int main(int argc, char *argv[])
{
int i,j;
int index;
int num_sep_bond_type1 = 0;
int num_sep_bond_type2 = 0;
int overflow_flag = 0; /*if overflow_flag ==1, reallocate memory */
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("[31mUsage: residuegen [0m input_file \n");
exit(1);
}
if (argc != 2) {
printf("[31mUsage: residuegen [0m input_file \n");
exit(1);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("Usage residuegen input_file\n");
exit(1);
}
if (argc != 2) {
printf("Usage residuegen input_file\n");
exit(1);
}
}
if ((fpin = fopen(argv[1], "r")) == NULL) {
fprintf(stdout, "Cannot open input file: %s, exit\n", argv[1]);
exit(1);
}
for(i=0; i<MAXSEPBOND; i++)
sepbond[i].type = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) break;
if (strncmp("ESP_FILE", line, 8) == 0) {
sscanf(&line[9], "%s", espfile);
continue;
}
if (strncmp("INPUT_FILE", line, 10) == 0) {
sscanf(&line[11], "%s", inputfile);
continue;
}
if (strncmp("CONF_NUM", line, 8) == 0) {
sscanf(&line[9], "%d", &confnum);
continue;
}
if (strncmp("SEP_BOND", line, 8) == 0) {
sscanf(&line[9], "%s%s%d", sepbond[sepbondnum].resat, sepbond[sepbondnum].capat, &sepbond[sepbondnum].type);
sepbondnum++;
continue;
}
if (strncmp("PSEUDO_HEAD_ATOM", line, 16) == 0) {
sscanf(&line[17], "%s", pseudo_head_name);
continue;
}
if (strncmp("PSEUDO_TAIL_ATOM", line, 16) == 0) {
sscanf(&line[17], "%s", pseudo_tail_name);
continue;
}
if (strncmp("NET_CHARGE", line, 10) == 0) {
sscanf(&line[11], "%lf", &netcharge);
continue;
}
if (strncmp("PREP_FILE", line, 9) == 0) {
sscanf(&line[10], "%s", prepfile);
continue;
}
if (strncmp("RESIDUE_FILE_NAME", line, 17) == 0) {
sscanf(&line[18], "%s", residue_file_name);
continue;
}
if (strncmp("RESIDUE_SYMBOL", line, 14) == 0) {
sscanf(&line[15], "%s", residue_symbol);
continue;
}
if (strncmp("ATOM_CHARGE", line, 11) == 0) {
if ( chargenum >= MAXCHARGE ) {
fprintf(stdout, "Error: MAXCHARGE is too small in residuegen.c\n"
" Increase MAXCHARGE and reinstall antechamber\n"
);
exit(1);
}
sscanf(&line[12], "%s%lf", charge[chargenum].name, &charge[chargenum].charge);
chargenum++;
continue;
}
}
fclose(fpin);
printf("\nINPUT_FILE:\t\t%s", inputfile);
printf("\nESP_FILE:\t\t%s", espfile);
printf("\nCONF_NUM:\t\t%d", confnum);
printf("\nNET_CHARGE:\t\t%-9.5lf", netcharge);
if(strcmp(pseudo_head_name, "PSEUDO_HEAD") != 0)
printf("\nPSEUDO_HEAD_NAME:\t\t%s", pseudo_head_name);
if(strcmp(pseudo_tail_name, "PSEUDO_TAIL") != 0)
printf("\nPSEUDO_TAIL_NAME:\t\t%s", pseudo_tail_name);
printf("\nThere are %d separating bonds", sepbondnum);
for(i=0;i<sepbondnum;i++)
printf("\nSEPBOND\t\t\t%d\t%s\t%s\t%d", i+1, sepbond[i].resat, sepbond[i].capat, sepbond[i].type);
printf("\nThere are %d predefined charges", chargenum);
for(i=0;i<chargenum;i++)
printf("\nATOM_CHARGE\t\t%d\t%s\t%9.5lf", i+1, charge[i].name, charge[i].charge);
printf("\nPREP_FILE: %s", prepfile);
/* read molecule information */
default_cinfo(&cinfo);
default_minfo(&minfo);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(inputfile, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
free(atom);
free(bond);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
int i;
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
atomicnum(atomnum, atom);
/* allocate memory*/
selectelement = (int *) malloc(sizeof(int) * atomnum);
if (selectelement == NULL) {
fprintf(stdout, "memory allocation error for *selectelement\n");
exit(1);
}
selectelement2 = (int *) malloc(sizeof(int) * atomnum);
if (selectelement2 == NULL) {
