void orient_princ(t_atoms *atoms, int isize, atom_id *index,
int natoms, rvec x[], rvec *v, rvec d)
{
int i, m;
rvec xcm, prcomp;
matrix trans;
calc_xcm(x, isize, index, atoms->atom, xcm, FALSE);
for (i = 0; i < natoms; i++)
{
rvec_dec(x[i], xcm);
}
principal_comp(isize, index, atoms->atom, x, trans, prcomp);
if (d)
{
copy_rvec(prcomp, d);
}
/* Check whether this trans matrix mirrors the molecule */
if (det(trans) < 0)
{
for (m = 0; (m < DIM); m++)
{
trans[ZZ][m] = -trans[ZZ][m];
}
}
rotate_atoms(natoms, NULL, x, trans);
if (v)
{
rotate_atoms(natoms, NULL, v, trans);
}
for (i = 0; i < natoms; i++)
{
rvec_inc(x[i], xcm);
}
}
/* move protein so that the anchor is aligned to a defined orientation */
int anchor2defined(PROT *prot_p, VECTOR *pos) {
float cos_theta, theta;
int i_res, i_conf, i_atom, na, ia;
ATOM **all_atoms; /* a list of pointers pointing to all atoms in prot */
ATOM *prot_anchor;
prot_anchor = prot_p->res[prot_p->n_res-1].conf[0].atom;
na = 0;
all_atoms = NULL;
for (i_res=0; i_res<prot_p->n_res; i_res++) {
for (i_conf=0; i_conf<prot_p->res[i_res].n_conf; i_conf++) {
for (i_atom=0; i_atom<prot_p->res[i_res].conf[i_conf].n_atom; i_atom++) {
ATOM *atom_p = &prot_p->res[i_res].conf[i_conf].atom[i_atom];
if (!atom_p->on) continue;
na++;
all_atoms = (ATOM **) realloc(all_atoms, na*sizeof(ATOM *));
all_atoms[na-1] = atom_p;
}
}
}
/* move anchor[0] to pos[0] */
VECTOR shift = vector_vminusv(pos[0], prot_anchor[0].xyz);
for (ia=0; ia<na; ia++) {
all_atoms[ia]->xyz = vector_vplusv(all_atoms[ia]->xyz, shift);
}
/* rotate anchor[1] to be aligned with pos[1] */
/* get i direction given by the defined orientaion (pos) and the current
protein position (prot_anchor) */
VECTOR vec_axis;
VECTOR pos_i, pos_j, pos_k;
VECTOR anchor_i, anchor_j;
pos_i = vector_normalize(vector_vminusv(pos[1],pos[0]));
anchor_i = vector_normalize(vector_vminusv(prot_anchor[1].xyz, prot_anchor[0].xyz));
cos_theta = vdotv(anchor_i, pos_i);
theta = acos(cos_theta);
vec_axis = vector_vplusv(pos[0],vector_vxv(anchor_i, pos_i));
rotate_atoms(pos[0], vec_axis, theta, na, all_atoms);
/* rotate anchor[2] to be aligned with pos[2] */
pos_j = vector_normalize(vector_vminusv(pos[2],pos[0]));
anchor_j = vector_normalize(vector_vminusv(prot_anchor[2].xyz, prot_anchor[0].xyz));
cos_theta = vdotv(anchor_j, pos_j);
theta = acos(cos_theta);
pos_k = vector_normalize(vector_vminusv(pos[3],pos[0]));
if (vdotv(vector_vxv(anchor_j,pos_j),pos_i) <0.)
theta = 2.*env.PI - theta;
rotate_atoms(pos[0], pos[1], theta, na, all_atoms);
free(all_atoms);
na = 0;
return 0;
}
/* Move the protein to the position so the membrane is between
z=+/- half_membrane_thichness */
int mem_position(PROT *prot_p, IPECE *ipece)
{
VECTOR *orig_r;
ATOM **all_atoms; /* a list of pointers pointing to all atoms in prot */
int i_res, i_conf, i_atom, na;
ATOM *atom_p;
VECTOR vec_orig, vec_i, vec_j, vec_k;
vec_orig.x = 0.; vec_orig.y = 0.; vec_orig.z = 0.;
vec_i.x=1.; vec_i.y=0.; vec_i.z=0.;
vec_j.x=0.; vec_j.y=1.; vec_j.z=0.;
vec_k.x=0.; vec_k.y=0.; vec_k.z=1.;
idum = time(NULL);
/* set up. add a residue to contain anchor vectors,
initialize all_atoms array, backup all atom coordinates to orig_r */
ins_res(prot_p, prot_p->n_res);
ins_conf(&prot_p->res[prot_p->n_res-1],0,4);
for (i_atom=0;i_atom<4;i_atom++) {
prot_p->res[prot_p->n_res-1].conf[0].atom[i_atom].on = 1;
}
prot_p->res[prot_p->n_res-1].conf[0].atom[0].xyz = vec_orig;
prot_p->res[prot_p->n_res-1].conf[0].atom[1].xyz = vector_rescale(vec_i,100.);
prot_p->res[prot_p->n_res-1].conf[0].atom[2].xyz = vector_rescale(vec_j,100.);
prot_p->res[prot_p->n_res-1].conf[0].atom[3].xyz = vector_rescale(vec_k,100.);
na = 0;
all_atoms = NULL;
orig_r = NULL;
for (i_res=0; i_res<prot_p->n_res; i_res++) {
for (i_conf=0; i_conf<prot_p->res[i_res].n_conf; i_conf++) {
for (i_atom=0; i_atom<prot_p->res[i_res].conf[i_conf].n_atom; i_atom++) {
atom_p = &prot_p->res[i_res].conf[i_conf].atom[i_atom];
if (!atom_p->on) continue;
na++;
orig_r = (VECTOR *) realloc(orig_r, na*sizeof(VECTOR));
