int cmp_conf_hv(CONF conf1, CONF conf2, float IDEN_THR) {
int iatom, jatom;
float IDEN_THR2 = IDEN_THR*IDEN_THR;
int n_hv1=0, n_hv2=0;
//if (strcmp(conf1.confName, conf2.confName)) return -1;
//if (conf1.n_atom != conf2.n_atom) return -1;
/* check if they same number of heavy atoms */
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (!conf1.atom[iatom].on) continue;
if (conf1.atom[iatom].name[1] == 'H') continue;
n_hv1++;
}
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (!conf2.atom[jatom].on) continue;
if (conf2.atom[jatom].name[1] == 'H') continue;
n_hv2++;
}
if (n_hv1!=n_hv2) return -1;
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (!conf1.atom[iatom].on) continue;
if (conf1.atom[iatom].name[1] == 'H') continue;
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (!conf2.atom[jatom].on) continue;
if (conf2.atom[jatom].name[1] == 'H') continue;
if (strncmp(conf1.atom[iatom].name+1, conf2.atom[jatom].name+1, 2) ) continue;
if (ddvv(conf1.atom[iatom].xyz, conf2.atom[jatom].xyz) < IDEN_THR2) break;
}
if (jatom == conf2.n_atom) return -1;
}
return 0;
}
int cmp_conf(CONF conf1, CONF conf2, float IDEN_THR) {
int iatom, jatom,n_on1,n_on2;
float IDEN_THR2 = IDEN_THR*IDEN_THR;
//if (strcmp(conf1.confName, conf2.confName)) return -1;
if (conf1.n_atom != conf2.n_atom) return -1;
n_on1 = 0;
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (conf1.atom[iatom].on) n_on1++;
}
n_on2 = 0;
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (conf2.atom[jatom].on) n_on2++;
}
if (n_on1 != n_on2) return -2;
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (!conf1.atom[iatom].on) continue;
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (!conf2.atom[jatom].on) continue;
if (strncmp(conf1.atom[iatom].name+1, conf2.atom[jatom].name+1, 2) ) continue;
if (fabs(conf1.atom[iatom].crg - conf2.atom[jatom].crg) > 1e-3) continue;
if (ddvv(conf1.atom[iatom].xyz, conf2.atom[jatom].xyz) < IDEN_THR2) break;
}
if (jatom == conf2.n_atom) return -1;
}
return 0;
}
float vdw(ATOM atom1, ATOM atom2)
{
float e = 0;
float d2, d6, d12; /* distance with power 2, 6, and 12 */
float C12, C6;
char pair[4];
VECTOR v1, v2;
FILE *debug_fp;
if (!atom1.on) return e;
if (!atom2.on) return e;
v1 = atom1.xyz;
v2 = atom2.xyz;
d2 = ddvv(v1, v2);
if (d2 > cutoff_far2)
e = VDW_ELIMIT_FAR; /* Cutoff */
else if (d2 < cutoff_near2)
e = VDW_ELIMIT_NEAR; /* Cutoff */
else
{ /* 12-6 L-J potential */
pair[0] = atom1.name[1]; /* element name */
pair[1] = '-';
pair[2] = atom2.name[1]; /* element name */
pair[3] = '\0';
if (param_get("VDWAMBER", "C12", pair, &C12)) {
param_get("VDWAMBER", "C12", "X-X", &C12);
debug_fp = fopen(env.debug_log,"a");
fprintf(debug_fp, "VDWAMBER C12 %s %16.6f\n", pair, C12);
fclose(debug_fp);
param_sav("VDWAMBER", "C12", pair, &C12,sizeof(C12));
}
if(param_get("VDWAMBER", "C6", pair, &C6)) {
param_get("VDWAMBER", "C6", "X-X", &C6);
debug_fp = fopen(env.debug_log,"a");
fprintf(debug_fp, "VDWAMBER C6 %s %16.6f\n", pair, C6);
fclose(debug_fp);
param_sav("VDWAMBER", "C6", pair, &C6,sizeof(C6));
}
d6 = d2*d2*d2;
d12 = d6*d6;
e = C12/d12 - C6/d6;
}
return e;