fprintf(stdout, "memory allocation error for *selectelement2\n");
exit(1);
}
flag = (int *) malloc(sizeof(int) * atomnum);
if (flag == NULL) {
fprintf(stdout, "memory allocation error for *flag\n");
exit(1);
}
/* find atom ids for predefined charges*/
for(i =0; i< chargenum; i++) {
charge[i].id = -1;
index = 0;
length = strlen(charge[i].name);
for(j =0; j< atomnum; j++)
if(strncmp(atom[j].name, charge[i].name,length) == 0) {
charge[i].id = j;
index = 1;
break;
}
if(index == 0) {
fprintf(stdout, "Error: the charge name, %s does not show up in the molecule\n", charge[i].name);
exit(1);
}
}
/* find atom ids for separted bonds*/
for(i =0; i<sepbondnum; i++) {
sepbond[i].resid = -1;
sepbond[i].capid = -1;
for(j =0; j< atomnum; j++) {
length = strlen(sepbond[i].resat);
if(strncmp(atom[j].name, sepbond[i].resat, length) == 0) {
sepbond[i].resid = j;
continue;
}
length = strlen(sepbond[i].capat);
if(strncmp(atom[j].name, sepbond[i].capat, length) == 0) {
sepbond[i].capid = j;
continue;
}
if(sepbond[i].resid != -1 && sepbond[i].capid != -1) break;
}
if(sepbond[i].resid == -1) {
fprintf(stdout, "Error: the ATOM_NAME1 %s of %d does not show up in the molecule\n", sepbond[i].resat, i+1);
exit(1);
}
if(sepbond[i].capid == -1) {
fprintf(stdout, "Error: the ATOM_NAME2 %s of %d does not show up in the molecule\n", sepbond[i].capat, i+1);
exit(1);
}
if(sepbond[i].type == 1) {
head_id = sepbond[i].resid;
pre_head_id = sepbond[i].capid;
num_sep_bond_type1 ++;
}
if(sepbond[i].type ==-1) {
tail_id = sepbond[i].resid;
post_tail_id = sepbond[i].capid;
num_sep_bond_type2 ++;
}
}
if(num_sep_bond_type1 > 1) {
fprintf(stdout, "Error: only one or none SEP_BOND has a type of '1'\n");
exit(1);
}
if(num_sep_bond_type2 > 1) {
fprintf(stdout, "Error: only one or none SEP_BOND has a type of '-1'\n");
exit(1);
}
/* find atom ids for terminal atoms */
num_terminal_atom = 0;
if(num_sep_bond_type1 == 1) num_terminal_atom ++;
if(num_sep_bond_type2 == 1) num_terminal_atom ++;
if(head_id == -1 && strcmp(pseudo_head_name, "PSEUDO_HEAD") != 0) {
for(i=0;i<atomnum;i++)
if(strcmp(atom[i].name, pseudo_head_name) == 0) {
head_id = i;
num_terminal_atom ++;
break;
}
}
if(tail_id == -1 && strcmp(pseudo_tail_name, "PSEUDO_TAIL") != 0) {
for(i=0;i<atomnum;i++)
if(strcmp(atom[i].name, pseudo_tail_name) == 0) {
tail_id = i;
num_terminal_atom ++;
break;
}
}
/* Now we allow a residue only has one cap (either the N or C-terminal) */
/*
if(num_terminal_atom != 0 && num_terminal_atom != 2) {
fprintf(stdout, "Error, the total number of terminal atoms must be zero or 2 (HEAD_ATOM / PSEUDO_HEAD_ATOM + TAIL_ATOM / PSEUDO_TAIL_ATOM)\n");
exit(0);
}
*/
/* find cap atoms and residue atoms*/
if(sepbondnum > 0) {
for(i=0;i<sepbondnum;i++) {
printf("\n\nCap Atoms for #%d separating bond (%s - %s) with a type of %d", i+1, sepbond[i].capat, sepbond[i].resat, sepbond[i].type);
group_atom1(i);
for (j = 0; j<atomnum; j++)
if(flag[j] == 1)
printf("\nATOM\t %d\t%s", j+1, atom[j].name);
}
printf("\n\nResidue Atoms");
group_atom2();
residueatnum = 0;
for (i = 0; i<atomnum; i++)
if(flag[i] == 1) {
residueatnum ++;
printf("\nATOM\t %d\t%s", i+1, atom[i].name);
}
}
else {
for (i = 0; i<atomnum; i++)
flag[i] = 1;
}
/* find main chain atoms when num_terminal_atom is 2, otherwise no main chain atoms are determined*/
if(num_terminal_atom == 2) {
printf("\n\n(PSEUDO) HEAD ATOM: %s", atom[head_id].name);
printf("\n\n(PSEUDO) TAIL ATOM: %s", atom[tail_id].name);
selectnum = 0;
for (i = 0; i<atomnum; i++) {
selectelement[i] = -1;
selectelement2[i] = -1;
}
