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;
}
int assign_crg(PROT prot) {
int k_res,k_conf,k_atom;
CONF *conf_p;
ATOM *atom_p;
FILE *debug_fp;
int err=0;
for (k_res=0; k_res<prot.n_res; k_res++) {
for (k_conf=0; k_conf<prot.res[k_res].n_conf; k_conf++) {
conf_p = &prot.res[k_res].conf[k_conf];
for (k_atom=0; k_atom<prot.res[k_res].conf[k_conf].n_atom; k_atom++) {
atom_p = &conf_p->atom[k_atom];
if (!atom_p->on) continue;
if ( param_get( "CHARGE", conf_p->confName, atom_p->name, &atom_p->crg) )
{
debug_fp = fopen(env.debug_log,"a");
if (!debug_fp) debug_fp = stdout;
fprintf(debug_fp, "CHARGE %s %s 0.000\n", conf_p->confName, atom_p->name);
fclose(debug_fp);
err = 1;
atom_p->crg = 0;
param_sav("CHARGE", conf_p->confName, atom_p->name, &atom_p->crg, sizeof(float));
}
//printf(" Debugging! residue %s%4d,conformer %s atom %s crg %f\n", prot.res[k_res].resName,prot.res[k_res].resSeq,conf_p->confName,atom_p->name,atom_p->crg);
}
}
}
if (err) printf(" Warning! assign_crg(): missing parameter(s), default value is used and saved in %s.\n", env.debug_log);
return 0;
}
int get_connect12_conf(int i_res, int i_conf, PROT prot) {
CONNECT connect;
FILE *debug_fp;
int i_atom;
int j_connect, k_connect, n_connect;
int j_res, j_conf, j_atom;
int k_lig, l_connect;
int n_ligs, n_conf;
int connect_found, lig_treated;
RES *res_p;
CONF *conf_p;
ATOM *atom_p,*jatom_p, *ligs[MAX_LIGS];
int ligs_res[MAX_LIGS];
int err = 0;
res_p = &prot.res[i_res];
conf_p = &prot.res[i_res].conf[i_conf];
/* Looping over all atoms */
for (i_atom=0; i_atom<prot.res[i_res].conf[i_conf].n_atom; i_atom++) {
atom_p = &prot.res[i_res].conf[i_conf].atom[i_atom];
if (!atom_p->on) continue;
for (j_connect=0; j_connect<MAX_CONNECTED; j_connect++) {
atom_p->connect12[j_connect] = NULL;
}
/* Error checking for connectivity parameter */
memset(atom_p->connect12, 0, MAX_CONNECTED*sizeof(void *));
if( param_get("CONNECT", conf_p->confName, atom_p->name, &connect) ) {
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp, " Error! get_connect12(): Can't find CONNECT parameter of conformer \"%s\" atom \"%s\"\n", conf_p->confName, atom_p->name);
fclose(debug_fp);
err++;
continue;
}
if( connect.n > MAX_CONNECTED ) {
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp, " Error! get_connect12(): Error in CONNECT parameter for conformer \"%s\" atom \"%s\", number of connected atoms is bigger than array size\nCheck parameter file or fix mcce.h with a bigger MAX_CONNECTED \n", conf_p->confName, atom_p->name);
fclose(debug_fp);
return USERERR;
}
lig_treated = 0; /* for each atom, ligand connectivy is checked at most once, no matter how many connectivities this atom has */
/* Looping over each connectivity member */
for (j_connect=0; j_connect<connect.n; j_connect++) {
connect_found = 0;
/* Ligand type connectivity or not */
if (!connect.atom[j_connect].ligand) { /* NOT ligand type */
if (!connect.atom[j_connect].res_offset) { /* If within the same residue (off_set is 0) */
j_res = i_res;
