/**
* Identify bends in the chain, where the kappa angle (virtual bond angle from
* c-alpha i-2, to i, to i+2) is greater than 70 degrees
* dssp-2.2.0/structure.cpp:1729
*/
static std::vector<int> calculate_bends(const float* xyz, const int* ca_indices,
const int* chain_ids, const int n_residues, std::vector<int>& skip)
{
std::vector<int> is_bend(n_residues, 0);
for (int i = 2; i < n_residues-2; i++) {
if (chain_ids[i-2] == chain_ids[i+2] && !skip[i-2] && !skip[i] && !skip[i+2]) {
fvec4 prev_ca(xyz[3*ca_indices[i-2]], xyz[3*ca_indices[i-2]+1], xyz[3*ca_indices[i-2]+2], 0);
fvec4 this_ca(xyz[3*ca_indices[i]], xyz[3*ca_indices[i]+1], xyz[3*ca_indices[i]+2], 0);
fvec4 next_ca(xyz[3*ca_indices[i+2]], xyz[3*ca_indices[i+2]+1], xyz[3*ca_indices[i+2]+2], 0);
fvec4 u_prime = prev_ca-this_ca;
fvec4 v_prime = this_ca-next_ca;
float cosangle = dot3(u_prime, v_prime)/sqrtf(dot3(u_prime, u_prime)*dot3(v_prime, v_prime));
float kappa = acosf(CLIP(cosangle, -1, 1));
is_bend[i] = kappa > (70 * (M_PI / 180.0));
}
}
return is_bend;
}
/**
* Identify bends in the chain, where the kappa angle (virtual bond angle from
* c-alpha i-2, to i, to i+2) is greater than 70 degrees
* dssp-2.2.0/structure.cpp:1729
*/
static std::vector<int> calculate_bends(const float* xyz, const int* ca_indices,
const int* chain_ids, const int n_residues, std::vector<int>& skip)
{
__m128 prev_ca, this_ca, next_ca, u_prime, v_prime, u, v;
float kappa;
std::vector<int> is_bend(n_residues, 0);
for (int i = 2; i < n_residues-2; i++) {
if (chain_ids[i-2] == chain_ids[i+2] && !skip[i-2] && !skip[i] && !skip[i+2]) {
prev_ca = load_float3(xyz + 3*ca_indices[i-2]);
this_ca = load_float3(xyz + 3*ca_indices[i]);
next_ca = load_float3(xyz + 3*ca_indices[i+2]);
u_prime = _mm_sub_ps(prev_ca, this_ca);
v_prime = _mm_sub_ps(this_ca, next_ca);
/* normalize the vectors u_prime and v_prime */
u = _mm_div_ps(u_prime, _mm_sqrt_ps(_mm_dp_ps2(u_prime, u_prime, 0x7F)));
v = _mm_div_ps(v_prime, _mm_sqrt_ps(_mm_dp_ps2(v_prime, v_prime, 0x7F)));
/* compute the arccos of the dot product. this gives the angle */
kappa = (float) acos(CLIP(_mm_cvtss_f32(_mm_dp_ps2(u, v, 0x71)), -1, 1));
is_bend[i] = kappa > (70 * (M_PI / 180.0));
}
}
return is_bend;
}