findpath(atom, 0, head_id);
printf("\n\nMain Chain Atoms");
for (j = 0; j < selectnum2 ; j++)
printf("\nATOM\t%d\t%s", j+1, atom[selectelement2[j]].name);
}
/* generate charge input file for respgen */
printf("\nGenerate charge input file for respgen ... \n");
if ((fpout = fopen("RESIDUE_GEN_RESPGEN.DAT", "w")) == NULL) {
fprintf(stdout, "Cannot open input file RESIDUE_GEN_RESPGEN.DAT, exit\n");
exit(1);
}
fprintf(fpout, "//predefined charges in a format of (CHARGE partical_charge atom_ID atom_name)");
for(i=0;i<chargenum;i++)
fprintf(fpout, "\nCHARGE %9.6lf\t%d\t%s", charge[i].charge, charge[i].id + 1, charge[i].name);
fprintf(fpout, "\n//charge groups in a format of (GROUP num_atom net_charge)");
fprintf(fpout, "\nGROUP\t%d\t%9.5lf\n", residueatnum, netcharge);
fprintf(fpout, "//atoms in the group in a format of (ATOM atom_ID atom_name)");
for (i = 0; i<atomnum; i++)
if(flag[i] == 1)
fprintf(fpout, "\nATOM\t%d\t%s", i+1, atom[i].name);
fclose(fpout);
/* generate main chain file for prepgen */
printf("\nGenerate main chain atom file for prepgen ... \n");
if ((fpout = fopen("RESIDUE_GEN_MAINCHAIN.DAT", "w")) == NULL) {
fprintf(stdout, "Cannot open input file RESIDUE_GEN_MAINCHAIN.DAT, exit\n");
exit(1);
}
if(head_id != -1 && pre_head_id != -1)
fprintf(fpout, "HEAD_NAME\t%s\n", atom[head_id].name);
if(tail_id != -1 && post_tail_id != -1)
fprintf(fpout, "TAIL_NAME\t%s\n", atom[tail_id].name);
for (i = 0; i < selectnum2 ; i++) {
if(head_id != -1 && pre_head_id != -1) {
length = strlen(atom[head_id].name);
if(strncmp(atom[selectelement2[i]].name, atom[head_id].name, length) == 0)
continue;
}
if(tail_id != -1 && post_tail_id != -1) {
length = strlen(atom[tail_id].name);
if(strncmp(atom[selectelement2[i]].name, atom[tail_id].name, length) == 0)
continue;
}
fprintf(fpout, "MAIN_CHAIN\t%s\n", atom[selectelement2[i]].name);
}
for (i = 0; i<atomnum; i++)
if(flag[i] == 1)
continue;
else
fprintf(fpout, "OMIT_NAME\t%s\n", atom[i].name);
if(pre_head_id != -1)
fprintf(fpout, "PRE_HEAD_TYPE\t%s\n", atom[pre_head_id].ambername);
if(post_tail_id != -1)
fprintf(fpout, "POST_TAIL_TYPE\t%s\n", atom[post_tail_id].ambername);
fprintf(fpout, "CHARGE\t%9.5lf\n", netcharge);
fflush(stdout);
fclose(fpout);
proceed();
printf("\n");
return (0);
}
int main(int argc, char *argv[])
{
int i;
int status = 0;
char command[MAXCHAR];
size_t copied_size;
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -l[0m maximum path length (default is -1, only recommand to use\n"
" when the program takes long time to finish or causes core dump.)\n"
" If applied, a value of 8 to 10 should good)\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp0[0m - evaluation the current charges \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n"
"[32m iresp0[0m - evaluation the current charges for polarizable model\n"
"[32m iresp1[0m- first stage of i_resp fitting \n"
"[32m iresp2[0m- second stage of i_resp fitting\n"
"[32m resp3[0m - one-stage resp fitting\n"
"[32m resp4[0m - calculating ESP from point charges\n"
"[32m resp5[0m - no-equalization\n"
"[31m -e[0m equalizing atomic charge, default is 1\n"
"[32m 0[0m not use \n"
"[32m 1[0m by atomic paths\n"
"[32m 2[0m by atomic paths and structural information, i.e. E/Z confirgurations\n"
"[31m -a[0m additional input data (predefined charges, atom groups etc).)\n"
"[31m -n[0m number of conformations (default is 1)\n"
"[31m -w[0m weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