if ( !param_get("IATOM", conf_p->confName, connect.atom[j_connect].name, &j_atom) ) {
/* First search atom in the same conformer */
j_conf = i_conf;
atom_p->connect12[j_connect] = &prot.res[j_res].conf[j_conf].atom[j_atom];
atom_p->connect12_res[j_connect] = j_res;
connect_found = 1;
}
else {
/* If not in same conformer, there are two situations:
1. atom is in side chain conformer, connecting to backbone;
2. atom is in backbone conformer, connecting to side chain; */
for (j_conf = 0; j_conf < prot.res[j_res].n_conf; j_conf++) {
if (j_conf == i_conf) continue;
if ( !param_get("IATOM", prot.res[j_res].conf[j_conf].confName, connect.atom[j_connect].name, &j_atom) ) {
atom_p->connect12[j_connect] = &prot.res[j_res].conf[j_conf].atom[j_atom];
atom_p->connect12_res[j_connect] = j_res;
connect_found = 1;
break;
}
}
if (!connect_found) {
char err_msg1[MAXCHAR_LINE];
char err_msg2[MAXCHAR_LINE];
sprintf(err_msg1," Error! get_connect12(): connectivity of atom \"%s %s %c%04d\" is not complete",
atom_p->name, conf_p->confName, res_p->chainID, res_p->resSeq);
sprintf(err_msg2," get_connect12(): atom %s in the same residue is not found", connect.atom[j_connect].name);
if (param_exist(err_msg1, "", "")) {
if (param_exist(err_msg2, "", "")) {
continue;
}
}
param_sav(err_msg1, "", "", "", 0);
param_sav(err_msg2, "", "", "", 0);
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp,"%s\n",err_msg1);
fprintf(debug_fp,"%s\n",err_msg2);
fclose(debug_fp);
err++;
}
}
}
else { /* Not in the same reside. */
j_res = i_res + connect.atom[j_connect].res_offset;
if (j_res < 0 || j_res >= prot.n_res) { /* j_res is out of residue list */
char err_msg1[MAXCHAR_LINE];
char err_msg2[MAXCHAR_LINE];
sprintf(err_msg1, " Error! get_connect12(): connectivity of atom \"%s %s %c%04d\" is not complete:\n",
atom_p->name, res_p->resName, res_p->chainID, res_p->resSeq);
sprintf(err_msg2, " get_connect12(): atom %s of residue i%+d is not found \n", connect.atom[j_connect].name,connect.atom[j_connect].res_offset);
if (param_exist(err_msg1, "", "")) {
if (param_exist(err_msg2, "", "")) {
continue;
}
}
param_sav(err_msg1, "", "", "", 0);
param_sav(err_msg2, "", "", "", 0);
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp,"%s\n",err_msg1);
fprintf(debug_fp,"%s\n",err_msg2);
fclose(debug_fp);
err++;
continue;
}
for (j_conf = 0; j_conf < prot.res[j_res].n_conf; j_conf++) {
if ( !param_get("IATOM", prot.res[j_res].conf[j_conf].confName, connect.atom[j_connect].name, &j_atom) ) {
if (!prot.res[j_res].conf[j_conf].atom[j_atom].on) {
atom_p->connect12[j_connect] = &prot.res[j_res].conf[j_conf].atom[j_atom];
atom_p->connect12_res[j_connect] = j_res;
connect_found = 1;
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp, " WARNING! get_connect12(): atom %s of residue i%+d is in connectivity list of atom \"%s %s %c%04d\", but it's not on\n",
connect.atom[j_connect].name,connect.atom[j_connect].res_offset,atom_p->name, res_p->resName, res_p->chainID, res_p->resSeq);
