/* CHARMM */
void wcharmm(char *filename, char *ifilename, int atomnum, ATOM * atom,
int bondnum, BOND * bond, CONTROLINFO cinfo, MOLINFO minfo)
{
char tmpchar[MAXCHAR];
size_t copied_size;
wac("ANTECHAMBER_PREP.AC0", atomnum, atom, bondnum, bond, cinfo,
minfo);
system("cp -rf ANTECHAMBER_PREP.AC0 ANTECHAMBER_PREP.AC");
/*part1: if intype is not prepi, prepc and ac, judge atom type*/
if ((strcmp(cinfo.intype, "prepi") != 0 &&
strcmp(cinfo.intype, "prepc") != 0 &&
strcmp(cinfo.intype, "5") != 0 &&
strcmp(cinfo.intype, "6") != 0 &&
strcmp(cinfo.intype, "ac") != 0 &&
strcmp(cinfo.intype, "1") != 0) || cinfo.prediction_index == 1
|| cinfo.prediction_index == 3) {
copied_size = build_exe_path(tmpchar, "atomtype",
sizeof tmpchar, 1);
strncat(tmpchar, " -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC"
" -p ", sizeof tmpchar - copied_size);
strncat(tmpchar, minfo.atom_type_def,
sizeof tmpchar - strlen(tmpchar) );
if(cinfo.intstatus == 2)
fprintf(stdout, "\nRunning: %s\n", tmpchar);
system(tmpchar);
}
copied_size = build_exe_path(tmpchar, "charmmgen", sizeof tmpchar, 1);
strncat(tmpchar, " -i ANTECHAMBER_PREP.AC -f ac -o ",
sizeof tmpchar - copied_size);
strncat(tmpchar, filename, sizeof tmpchar - strlen(tmpchar) );
strcat(tmpchar, " -r ");
strcat(tmpchar, minfo.resname);
if(cinfo.intstatus == 2)
fprintf(stdout, "\nRunning: %s\n", tmpchar);
system(tmpchar);
/* system("rm -f ANTECHAMBER_PREP.AC");*/
}
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[]) {
int i,j,k;
int overflow_flag = 0;
int count;
int atid1, atid2;
int resid1, resid2;
int oldresid;
int suc;
double sum;
double x,y,z;
char line[MAXCHAR];
char defstr[MAXCHAR];
char atomname[MAXCHAR];
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: match -i [0m input file name \n"
"[31m -r [0m reference file name \n"
"[31m -f [0m format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
"[31m -o [0m output file name\n"
"[31m -l [0m run log file name, default is \"match.log\"\n"
"[31m -s [0m selection mode\n"
"[34m 0:[0m use all atoms (the default)\n"
"[34m 1:[0m specify atom names\n"
"[34m 2:[0m use atom defination file\n"
"[34m 3:[0m use residue defination file - original residue IDs\n"
"[34m 4:[0m use residue defination file - renumbered residue IDs\n"
"[31m -ds [0mdefinition string if selection modes of '1' or '3' or '4'\n"
"[31m [0me.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
"[31m -df [0mdefinition file if selection mode of '2' or '3' or '4'\n"
"[31m [0mrecords take a form of 'ATOM atom_id_input atom_id_reference'\n"
"[31m [0mor 'RES res_id_input res_id_reference'\n"
"[31m -n [0m number of atoms participating ls-fitting,\n"
"[31m [0m default is -1, which implies to use all the selected atoms\n"
"[31m -m [0m matrix file, default is \"match.matrix\"\n"
"[31m -t [0m job type:\n"
"[35m 0:[0m calculate rms only, need -i and -r\n"
"[35m 1:[0m lsfit, need -i, -r and -o the default\n"
"[35m 2:[0m translation/rotation, need -i, -o and -m\n");
exit(0);
}
if (argc != 23 && argc != 21 && argc != 19 && argc != 17 && argc != 15 && argc != 13 && argc != 11 && argc !=9 && argc !=7 && argc !=5) {
printf
("[31mUsage: match -i [0m input file name \n"
"[31m -r [0m reference file name \n"
"[31m -f [0m format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
"[31m -o [0m output file name\n"
"[31m -l [0m run log file name, default is \"match.log\"\n"
"[31m -s [0m selection mode\n"
"[34m 0:[0m use all atoms (the default)\n"
"[34m 1:[0m specify atom names\n"
"[34m 2:[0m use atom defination file\n"
"[34m 3:[0m use residue defination file - original residue IDs\n"