if (argc != 7 && argc != 9 && argc != 11 && argc != 13 && argc != 15 && argc != 17) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -l[0m maximum path length (default is -1, only recommand to use\n"
" when the program takes long time to finish or causes core dump.)\n"
" If applied, a value of 8 to 10 should good)\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp0[0m - evaluation the current charges \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n"
"[32m iresp0[0m - evaluation the current charges for polarizable model\n"
"[32m iresp1[0m- first stage of i_resp fitting \n"
"[32m iresp2[0m- second stage of i_resp fitting\n"
"[32m resp3[0m - one-stage resp fitting\n"
"[32m resp4[0m - calculating ESP from point charges\n"
"[32m resp5[0m - no-equalization\n"
"[31m -e[0m equalizing atomic charge, default is 1\n"
"[32m 0[0m not use \n"
"[32m 1[0m by atomic paths\n"
"[32m 2[0m by atomic paths and structural information, i.e. E/Z confirgurations\n"
"[31m -a[0m additional input data (predefined charges, atom groups etc).)\n"
"[31m -n[0m number of conformations (default is 1)\n"
"[31m -w[0m weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -l maximum path length (default is -1, only recommand to use\n");
printf(" when the program takes long time to finish or causes core dump.)\n");
printf(" If applied, a value of 8 to 10 should good)\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp0 - evaluation the current charges \n");
printf(" resp1 - first stage resp fitting\n");
printf(" resp2 - second stage resp fitting \n");
printf(" iresp0 - evaluation the current charges for polarizable model \n");
printf(" iresp1- first stage of i_resp fitting\n");
printf(" iresp2- second stage of i_resp fitting \n");
printf(" resp3 - one-stage resp fitting\n");
printf(" resp4 - calculating ESP from point charges \n");
printf(" resp5 - no-equalization \n");
printf(" -e equalizing atomic charge, default is 1\n");
printf(" 0 not use \n");
printf(" 1 by atomic paths\n");
printf(" 2 by atomic paths and structural information, i.e. E/Z confirgurations\n");
printf(" -a additional input data (predefined charges, atom groups etc).)\n");
printf(" -n number of conformations (default is 1)\n");
printf(" -w weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
if (argc != 7 && argc != 9 && argc != 11 && argc != 13 && argc != 15 && argc != 17) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -l maximum path length (default is -1, only recommand to use\n");
printf(" when the program takes long time to finish or causes core dump.)\n");
printf(" If applied, a value of 8 to 10 should good)\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp0 - evaluation the current charges \n");
printf(" resp1 - first stage resp fitting\n");
printf(" resp2 - second stage resp fitting \n");
printf(" iresp0 - evaluation the current charges for polarizable model \n");
printf(" iresp1- first stage of i_resp fitting\n");
printf(" iresp2- second stage of i_resp fitting \n");
printf(" resp3 - one-stage resp fitting\n");
printf(" resp4 - calculating ESP from point charges \n");
printf(" resp5 - no-equalization \n");
printf(" -e equalizing atomic charge, default is 1\n");
printf(" 0 not use \n");
printf(" 1 by atomic paths\n");
printf(" 2 by atomic paths and structural information, i.e. E/Z confirgurations\n");
printf(" -a additional input data (predefined charges, atom groups etc).)\n");
printf(" -w weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
}
method = -1;
max_path_length = -1;
for (i = 1; i < argc; i += 2) {
if (strcmp(argv[i], "-i") == 0)
strcpy(ifilename, argv[i + 1]);