fclose(debug_fp);
break;
}
if (BOND_THR > dvv(atom_p->xyz, prot.res[j_res].conf[j_conf].atom[j_atom].xyz)) {
atom_p->connect12[j_connect] = &prot.res[j_res].conf[j_conf].atom[j_atom];
atom_p->connect12_res[j_connect] = j_res;
connect_found = 1;
break;
}
}
}
if (!connect_found) {
char err_msg1[MAXCHAR_LINE];
char err_msg2[MAXCHAR_LINE];
sprintf(err_msg1, " Error! get_connect12(): connectivity of atom \"%s %s %c%04d\" is not complete:\n",
atom_p->name, res_p->resName, res_p->chainID, res_p->resSeq);
sprintf(err_msg2, " get_connect12(): atom %s of residue i%+d is not found \n", connect.atom[j_connect].name,connect.atom[j_connect].res_offset);
if (param_exist(err_msg1, "", "")) {
if (param_exist(err_msg2, "", "")) {
continue;
}
}
param_sav(err_msg1, "", "", "", 0);
param_sav(err_msg2, "", "", "", 0);
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp,"%s\n",err_msg1);
fprintf(debug_fp,"%s\n",err_msg2);
fclose(debug_fp);
err++;
}
}
}
else { /* Ligand type connectivity */
if (lig_treated) continue;
/* Loop over all atoms and find all atom within bond threshold */
n_ligs = 0;
for (j_res=0; j_res < prot.n_res; j_res++) {
if (j_res == i_res) continue;
if ( prot.res[j_res].n_conf>2 ) n_conf=2;
else n_conf = prot.res[j_res].n_conf;
for (j_conf=0; j_conf < n_conf; j_conf++) { /* searching is localized in backbone and first side chain */
for (j_atom=0; j_atom<prot.res[j_res].conf[j_conf].n_atom; j_atom++) {
jatom_p = &prot.res[j_res].conf[j_conf].atom[j_atom];
if (!jatom_p->on) continue;
if (BOND_THR > dvv(atom_p->xyz, jatom_p->xyz)) {
n_ligs++;
ligs[n_ligs-1] = jatom_p;
ligs_res[n_ligs-1] = j_res;
}
}
}
}
/* Go over connectivity list and put connected atoms in for those atom name is defined */
for (k_connect=j_connect; k_connect<connect.n; k_connect++) {
if (!connect.atom[k_connect].ligand) continue;
if (atom_p->connect12[k_connect]) continue;
if (strchr(connect.atom[k_connect].name, '?')) continue; /* If atom name in parameter is a '?', then go to next one */
for (k_lig=0; k_lig<n_ligs; k_lig++) {
if (strcmp(ligs[k_lig]->name, connect.atom[k_connect].name)) continue;
/* Check if ligand atom is already in the connectivity list, this is for the case one atom connect to over one atom with same name */
for (l_connect=j_connect; l_connect<connect.n; l_connect++) {
if (ligs[k_lig] == atom_p->connect12[l_connect]) break;
}
if (l_connect < connect.n) continue;
/* Adding ligs[k_lig] into list */
atom_p->connect12[k_connect] = ligs[k_lig];
atom_p->connect12_res[k_connect] = ligs_res[k_lig];
break;
}
}
/* Then go over connectivity list again and put atoms in for those atom name is not defined */
for (k_connect=j_connect; k_connect<connect.n; k_connect++) {
int k_lig_add;
float lig_dist;
if (!connect.atom[k_connect].ligand) continue;
if (atom_p->connect12[k_connect]) continue;
if (!strchr(connect.atom[k_connect].name, '?')) continue; /* If atom name in parameter is not a '?', then go to next one */
k_lig_add = -1;
lig_dist = BOND_THR;
for (k_lig=0; k_lig<n_ligs; k_lig++) {