"[34m 4:[0m use residue defination file - renumbered residue IDs\n"
"[31m -ds [0mdefinition string if selection modes of '1' or '3' or '4'\n"
"[31m [0me.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
"[31m -df [0mdefinition file if selection mode of '2' or '3' or '4'\n"
"[31m [0mrecords take a form of 'ATOM atom_id_input atom_id_reference'\n"
"[31m [0mor 'RES res_id_input res_id_reference'\n"
"[31m -n [0m number of atoms participating ls-fitting,\n"
"[31m [0m default is -1, which implies to use all the selected atoms\n"
"[31m -m [0m matrix file, default is \"match.matrix\"\n"
"[31m -t [0m job type:\n"
"[35m 0:[0m calculate rms only, need -i and -r\n"
"[35m 1:[0m lsfit, need -i, -r and -o the default\n"
"[35m 2:[0m translation/rotation, need -i, -o and -m\n");
exit(0);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf
("Usage: match -i input file name \n"
" -r reference file name \n"
" -f format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
" -o output file name\n"
" -l run log file name, default is \"match.log\"\n"
" -s selection mode\n"
" 0: use all atoms (the default)\n"
" 1: specify atom names\n"
" 2: use atom defination file\n"
" 3: use residue defination file - original residue IDs\n"
" 4: use residue defination file - renumbered residue IDs\n"
" -ds definition string if selection modes of '1' or '3' or '4'\n"
" e.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
" -df definition file if selection mode of '2' or '3' or '4'\n"
" records take a form of 'ATOM atom_id_input atom_id_reference'\n"
" or 'RES res_id_input res_id_reference'\n"
" -n number of atoms participating ls-fitting,\n"
" default is -1, which implies to use all the selected atoms\n"
" -m matrix file, default is \"match.matrix\"\n"
" -t job type:\n"
" 0: calculate rms only, need -i and -r\n"
" 1: lsfit, need -i, -r and -o the default\n"
" 2: translation/rotation, need -i, -o and -m\n");
exit(0);
}
if (argc != 23 && argc != 21 && argc != 19 && argc != 17 && argc != 15 && argc != 13 && argc != 11 && argc !=9 && argc !=7 && argc !=5) {
printf
("Usage: match -i input file name \n"
" -r reference file name \n"
" -f format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
" -o output file name\n"
" -l run log file name, default is \"match.log\"\n"
" -s selection mode\n"
" 0: use all atoms (the default)\n"
" 1: specify atom names\n"
" 2: use atom defination file\n"
" 3: use residue defination file - original residue IDs\n"
" 4: use residue defination file - renumbered residue IDs\n"
" -ds definition string if selection modes of '1' or '3' or '4'\n"
" e.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
" -df definition file if selection mode of '2' or '3' or '4'\n"
" records take a form of 'ATOM atom_id_input atom_id_reference'\n"
" or 'RES res_id_input res_id_reference'\n"
" -n number of atoms participating ls-fitting,\n"
" default is -1, which implies to use all the selected atoms\n"
" -m matrix file, default is \"match.matrix\"\n"
" -t job type:\n"
" 0: calculate rms only, need -i and -r\n"
" 1: lsfit, need -i, -r and -o the default\n"
" 2: translation/rotation, need -i, -o and -m\n");
exit(0);
}
}
for (i = 1; i < argc; i += 2) {
if (strcmp(argv[i], "-i") == 0) {
strcpy(ifilename, argv[i + 1]);
iinput = 1;
}
if (strcmp(argv[i], "-f") == 0)
format=atoi(argv[i+1]);
if (strcmp(argv[i], "-o") == 0) {
strcpy(ofilename, argv[i + 1]);
ioutput = 1;
}
if (strcmp(argv[i], "-r") == 0) {
strcpy(rfilename, argv[i + 1]);
iref = 1;
}
if (strcmp(argv[i], "-s") == 0)
stype = atoi(argv[i+1]);
if (strcmp(argv[i], "-ds") == 0)
strcpy(def_atomname_str, argv[i + 1]);