if (strcmp(argv[i], "-o") == 0)
strcpy(ofilename, argv[i + 1]);
if (strcmp(argv[i], "-a") == 0) {
strcpy(afilename, argv[i + 1]);
iaddinfo = 1;
}
if (strcmp(argv[i], "-n") == 0)
nconf = atoi(argv[i+1]);
if (strcmp(argv[i], "-l") == 0)
max_path_length = atoi(argv[i+1]);
if (strcmp(argv[i], "-f") == 0) {
if (strcmp("resp", argv[i + 1]) == 0)
method = -1;
if (strcmp("resp0", argv[i + 1]) == 0)
method = 0;
if (strcmp("resp1", argv[i + 1]) == 0) {
method = 1;
weight = 0.0005;
}
if (strcmp("resp2", argv[i + 1]) == 0) {
method = 2;
weight = 0.001;
}
if (strcmp("resp3", argv[i + 1]) == 0)
method = 3;
if (strcmp("iresp1", argv[i + 1]) == 0) {
method = 4;
weight = 0.0005;
}
if (strcmp("iresp2", argv[i + 1]) == 0) {
method = 5;
weight = 0.001;
}
if (strcmp("resp4", argv[i + 1]) == 0) {
method = 6;
weight = 0.000;
}
if (strcmp("iresp0", argv[i + 1]) == 0)
method = 7;
if (strcmp("resp5", argv[i + 1]) == 0) {
method = 8;
weight = 0.0005;
}
}
if (strcmp(argv[i], "-w") == 0)
weight = atof(argv[i+1]);
if (strcmp(argv[i], "-e") == 0)
iequ = atoi(argv[i+1]);
}
if(nconf < 1) {
printf("\nNumber of conformations must be equal to or larger than 1");
exit(1);
}
if(iequ != 0 && iequ != 1 && iequ !=2)
iequ = 1;
default_cinfo(&cinfo);
default_minfo(&minfo);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
free(atom);
free(bond);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
int i;
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
atomicnum(atomnum, atom);
adjustatomname(atomnum, atom, 1);
if(minfo.dcharge >= -9990) charge = minfo.dcharge;
equ_atom_id = (int *) malloc(sizeof(int) * atomnum);
if (equ_atom_id == NULL) {
fprintf(stdout, "memory allocation error for *equ_atom_id\n");
exit(1);
}
for (i = 0; i < atomnum; i++)
equ_atom_id[i] = -1;
if(method == 3) {
atqwt = (double *) malloc(sizeof(double) * atomnum);
if (atqwt == NULL) {
fprintf(stdout, "memory allocation error for *atqwt\n");
exit(1);
}
refcharge = (double *) malloc(sizeof(double) * atomnum);
if (refcharge == NULL) {
fprintf(stdout, "memory allocation error for *refcharge\n");
exit(1);
}
for(i=0;i<atomnum;i++) {
atqwt[i] = 0;
refcharge[i] = 0;
}
// now read in atomic weights and reference charge parameters
pfilename[0] = '\0';
strcpy(pfilename, amberhome);
strcat(pfilename, "/dat/antechamber/RESPPARM.DAT");
readparm(pfilename);
wac("ANTECHAMBER_RESP.AC", atomnum, atom, bondnum, bond, cinfo, minfo);
copied_size = build_exe_path(command,
"atomtype -i ANTECHAMBER_RESP.AC -o ANTECHAMBER_RESP_AT.AC -d ",
sizeof command, 1 );
dfilename[0] = '\0';
strcpy(dfilename, amberhome);
strcat(dfilename, "/dat/antechamber/ATOMTYPE_RESP.DEF");
strncat(command, dfilename, MAXCHAR - copied_size );
if (cinfo.intstatus == 2)
fprintf(stdout, "Running: %s\n", command);
status = system(command);
if(status != 0) {
fprintf(stdout, "Error: cannot run \"%s\" in respgen.c properly, exit\n", command);
exit(1);
}
assignparm("ANTECHAMBER_RESP_AT.AC");
}
if(iequ == 1)
identify_equatom(atomnum, atom, equ_atom_id, max_path_length, bondnum, bond, 0);
if(iequ == 2)
identify_equatom(atomnum, atom, equ_atom_id, max_path_length, bondnum, bond, 1);
icharge = (int *) malloc(sizeof(int) * atomnum);
if (icharge == NULL) {
fprintf(stdout, "memory allocation error for *icharge in respin()\n");
exit(1);
}
pcharge = (double *) malloc(sizeof(double) * atomnum);
if (pcharge == NULL) {
fprintf(stdout, "memory allocation error for *pcharge in respin()\n");
exit(1);
}
for(i=0;i<atomnum;i++) {
pcharge[i] = 0.0;
icharge[i] = 0;
}
if(iaddinfo == 1) {