if (ligs[k_lig]->name[1] == 'H') continue; /* If it's a proton, then not considered */
/* Check if ligand atom is already in the connectivity list, this is for the case one atom connect to over one atom with same name */
for (l_connect=j_connect; l_connect<connect.n; l_connect++) {
if (ligs[k_lig] == atom_p->connect12[l_connect]) break;
}
if (l_connect < connect.n) continue;
if (dvv(atom_p->xyz,ligs[k_lig]->xyz) < lig_dist) {
lig_dist = dvv(atom_p->xyz,ligs[k_lig]->xyz);
k_lig_add = k_lig;
}
}
/* Adding ligs[k_lig] into list */
if (k_lig_add >= 0) {
atom_p->connect12[k_connect] = ligs[k_lig_add];
atom_p->connect12_res[k_connect] = ligs_res[k_lig_add];
}
}
/* Go over connectivity list to check if there is empty slot */
for (k_connect=j_connect; k_connect<connect.n; k_connect++) {
if (!connect.atom[k_connect].ligand) continue;
if (atom_p->connect12[k_connect]) continue;
char err_msg1[MAXCHAR_LINE];
sprintf(err_msg1, " Warning! get_connect12(): An empty ligand connectivity slot found for atom %s in residue %s %d to atom %s\n", atom_p->name, res_p->resName, res_p->resSeq, connect.atom[k_connect].name);
if (param_exist(err_msg1, "", "")) {
continue;
}
param_sav(err_msg1, "", "", "", 0);
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp,"%s\n",err_msg1);
fclose(debug_fp);
}
/* Check if all ligand atoms are in the connectivity list */
for (k_lig=0; k_lig<n_ligs; k_lig++) {
if (ligs[k_lig]->name[1] == 'H') continue; /* If it's a proton, then not considered */
/* Check if ligand atom is already in the connectivity list, this is for the case one atom connect to over one atom with same name */
for (l_connect=j_connect; l_connect<connect.n; l_connect++) {
if (ligs[k_lig] == atom_p->connect12[l_connect]) break;
}
if (l_connect < connect.n) continue;
char err_msg1[MAXCHAR_LINE];
sprintf(err_msg1, " Warning! get_connect12(): An atom (%s in residue %s %d) within bond threshold to atom %s in residue %s %d is not put in the connectivity list \n",ligs[k_lig]->name, ligs[k_lig]->resName, ligs[k_lig]->resSeq, atom_p->name, res_p->resName, res_p->resSeq);
if (param_exist(err_msg1, "", "")) {
continue;
}
param_sav(err_msg1, "", "", "", 0);
debug_fp = fopen(env.debug_log, "a");
fprintf(debug_fp,"%s\n",err_msg1);
fclose(debug_fp);
}
lig_treated = 1;
/* END of treating ligand type */
}
/* If connecting to a dummy atom, it could be the case connecting to NTR or CTR */
if (!atom_p->connect12[j_connect]) continue;
if ( atom_p->connect12[j_connect]->on) continue;
if (strcmp(connect.atom[j_connect].name, " CA ") && strcmp(connect.atom[j_connect].name, " C ")) continue;
//printf(" Debugging! residue %s%4d,conformer %s, on=%d\n", res_p->resName,res_p->resSeq,conf_p->confName,atom_p->connect12[j_connect]->on);
connect_found = 0;
for (j_res=0; j_res<prot.n_res; j_res++) {
if (strcmp(prot.res[j_res].resName, "NTR"))
if (strcmp(prot.res[j_res].resName, "NTG"))
if (strcmp(prot.res[j_res].resName, "CTR")) continue;
