping */
/* around */
for (k = k_closest_neighbor; k < n_neighbor_indices + k_closest_neighbor; k++) {
k_prime = k % n_neighbor_indices;
r = _mm_set1_ps(atom_radii[neighbor_indices[k_prime]]);
r_jk = _mm_sub_ps(r_j, load_float3(frame+3*neighbor_indices[k_prime]));
if (_mm_extract_epi16(CAST__M128I(_mm_cmplt_ps(_mm_dp_ps(r_jk, r_jk, 0xFF), _mm_mul_ps(r, r))), 0)) {
k_closest_neighbor = k;
is_accessible = 0;
break;
}
}
if (is_accessible) {
areas[i]++;
}
}
areas[i] *= constant * (atom_radii[i])*(atom_radii[i]);
}
}