if ((fpaddinfo = fopen(afilename, "r")) == NULL) {
fprintf(stdout, "Cannot open the additional file %s to read in main(), exit\n", afilename);
exit(1);
}
if ((fpcharge = fopen("QIN", "w")) == NULL) {
fprintf(stdout, "Cannot open file QIN, exit\n");
exit(1);
}
readinfo();
}
respin(method);
if(iaddinfo == 1) {
fclose(fpcharge);
fclose(fpaddinfo);
}
printf("\n");
/*
free(atom);
free(selectindex);
free(selectelement);
free(equ_atom_id);
free(pathnum);
free(pathatomnum);
for (i =0 ;i <atomnum; i++) free(pathscore[i]);
*/
return (0);
}
int main(int argc, char *argv[])
{
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n");
exit(0);
}
if (argc != 7) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n");
exit(0);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp1 - first stage resp fitting\n");
printf
(" resp2 - second stage resp fitting \n");
exit(0);
}
if (argc != 7) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp1 - first stage resp fitting\n");
printf
(" resp2 - second stage resp fitting \n");
exit(0);
}
}
method = 0;
for (i = 1; i < argc; i += 2) {
if (strcmp(argv[i], "-i") == 0)
strcpy(ifilename, argv[i + 1]);
if (strcmp(argv[i], "-o") == 0)
strcpy(ofilename, argv[i + 1]);
if (strcmp(argv[i], "-f") == 0) {
if (strcmp("resp", argv[i + 1]) == 0)
method = 0;
if (strcmp("resp1", argv[i + 1]) == 0)
method = 1;
if (strcmp("resp2", argv[i + 1]) == 0)
method = 2;
}
}
default_minfo(&minfo);
default_cinfo(&cinfo);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stderr, "memory allocation error for *atom\n");
exit(0);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stderr, "memory allocation error for *bond\n");
exit(0);
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
free(atom);
free(bond);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stderr, "memory allocation error for *atom\n");
exit(0);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stderr, "memory allocation error for *bond\n");
exit(0);
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
atomicnum(atomnum, atom);
adjustatomname(atomnum, atom, 1);
if(minfo.dcharge >= -9990) charge = minfo.dcharge;
selectindex = (int *) malloc(sizeof(int) * atomnum);
if (selectindex == NULL) {
fprintf(stderr, "memory allocation error for *selectindex\n");
exit(0);
}
equatomno = (int *) malloc(sizeof(int) * atomnum);
if (equatomno == NULL) {
fprintf(stderr, "memory allocation error for *equatomno\n");
exit(0);
}
pathnum = (int *) malloc(sizeof(int) * atomnum);
if (pathnum == NULL) {
fprintf(stderr, "memory allocation error for *pathnum\n");
exit(0);
}
selectelement = (int *) malloc(sizeof(int) * atomnum);
if (selectelement == NULL) {
fprintf(stderr, "memory allocation error for *selectelement\n");
exit(0);
}
pathatomnum = (int *) malloc(sizeof(int) * atomnum);
if (pathatomnum == NULL) {
fprintf(stderr, "memory allocation error for *pathatomnum\n");
exit(0);
}
if(atomnum > MAX_RESP_ATOM) {
fprintf(stderr, "The number of atoms (%d) exceed the MAX_RESP_ATOM (%d) defined in respgen.c, extend MAX_RESP_ATOM and recompile the program\n, atomnum, MAX_RESP_ATOM");
exit(0);
}
for (i = 0; i < atomnum; i++) {
pathatomnum[i] = MAXPATHATOMNUM;
pathscore[i] = (double *) calloc(pathatomnum[i], sizeof(double));
if (pathscore == NULL) {
fprintf(stderr, "memory allocation error for *pathscore[%d]\n",
i + 1);
exit(0);
}
}
equatom();
respin(method);
printf("\n");
/*
free(atom);
free(selectindex);
free(selectelement);
free(equatomno);
free(pathnum);
free(pathatomnum);
for (i =0 ;i <atomnum; i++) free(pathscore[i]);
*/
return (0);
}