for (j_conf=0; j_conf<prot.res[j_res].n_conf; j_conf++) {
for (j_atom=0; j_atom<prot.res[j_res].conf[j_conf].n_atom; j_atom++) {
jatom_p = &prot.res[j_res].conf[j_conf].atom[j_atom];
if (!jatom_p->on) continue;
if (strcmp(connect.atom[j_connect].name, jatom_p->name)) continue;
if (BOND_THR > dvv(atom_p->xyz, jatom_p->xyz)) {
atom_p->connect12[j_connect] = jatom_p;
atom_p->connect12_res[j_connect] = j_res;
connect_found = 1;
break;
}
}
if (connect_found) break;
}
if (connect_found) break;
}
}
/* Move NULL pointer to the end of the array */
n_connect = connect.n;
for (j_connect=0; j_connect < n_connect-1; j_connect++) {
if (!atom_p->connect12[j_connect]) {
for (k_connect=j_connect; k_connect<n_connect-1; k_connect++) {
atom_p->connect12[k_connect] = atom_p->connect12[k_connect+1];
atom_p->connect12_res[k_connect] = atom_p->connect12_res[k_connect+1];
}
atom_p->connect12[n_connect-1] = NULL;
atom_p->connect12_res[n_connect-1] = 0;
j_connect--;
n_connect--;
}
}
}
return 0;
}
int head3lst_param(EMATRIX ematrix)
{ int kc;
float rxn0, extra, em0, pka0;
char sbuff[6];
int H, e;
for (kc=0; kc<ematrix.n; kc++) {
strncpy(sbuff, ematrix.conf[kc].uniqID, 5); sbuff[5] = '\0';
if (param_get("EM", sbuff, "", &em0)) {
printf(" WARNING: No EM entry for %s, set to 0.\n", sbuff);
fflush(stdout);
em0 = 0.0;
param_sav("EM", sbuff, "", &em0, sizeof(float));
}
ematrix.conf[kc].Em = em0;
if (param_get("PKA", sbuff, "", &pka0)) {
printf(" WARNING: No PKA entry for %s, set to 0.\n",sbuff);
fflush(stdout);
pka0 = 0.0;
param_sav("PKA",sbuff, "", &pka0, sizeof(float));
}
ematrix.conf[kc].pKa = pka0;
if (param_get("PROTON",sbuff, "", &H)) {
printf(" WARNING: no PROTON for %s, 0 assumed\n",sbuff);
H = 0;
param_sav("PROTON",sbuff, "", &H, sizeof(int));
}
ematrix.conf[kc].H = H;
if (param_get("ELECTRON",sbuff, "", &e)) {
printf(" WARNING: no ELECTRON for %s, 0 assumed\n",sbuff);
e = 0;
param_sav("ELECTRON",sbuff, "", &e, sizeof(int));
}
ematrix.conf[kc].e = e;
if (!strcmp(env.pbe_solver, "delphi") && !strcmp(env.rxn_method, "surface")) {
if (param_get("RXN",sbuff, "", &rxn0)) {
printf(" WARNING: No RXN entry for %s, set to 0.\n",sbuff);
fflush(stdout);
rxn0 = 0.0;
param_sav("RXN",sbuff, "", &rxn0, sizeof(float));
}
ematrix.conf[kc].E_rxn0 = rxn0; /*this is the case with delphi*/
}
else ematrix.conf[kc].E_rxn0 = 0.0; /*this is the case with apbs*/
if (param_get("EXTRA",sbuff, "", &extra)) {
/* printf(" WARNING: No EXTRA entry for %s, set to 0.\n",sbuff); */
fflush(stdout);
extra = 0.0;
param_sav("EXTRA",sbuff, "", &extra, sizeof(float));
}
ematrix.conf[kc].E_extra = extra;
/*if we calculate rxn with self energies, then we don't need rxn0*/
ematrix.conf[kc].E_dsolv = ematrix.conf[kc].E_rxn - ematrix.conf[kc].E_rxn0;
/* label unrealistic values */
if (ematrix.conf[kc].E_vdw0 > 999.0) ematrix.conf[kc].E_vdw0 = 999.0;
if (ematrix.conf[kc].E_vdw1 > 999.0) ematrix.conf[kc].E_vdw1 = 999.0;
}
return 0;
}
int make_matrices(PROT prot, char *dir)
{
int i, kr, kc, counter, verbose;
int n_conf, n_dummies;