}
float dist_conf_hv(CONF conf1, CONF conf2) {
int iatom, jatom;
float max_dist = 999.;
float next_test_dist, test_dist2;
int n_hv1=0, n_hv2=0;
/* check if they have the same number of heavy atoms */
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (!conf1.atom[iatom].on) continue;
if (conf1.atom[iatom].name[1] == 'H') continue;
n_hv1++;
}
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (!conf2.atom[jatom].on) continue;
if (conf2.atom[jatom].name[1] == 'H') continue;
n_hv2++;
}
if (n_hv1!=n_hv2) return 999.;
next_test_dist = max_dist;
while (1) {
test_dist2 = next_test_dist*next_test_dist - 1e-4;
next_test_dist = 0.;
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (!conf1.atom[iatom].on) continue;
if (conf1.atom[iatom].name[1] == 'H') continue;
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (!conf2.atom[jatom].on) continue;
if (conf2.atom[jatom].name[1] == 'H') continue;
if (strncmp(conf1.atom[iatom].name+1, conf2.atom[jatom].name+1, 2) ) continue;
if (ddvv(conf1.atom[iatom].xyz, conf2.atom[jatom].xyz) < test_dist2) break;
}
if (jatom >= conf2.n_atom) break; /* can't find a jatom within test_dist to match iatom */
else {
/* next test threshold is the maximum of all distances btw matched iatom and jatom */
if (dvv(conf1.atom[iatom].xyz, conf2.atom[jatom].xyz) > next_test_dist) {
next_test_dist = dvv(conf1.atom[iatom].xyz, conf2.atom[jatom].xyz);
}
}
}
if (iatom < conf1.n_atom) { /* test_dist in the current loop is shorter than the distance btw i and j */
break;
}
}
return sqrt(test_dist2+1e-4);
}
float vdw_sim(ATOM atom1, ATOM atom2)
{ float f1 = env.vdwf1, f2 = env.vdwf2;
/* vdw constants
* vdw = epsilon((sigma/(r1+r2))^12 - (sigma/(r1+r2))^6)
* f1: sigma=f1*(r1+r2)
* f2: epsilon=f2
*/
float e = 0;
float d2, d6, d12; /* distance with power 2, 6, and 12 */
float C12, C6;
float s, s6, s12;
VECTOR v1, v2;
if (!atom1.on) return e;
if (!atom2.on) return e;
v1 = atom1.xyz;
v2 = atom2.xyz;
d2 = ddvv(v1, v2);
if (d2 > cutoff_far2)
e = VDW_ELIMIT_FAR; /* Cutoff */
else if (d2 < cutoff_near2)
e = VDW_ELIMIT_NEAR; /* Cutoff */
else
{ /* 12-6 L-J potential */
d6 = d2*d2*d2;
d12 = d6*d6;
s = f1*(atom1.rad+atom1.rad);
s6 = s*s*s*s*s*s;
s12= s6*s6;
C12=f2*s12;
C6 =f2*s6;
e = C12/d12 - C6/d6;
}
return e;
}
VECTOR vdw_frc(VECTOR v1, VECTOR v2, float C6, float C12) {
VECTOR frc;
float d2, d4, d8, d14;
VECTOR frc6,frc12;
d2 = ddvv(v1, v2);
if (d2 > cutoff_far2) {frc.x=0;frc.y=0;frc.z=0;return frc;}
if (d2 < cutoff_near2) d2 = cutoff_near2;
d4 = d2*d2;
d8 = d4*d4;
d14 = d8*d4*d2;
frc12 = vector_rescale(vector_vminusv(v2,v1), (-12.*C12/d14));
frc6 = vector_rescale(vector_vminusv(v2,v1), ( 6.*C6/d8));
frc = vector_vplusv(frc12, frc6);
return frc;
}
float rmsd_conf_hv(CONF conf1, CONF conf2) {
int iatom, jatom;
int n_hv1=0, n_hv2=0;
float sum_distsq;
/* check if they have the same number of heavy atoms */
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (!conf1.atom[iatom].on) continue;
if (conf1.atom[iatom].name[1] == 'H') continue;
n_hv1++;
}
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (!conf2.atom[jatom].on) continue;