orig_r[na-1] = atom_p->xyz;
all_atoms = (ATOM **) realloc(all_atoms, na*sizeof(ATOM *));
all_atoms[na-1] = atom_p;
atom_p->i_atom_prot = na-1;
}
}
}
/* move the center of the protein to the origin */
VECTOR center;
center = vec_orig;
int ia;
for (ia=0; ia<na; ia++) {
center = vector_vplusv(center, all_atoms[ia]->xyz);
}
center = vector_rescale(center, 1./na);
for (ia=0; ia<na; ia++) {
all_atoms[ia]->xyz = vector_vminusv(all_atoms[ia]->xyz, center);
}
float score, min_score;
int best_pos;
/* get the initial score for the protein */
probe(*prot_p, ipece);
/* collect atoms used for calculating scores */
get_scored_atoms(*prot_p, ipece);
min_score = calc_score(ipece);
best_pos = 1;
/* rotate around x axis by 90� to calculate score again */
rotate_atoms(vec_orig, vec_i, env.PI/2., ipece->n_scored_atom, ipece->scored_atoms);
score = calc_score(ipece);
if (score < min_score) {
min_score = score;
best_pos = 2;
}
rotate_atoms(vec_orig, vec_i, -env.PI/2., ipece->n_scored_atom, ipece->scored_atoms);
/* rotate around y axis by 90� to calculate score again */
rotate_atoms(vec_orig, vec_j, env.PI/2., ipece->n_scored_atom, ipece->scored_atoms);
score = calc_score(ipece);
if (score < min_score) {
min_score = score;
best_pos = 3;
}
rotate_atoms(vec_orig, vec_j, -env.PI/2., ipece->n_scored_atom, ipece->scored_atoms);
/* choose the lowest scored position to start with */
if (best_pos == 2) {
rotate_atoms(vec_orig, vec_i, env.PI/2., na, all_atoms);
rotate_atoms(vec_orig, vec_i, env.PI/2., ipece->n_scored_atom, ipece->scored_atoms);
}
if (best_pos == 3) {
rotate_atoms(vec_orig, vec_j, env.PI/2., na, all_atoms);
rotate_atoms(vec_orig, vec_j, env.PI/2., ipece->n_scored_atom, ipece->scored_atoms);
}
/* randomly translate the protein in z direction or rotation around an axis
on x-y plane to find the lowest scored position.
sampling the positions in a way similar as monte carlo */
VECTOR vec_trans = vec_orig;
VECTOR vec_axis = vec_orig;
score = calc_score(ipece);
min_score = score;
for (ia=0;ia<4;ia++) {
ipece->membrane_position[ia] = prot_p->res[prot_p->n_res-1].conf[0].atom[ia].xyz;
}
int iter;
for (iter=0;iter<ipece->n_iteration;iter++) {
float new_score, delta_score;
/* translation */
if (ran2(&idum) < 0.5) {
vec_trans.z = 2.*(ran2(&idum) - 0.5)*ipece->translation_max;
translate_atoms(vec_trans, ipece->n_scored_atom, ipece->scored_atoms);
new_score = calc_score(ipece);
delta_score = new_score - score;
if (ran2(&idum) < exp(-ipece->beta * delta_score)) {
translate_atoms(vec_trans, na, all_atoms);
score = new_score;
}
else {
vec_trans.z = -vec_trans.z;
translate_atoms(vec_trans, ipece->n_scored_atom, ipece->scored_atoms);
}
}
/* rotation */
else {
float phi, theta;
phi = ran2(&idum)*2.*env.PI;
theta = ran2(&idum)*ipece->rotation_max; /* rotation_max has been
converted to radian in
parameter reading process */
vec_axis.x = cos(phi);
vec_axis.y = sin(phi);
rotate_atoms(vec_orig, vec_axis, theta, ipece->n_scored_atom, ipece->scored_atoms);
new_score = calc_score(ipece);
delta_score = new_score - score;
if (ran2(&idum) < exp(-ipece->beta * delta_score)) {
rotate_atoms(vec_orig, vec_axis, theta, na, all_atoms);
score = new_score;
}
else {
vec_trans.z = -vec_trans.z;
rotate_atoms(vec_orig, vec_axis, -theta, ipece->n_scored_atom, ipece->scored_atoms);
}
}
if (score < min_score) {
min_score = score;
for (ia=0;ia<4;ia++) {
ipece->membrane_position[ia] = prot_p->res[prot_p->n_res-1].conf[0].atom[ia].xyz;
}
}
/*
printf("\n");
for (i=0;i<4;i++) {
printf(" %10.6f %10.6f %10.6f\n",
prot_p->res[prot_p->n_res-1].conf[0].atom[i].xyz.x,
prot_p->res[prot_p->n_res-1].conf[0].atom[i].xyz.y,
prot_p->res[prot_p->n_res-1].conf[0].atom[i].xyz.z);
}
*/
}
ipece->mem_position_defined = 1;
/* move the protein back to orginal position */
for (ia=0; ia<na; ia++) {
all_atoms[ia]->xyz = orig_r[ia];
}
/* free memory */
free_scored_atoms(ipece);
free_probe(ipece);
free(all_atoms);
free(orig_r);
na = 0;
/* delete the extra anchor residue */
del_res(prot_p, prot_p->n_res-1);
return 0;
}