char fname[MAXCHAR_LINE];
FILE *fp;
char sbuff[MAXCHAR_LINE];
char sbuff2[MAXCHAR_LINE];
char confName[6];
int natom;
int serial;
char uniqID[15];
char dummy;
EMATRIX ematrix;
if (verbose != 1) {
verbose = 0;
}
n_conf = 0;
for (kr=0; kr<prot.n_res; kr++) {
n_conf+=(prot.res[kr].n_conf-1);
}
/* Try to load an existing energy table */
ematrix.n = 0; /* the load_energies program relies on n to determine the validation of pointers */
if (load_energies(&ematrix, dir, verbose) == n_conf) { /* partial run exits */
printf(" File %s/%s exists, energy calculation will update this file\n", dir, ENERGY_TABLE);
}
else { /* initialize a new one with current run */
free_ematrix(&ematrix); /* if ematrix.n is 0, nothing would happen */
ematrix.n = n_conf;
if (!(ematrix.conf = (CONF_HEAD *) calloc(ematrix.n, sizeof(CONF_HEAD)))) {
printf(" Allocate memory error\n");
return USERERR;
}
if (!(ematrix.pw = (PAIRWISE **) calloc(ematrix.n, sizeof(PAIRWISE *)))) {
printf(" Allocate memory error\n");
return USERERR;
}
for (i=0; i<ematrix.n; i++) {
if (!(ematrix.pw[i] = (PAIRWISE *) calloc(ematrix.n, sizeof(PAIRWISE)))) {
printf(" Allocate memory error\n");
return USERERR;
}
}
for (i=0; i<ematrix.n; i++) {
ematrix.conf[i].on = 'f';
}
}
counter = 0; n_dummies = 0;
for (kr=0; kr<prot.n_res; kr++) {
for (kc=1; kc<prot.res[kr].n_conf; kc++) {
strcpy(ematrix.conf[counter].uniqID, prot.res[kr].conf[kc].uniqID);
strcpy(ematrix.conf[counter].history, prot.res[kr].conf[kc].history);
strncpy(confName, ematrix.conf[counter].uniqID, 5); confName[5] = '\0';
if (param_get("NATOM", confName, "", &natom)) {
printf(" WARNING: no NATOM for %s, 0 assumed\n", confName);
natom = 0;
param_sav("NATOM", confName, "", &natom, sizeof(int));
}
if (natom == 0) { /* dummy */
n_dummies ++;
ematrix.conf[counter].on = 't';
counter ++;
continue;
}
ematrix.conf[counter].netcrg = prot.res[kr].conf[kc].netcrg;
if (env.recalc_tors)
ematrix.conf[counter].E_tors = torsion_conf(&prot.res[kr].conf[kc]);
/* other parameters will be updated by head3lst_update once uniqID is defined*/
counter++;
}
}
/* updating self energy terms for conformers in current delphi */
refresh_prot(prot);
counter = 0; n_dummies = 0;
for (kr=0; kr<prot.n_res;kr++) {
for (kc=1; kc<prot.res[kr].n_conf; kc++) {
strncpy(confName, ematrix.conf[counter].uniqID, 5); confName[5] = '\0';
if (param_get("NATOM", confName, "", &natom)) {
printf(" WARNING: no NATOM for %s, 0 assumed\n", confName);
natom = 0;
param_sav("NATOM", confName, "", &natom, sizeof(int));
}
if (natom == 0) { /* dummy */
n_dummies ++;
ematrix.conf[counter].on = 't';
counter ++;
continue;
}
if (((counter-n_dummies+1) >= env.pbe_start && (counter-n_dummies+1) <= env.pbe_end)) {
ematrix.conf[counter].E_vdw0 = prot.res[kr].conf[kc].E_vdw0;
ematrix.conf[counter].E_vdw1 = prot.res[kr].conf[kc].E_vdw1;
ematrix.conf[counter].E_tors = prot.res[kr].conf[kc].E_tors;
ematrix.conf[counter].E_epol = prot.res[kr].conf[kc].E_epol;
ematrix.conf[counter].E_rxn = prot.res[kr].conf[kc].E_rxn;