if (conf2.atom[jatom].name[1] == 'H') continue;
n_hv2++;
}
if (n_hv1!=n_hv2) return 999.;
if (n_hv1 == 0) return 0.;
sum_distsq = 0.;
for (iatom = 0; iatom<conf1.n_atom; iatom++) {
if (!conf1.atom[iatom].on) continue;
if (conf1.atom[iatom].name[1] == 'H') continue;
for (jatom = 0; jatom<conf2.n_atom; jatom++) {
if (!conf2.atom[jatom].on) continue;
if (conf2.atom[jatom].name[1] == 'H') continue;
if (!strcmp(conf1.atom[iatom].name, conf2.atom[jatom].name)) break;
}
if (jatom >= conf2.n_atom) return 999.; /* can't find a jatom to match iatom */
sum_distsq += ddvv(conf1.atom[iatom].xyz, conf2.atom[jatom].xyz);
}
return sqrt(sum_distsq/(float) n_hv1);
}
int mkacc(ATOM *atom)
{
VECTOR point;
int i, j, k, l, m;
float d_square;
int count;
int ix, iy, iz;
int ax, ay, az; /* the grid index of this atom */
int status;
count = num_pts;
ax = (int) ((atom -> xyz.x - xyz_min.x) / grid_interval);
ay = (int) ((atom -> xyz.y - xyz_min.y) / grid_interval);
az = (int) ((atom -> xyz.z - xyz_min.z) / grid_interval);
/* loop over each point */
for (m = 0; m < num_pts; m++) {
status = TRUE;
point.x = point_preset[m][0] * atom -> rad + atom -> xyz.x;
point.y = point_preset[m][1] * atom -> rad + atom -> xyz.y;
point.z = point_preset[m][2] * atom -> rad + atom -> xyz.z;
/* find out which grid this point belongs to */
ix = (int) ((point.x - xyz_min.x) / grid_interval);
iy = (int) ((point.y - xyz_min.y) / grid_interval);
iz = (int) ((point.z - xyz_min.z) / grid_interval);
if (grid[ix][iy][iz].n_atom >= 1) {
for (l = 0; l < grid[ix][iy][iz].n_atom; l++) {
if (grid[ix][iy][iz].atom[l].on &&
status == TRUE &&
(ix != ax || iy != ay || iz != az ||
memcmp(atom, &(grid[ix][iy][iz].atom[l]), sizeof(ATOM)))) {
d_square = ddvv(point, grid[ix][iy][iz].atom[l].xyz);
if (d_square < grid[ix][iy][iz].atom[l].rad * grid[ix][iy][iz].atom[l].rad) {
status = FALSE;
count --;
}
}
}
}
for (i = ix - 1; i <= ix + 1; i++) {
if (status == FALSE) break;
for (j = iy - 1; j <= iy + 1; j++) {
if (status == FALSE) break;
for (k = iz - 1; k <= iz + 1; k++) {
if (status == FALSE) break;
for (l = 0; l < grid[i][j][k].n_atom; l++) {
if (grid[i][j][k].atom[l].on && status == TRUE) {
if (i != ax || j != ay || k != az ||
memcmp(atom, &(grid[i][j][k].atom[l]), sizeof(ATOM))) {
d_square = ddvv(point, grid[i][j][k].atom[l].xyz);
if (d_square < grid[i][j][k].atom[l].rad * grid[i][j][k].atom[l].rad) {
status = FALSE;
count --;
}
}
}
}
}
}
}
}
atom->sas = (float) count/num_pts;
return 0;
}
int relax_water(PROT prot) {
int i_res,i_conf,i_atom,j_res,j_conf,j_atom,k_res,k_conf,k_atom;
int n_conf, add, counter;
FILE *debug_fp;
for (i_res=0; i_res<prot.n_res; i_res++) {
RES *ires_p = &prot.res[i_res];
if (strcmp(prot.res[i_res].resName, "HOH")) continue;
n_conf = prot.res[i_res].n_conf;
counter = 0;
for (i_conf=1; i_conf<n_conf; i_conf++) {
CONF *iconf_p = &prot.res[i_res].conf[i_conf];
if (!iconf_p->n_atom) continue;
for (j_res=0; j_res<prot.n_res; j_res++) {
if (!strcmp(prot.res[j_res].resName, "HOH")) continue;
for (j_conf=0; j_conf<prot.res[j_res].n_conf; j_conf++) {
CONF *jconf_p = &prot.res[j_res].conf[j_conf];
ATOM *iatom_p;