if (strcmp(argv[i], "-df") == 0)
strcpy(def_filename, argv[i + 1]);
if (strcmp(argv[i], "-m") == 0) {
strcpy(mfilename, argv[i + 1]);
imatrix = 1;
}
if (strcmp(argv[i], "-t") == 0)
jobtype = atoi(argv[i+1]);
if (strcmp(argv[i], "-n") == 0)
nsel = atoi(argv[i+1]);
if (strcmp(argv[i], "-l") == 0)
strcpy(lfilename, argv[i + 1]);
}
if(jobtype !=0 && jobtype != 1 && jobtype != 2) jobtype = 1;
if(format != 1 && format != 2 && format != 3 && format != 4 && format != 5) format = 1;
if(jobtype == 0)
if(iinput == 0 || iref == 0) {
fprintf(stderr, "RMS calculation needs an input and a reference files, exit\n");
exit(0);
}
if(jobtype == 1)
if(iinput == 0 || ioutput == 0 || iref == 0) {
fprintf(stderr, "The least-square fitting calculation needs an input, an output and a reference files, exit\n");
exit(0);
}
if(jobtype == 2)
if(iinput == 0 || ioutput == 0) {
fprintf(stderr, "The translation/rotation job needs an input and an output files, exit\n");
exit(0);
}
if(jobtype == 0 || jobtype == 1) {
if ((fplog = fopen(lfilename, "w")) == NULL) {
fprintf(stderr, "Cannot open log file %s to write, exit\n", lfilename);
exit(1);
}
}
/* read in input files*/
memory(0, MAXATOM, MAXBOND, MAXRING);
if(format == 1) {
overflow_flag = rpdb(ifilename, &atomnum, atom, cinfo, minfo, 0);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rpdb(ifilename, &atomnum, atom, cinfo, minfo, 0);
}
}
if(format == 2) {
overflow_flag = rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
}
if(format == 3) {
overflow_flag = rmol2(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo, 0);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag =
rmol2(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo, 0);
}
}
if(format == 4) {
overflow_flag = rmdl(ifilename, &atomnum, atom, &bondnum, bond, cinfo, minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rmdl(ifilename, &atomnum, atom, &bondnum, bond, cinfo, minfo);
}
}
if(format == 5) {
overflow_flag = rrst(ifilename, &atomnum, atom, cinfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rrst(ifilename, &atomnum, atom, cinfo);
}
}
free(bond);
free(ring);
free(arom);
cinfo.maxatom = MAXATOM;
cinfo.maxbond = MAXBOND;
cinfo.maxring = MAXRING;
ref_memory(0, MAXATOM, MAXBOND, MAXRING);
if(format == 1) {
overflow_flag = rpdb(rfilename, &refatomnum, refatom, cinfo, minfo, 0);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rpdb(rfilename, &refatomnum, refatom, cinfo, minfo, 0);
}
}
if(format == 2) {
overflow_flag = rac(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rac(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo);
}
}
if(format == 3) {
overflow_flag = rmol2(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo, 0);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rmol2(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo, 0);
}
}
if(format == 4) {
overflow_flag = rmdl(rfilename, &refatomnum, refatom, &refbondnum, refbond, cinfo, minfo);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rmdl(rfilename, &refatomnum, refatom, &refbondnum, refbond, cinfo, minfo);
}
}
if(format == 5) {
overflow_flag = rrst(rfilename, &refatomnum, refatom, cinfo);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rrst(rfilename, &refatomnum, refatom, cinfo);
}
}
free(refbond);
free(refring);
free(refarom);
if(debug == 1) {
for(i=0;i<atomnum;i++)
printf("ATOM %5d %5s %5s %5d %8.3lf %8.3lf %8.3lf\n", i+1, atom[i].name, atom[i].aa, atom[i].resno, atom[i].x, atom[i].y, atom[i].z);
for(i=0;i<refatomnum;i++)
printf("ATOM %5d %5s %5s %5d %8.3lf %8.3lf %8.3lf\n", i+1, refatom[i].name, refatom[i].aa, refatom[i].resno, refatom[i].x, refatom[i].y, refatom[i].z);