if (!strcmp(env.pbe_solver, "apbs") || !strcmp(env.rxn_method, "self")) ematrix.conf[counter].E_rxn0 = 0.0;
ematrix.conf[counter].E_dsolv = ematrix.conf[counter].E_rxn - ematrix.conf[counter].E_rxn0;
}
counter++;
}
}
head3lst_param(ematrix); /* fine tune and complete the rest param */
/* updating the pw of matrix */
n_dummies = 0;
for (kc=0; kc<ematrix.n; kc++) {
/* dummy conformer doesn't have opp file */
strncpy(confName, ematrix.conf[kc].uniqID, 5); confName[5] = '\0';
if (param_get("NATOM", confName, "", &natom)) {
printf(" WARNING: no NATOM for %s, 0 assumed\n", confName);
natom = 0;
param_sav("NATOM", confName, "", &natom, sizeof(int));
}
if (natom == 0) { /* dummy */
n_dummies ++;
ematrix.conf[kc].on = 't';
for (i=0; i<ematrix.n; i++) {
ematrix.pw[kc][i].ele = ematrix.pw[kc][i].vdw = ematrix.pw[kc][i].crt = ematrix.pw[kc][i].ori = 0.0;
ematrix.pw[kc][i].mark[0] = '\0';
}
continue;
}
if (((kc-n_dummies+1) >= env.pbe_start && (kc-n_dummies+1) <= env.pbe_end)) { /* in current calculation */
ematrix.conf[kc].on = 't';
sprintf(fname, "%s.opp", ematrix.conf[kc].uniqID);
if (!(fp = fopen(fname, "r"))) {
printf(" FATAL: read file error %s\n", fname);
return USERERR;
}
/* load pairwise energy */
for (i=0; i<ematrix.n; i++) {
/* Skip dummies */
while (1) { /* a mismatch, dummy */
strncpy(confName, ematrix.conf[i].uniqID, 5); confName[5] = '\0';
if (param_get("NATOM", confName, "", &natom)) {
printf(" FATAL: no NATOM for %s\n", confName);
return USERERR;
}
if (natom == 0) {
ematrix.pw[kc][i].ele = ematrix.pw[kc][i].vdw = ematrix.pw[kc][i].crt = ematrix.pw[kc][i].ori = 0.0;
ematrix.pw[kc][i].mark[0] = '\0';
dummy = 1;
i++; /* skip to the next valid */
}
else {
dummy = 0;
break; /* break as non dummy */
}
if (i>=ematrix.n) break; /* break as done, dummy would continue */
}
if (dummy) break;
/* everything reaches here is non dummy */
if (!fgets(sbuff, sizeof(sbuff), fp)) {
printf(" FATAL: Unexpected end of file %s.\n", fname);
return USERERR;
}
strncpy(sbuff2, sbuff, 5); sbuff2[5] = '\0';
serial = atoi(sbuff2);
strncpy(uniqID, sbuff+6, 14); uniqID[14] = '\0';
strncpy(sbuff2, sbuff+20, 10); sbuff2[10] = '\0';
ematrix.pw[kc][i].crt = atof(sbuff2);
strncpy(sbuff2, sbuff+30, 10); sbuff2[10] = '\0';
ematrix.pw[kc][i].vdw = atof(sbuff2);
strncpy(sbuff2, sbuff+40, 10); sbuff2[10] = '\0';
ematrix.pw[kc][i].ori = atof(sbuff2);
strncpy(ematrix.pw[kc][i].mark, sbuff+50, 3);
*(strchr(ematrix.pw[kc][i].mark,'\n')) = '\0';
//sscanf(sbuff, "%d %s %f %f %f %s", &serial, uniqID, &pairwise_raw[kc][i].ele, &pairwise_raw[kc][i].vdw, &pairwise_raw[kc][i].ori, pairwise_raw[kc][i].mark);
if (strcmp(uniqID, ematrix.conf[i].uniqID)) {
printf(" FATAL: Mismatch %s in protein structure and %s in %s.\n", ematrix.conf[i].uniqID,
uniqID,
fname);
return USERERR;
}
}
fclose(fp);
}
}
if (write_energies(&ematrix, dir, verbose)) {
printf(" Error in writing energy lookuptable %s/%s\n", dir, ENERGY_TABLE);
return USERERR;
}
free_ematrix(&ematrix);
return 0;
}