CONF conf;
conf.n_atom = iconf_p->n_atom;
conf.atom = (ATOM *) malloc(conf.n_atom*sizeof(ATOM));
cpy_conf(&conf,iconf_p);
for (i_atom=0;i_atom<conf.n_atom;i_atom++) {
if (!conf.atom[i_atom].on) continue;
if (conf.atom[i_atom].name[1] == 'O') break;
}
if (i_atom<conf.n_atom) iatom_p = &conf.atom[i_atom];
else break;
add = 0;
for (j_atom=0; j_atom<prot.res[j_res].conf[j_conf].n_atom; j_atom++) {
ATOM *jatom_p = &jconf_p->atom[j_atom];
if (!jatom_p->on) continue;
if (jatom_p->name[1] == 'H') continue;
if (ddvv(iatom_p->xyz,jatom_p->xyz) > RELAX_THR2) continue;
add = 1;
for (i_atom=0;i_atom<conf.n_atom;i_atom++) {
if (!conf.atom[i_atom].on) continue;
conf.atom[i_atom].xyz =
vector_vplusv(jatom_p->xyz,
vector_rescale(vector_normalize(
vector_vminusv(conf.atom[i_atom].xyz, jatom_p->xyz)), env.water_relax_thr));
}
/*
ins_conf(ires_p, ires_p->n_conf, iconf_p->n_atom);
iconf_p = &prot.res[i_res].conf[i_conf];
if (cpy_conf(&ires_p->conf[ires_p->n_conf-1], &ires_p->conf[i_conf])) {printf(" Error! relax_water(): couldn't copy the conformer \"%s\" in residue %s %d, to new position k_conf = %d\n",ires_p->conf[i_conf].confName,ires_p->resName, ires_p->resSeq, ires_p->n_conf-1); return USERERR;}
for (i_conf2=1; i_conf2<ires_p->n_conf-1; i_conf2++) {
if (!cmp_conf(ires_p->conf[i_conf2], ires_p->conf[ires_p->n_conf-1],0.05)) break;
}
if ( i_conf2 < ires_p->n_conf-1 ) {
del_conf(ires_p, ires_p->n_conf-1);
iconf_p = &prot.res[i_res].conf[i_conf];
continue;
}
*/
//printf(" Debugging! residue %s%4d nconf=%d, residue %s%4d, distance %8.3f\n", prot.res[i_res].resName,prot.res[i_res].resSeq,ires_p->n_conf, prot.res[j_res].resName,prot.res[j_res].resSeq,dvv(iatom_p->xyz,jatom_p->xyz));
}
if (add) {
for (j_atom=0; j_atom<prot.res[j_res].conf[j_conf].n_atom; j_atom++) {
ATOM *jatom_p = &jconf_p->atom[j_atom];
if (!jatom_p->on) continue;
if (jatom_p->name[1] == 'H') continue;
if (ddvv(iatom_p->xyz,jatom_p->xyz) > RELAX_THR2) continue;
add = 0;
}
}
if (add) {
for (k_conf=1; k_conf<ires_p->n_conf; k_conf++) {
if (!cmp_conf(ires_p->conf[k_conf], conf, 0.05)) break;
}
if ( k_conf<ires_p->n_conf ) add = 0;
}
if (add) {
for (k_res=0; k_res<prot.n_res; k_res++) {
k_conf = 0;
for (k_atom=0; k_atom<prot.res[k_res].conf[k_conf].n_atom; k_atom++) {
ATOM *katom_p = &prot.res[k_res].conf[k_conf].atom[k_atom];
if (!katom_p->on) continue;
if (katom_p->name[1] == 'H') continue;
if (ddvv(iatom_p->xyz,katom_p->xyz) > RELAX_THR2) continue;
add = 0;
}
}
}
if (add) {
counter++;
ins_conf(ires_p, ires_p->n_conf, conf.n_atom);
iconf_p = &prot.res[i_res].conf[i_conf];
if (cpy_conf(&ires_p->conf[ires_p->n_conf-1], &conf)) {printf(" Error! relax_water(): couldn't copy a new conformer \"%s\" in residue %s %d, to new position k_conf = %d\n",conf.confName,ires_p->resName, ires_p->resSeq, ires_p->n_conf-1); return USERERR;}
debug_fp = fopen(env.debug_log,"a");
fprintf(debug_fp,"add conformer to HOH %c%04d to relax against %s %c%04d\n",ires_p->chainID,ires_p->resSeq,prot.res[j_res].resName,prot.res[j_res].chainID,prot.res[j_res].resSeq);
fclose(debug_fp);
}
free(conf.atom);
}
}
}
}
return 0;
}