}
if(jobtype == 0 || jobtype == 1) {
fit_atom = (FITATOM *) malloc(sizeof(FITATOM) * atomnum);
if (fit_atom == NULL) {
fprintf(stderr, "memory allocation error for *fit_atom\n");
exit(1);
}
fit_refatom = (FITATOM *) malloc(sizeof(FITATOM) * refatomnum);
if (fit_refatom == NULL) {
fprintf(stderr, "memory allocation error for *fit_refatom\n");
exit(1);
}
if(stype == 0) {
for(i=0;i<atomnum;i++) {
fit_atom[i].x=atom[i].x;
fit_atom[i].y=atom[i].y;
fit_atom[i].z=atom[i].z;
}
for(i=0;i<refatomnum;i++) {
fit_refatom[i].x=refatom[i].x;
fit_refatom[i].y=refatom[i].y;
fit_refatom[i].z=refatom[i].z;
}
fit_atomnum = atomnum;
fit_refatomnum = refatomnum;
}
if(stype == 1) {
count = 0;
for(i=0;i <= strlen(def_atomname_str);i++) {
if(def_atomname_str[i]==' ') continue;
if(def_atomname_str[i]==',') def_atomname_str[i] = ' ';
defstr[count] = def_atomname_str[i];
count++;
}
sscanf(defstr, "%s", atomname);
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
for(i=1;i<strlen(defstr);i++)
if(defstr[i] == ' ') {
sscanf(&defstr[i], "%s", atomname);
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
}
for(i=0;i<atomnum;i++) {
suc = 0;
for(j=0;j<ndef_atomname;j++) {
if(strcmp(def_atomname[j].str, atom[i].name) == 0) {
suc = 1;
break;
}
if(strcmp(def_atomname[j].str, "HET") == 0)
if(atom[i].name[0] != 'H') {
suc = 1;
break;
}
}
if(suc == 1) {
fit_atom[fit_atomnum].x=atom[i].x;
fit_atom[fit_atomnum].y=atom[i].y;
fit_atom[fit_atomnum].z=atom[i].z;
fit_atomnum++;
}
}
for(i=0;i<refatomnum;i++) {
suc = 0;
for(j=0;j<ndef_atomname;j++) {
if(strcmp(def_atomname[j].str, refatom[i].name) == 0) {
suc = 1;
break;
}
if(strcmp(def_atomname[j].str, "HET") == 0)
if(refatom[i].name[0] != 'H') {
suc = 1;
break;
}
}
if(suc == 1) {
fit_refatom[fit_refatomnum].x=refatom[i].x;
fit_refatom[fit_refatomnum].y=refatom[i].y;
fit_refatom[fit_refatomnum].z=refatom[i].z;
fit_refatomnum++;
}
}
}
if(stype == 2) {
if ((fpdef = fopen(def_filename, "r")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", def_filename);
exit(1);
}
count = 0;
for(;;) {
if (fgets(line, MAXCHAR, fpdef) == NULL) break;
if(strncmp(line, "ATOM", 4) == 0) {
sscanf(&line[4], "%d%d", &atid1, &atid2);
atid1--;
atid2--;
fit_atom[count].x=atom[atid1].x;
fit_atom[count].y=atom[atid1].y;
fit_atom[count].z=atom[atid1].z;
fit_refatom[count].x=refatom[atid2].x;
fit_refatom[count].y=refatom[atid2].y;
fit_refatom[count].z=refatom[atid2].z;
count++;
}
}
fit_atomnum = count;
fit_refatomnum = count;
fclose(fpdef);
}
if(stype == 3 || stype == 4) {
/*first of all, read in atom name definition strings*/
count = 0;
for(i=0;i <= strlen(def_atomname_str);i++) {
if(def_atomname_str[i]==' ') continue;
if(def_atomname_str[i]==',') def_atomname_str[i] = ' ';
defstr[count] = def_atomname_str[i];
count++;
}
sscanf(defstr, "%s", atomname);
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
for(i=1;i<strlen(defstr);i++)
if(defstr[i] == ' ') {
sscanf(&defstr[i], "%s", atomname);
if(strcmp(atomname, "HET") == 0) {
fprintf(stderr, "Warning: HET cannot be defined with -s of 3\n");
continue;
}
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
}
if(debug == 1) {
for(i=0;i<ndef_atomname;i++)
printf("DEF %5d %5s\n", i+1, def_atomname[i].str);
}
if(stype == 4) {
count = 0;
oldresid = -99999;
for(i=0;i<atomnum;i++) {
if(atom[i].resno != oldresid) {
oldresid = atom[i].resno;
count++;
}
atom[i].resno = count;
}
count = 0;
oldresid = -99999;
for(i=0;i<refatomnum;i++) {
if(refatom[i].resno != oldresid) {
oldresid = refatom[i].resno;
count++;
}
refatom[i].resno = count;
}
