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);
}