}
/* now working on residue definition file */
if ((fpdef = fopen(def_filename, "r")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", def_filename);
exit(1);
}
count = 0;
for(;;) {
if (fgets(line, MAXCHAR, fpdef) == NULL) break;
if(strncmp(line, "RES", 3) == 0) {
sscanf(&line[3], "%d%d", &resid1, &resid2);
if(debug == 1)
printf("RES %5d %5d\n", resid1, resid2);
for(i=0; i< ndef_atomname; i++) {
atid1 = -1;
atid2 = -1;
for(j=0;j<atomnum;j++)
if(strcmp(def_atomname[i].str, atom[j].name) == 0 && atom[j].resno == resid1) {
atid1 = j;
break;
}
for(j=0;j<refatomnum;j++)
if(strcmp(def_atomname[i].str, refatom[j].name) == 0 && refatom[j].resno == resid2) {
atid2 = j;
break;
}
if(atid1 >= 0 && atid2 >= 0) {
fit_atom[count].x=atom[atid1].x;
fit_atom[count].y=atom[atid1].y;
fit_atom[count].z=atom[atid1].z;
fit_refatom[count].x=refatom[atid2].x;
fit_refatom[count].y=refatom[atid2].y;
fit_refatom[count].z=refatom[atid2].z;
count++;
}
}
}
}
fit_atomnum = count;
fit_refatomnum = count;
fclose(fpdef);
}
if(fit_atomnum != fit_refatomnum || fit_atomnum <=0) {
fprintf(stderr, "\nThe numumber of fitting atoms in input file (%d) is different from the number of fitting atoms in ref file (%d)", fit_atomnum, fit_refatomnum);
exit(0);
}
if(nsel > 0 && fit_atomnum > nsel) fit_atomnum = nsel;
if(fit_atomnum <= 0) {
fprintf(stderr, "\nThe number of fitting atoms is smaller than or equal to zero, exit!");
exit(1);
}
sum = 0;
for(i=0;i<fit_atomnum;i++) {
sum+=(fit_atom[i].x-fit_refatom[i].x) * (fit_atom[i].x-fit_refatom[i].x);
sum+=(fit_atom[i].y-fit_refatom[i].y) * (fit_atom[i].y-fit_refatom[i].y);
sum+=(fit_atom[i].z-fit_refatom[i].z) * (fit_atom[i].z-fit_refatom[i].z);
}
rms = sqrt(sum/fit_atomnum);
fprintf(fplog, "The rmsd before least-square fitting is %9.4lf\n", rms);
fprintf(fplog, "Number of atoms participate least-square fitting is %9d\n", fit_atomnum);
fprintf(stdout, "\nThe rmsd before least-square fitting is %9.4lf", rms);
fprintf(stdout, "\nNumber of atoms participate least-square fitting is %9d", fit_atomnum);
if(jobtype == 0) {
fclose(fplog);
return 0;
}
if ((fpmatrix = fopen(mfilename, "w")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", mfilename);
exit(1);
}
rms = lsfit(fit_refatom, fit_atom, fit_atomnum) ;
for(i=0;i<fit_atomnum;i++) {
x=CG0[0]+ROT[0][0]*(fit_atom[i].x-CG1[0])+ ROT[0][1]*(fit_atom[i].y-CG1[1])+ ROT[0][2]*(fit_atom[i].z-CG1[2]);
y=CG0[1]+ROT[1][0]*(fit_atom[i].x-CG1[0])+ ROT[1][1]*(fit_atom[i].y-CG1[1])+ ROT[1][2]*(fit_atom[i].z-CG1[2]);
z=CG0[2]+ROT[2][0]*(fit_atom[i].x-CG1[0])+ ROT[2][1]*(fit_atom[i].y-CG1[1])+ ROT[2][2]*(fit_atom[i].z-CG1[2]);
sum =(x-fit_refatom[i].x) * (x-fit_refatom[i].x);
sum+=(y-fit_refatom[i].y) * (y-fit_refatom[i].y);
sum+=(z-fit_refatom[i].z) * (z-fit_refatom[i].z);
sum = sqrt(sum);
fprintf(fplog, "ATOM %5d %9.3lf %9.3lf %9.3lf ", i+1, fit_atom[i].x, fit_atom[i].y, fit_atom[i].z);
fprintf(fplog, "REFATOM %9.3lf %9.3lf %9.3lf %9.3lf\n", fit_refatom[i].x, fit_refatom[i].y, fit_refatom[i].z, sum);
}
fclose(fpmatrix);
fprintf(fplog, "\nThe rmsd after least-square fitting is %9.4lf\n", rms);
fprintf(stdout, "\nThe rmsd after least-square fitting is %9.4lf\n", rms);
fclose(fplog);
}
if(jobtype == 2)
rmatrix(mfilename);
if(jobtype == 1 || jobtype == 2) {
for(i=0;i<atomnum;i++) {
x=CG0[0]+ROT[0][0]*(atom[i].x-CG1[0])+ ROT[0][1]*(atom[i].y-CG1[1])+ ROT[0][2]*(atom[i].z-CG1[2]);
y=CG0[1]+ROT[1][0]*(atom[i].x-CG1[0])+ ROT[1][1]*(atom[i].y-CG1[1])+ ROT[1][2]*(atom[i].z-CG1[2]);
z=CG0[2]+ROT[2][0]*(atom[i].x-CG1[0])+ ROT[2][1]*(atom[i].y-CG1[1])+ ROT[2][2]*(atom[i].z-CG1[2]);
atom[i].x = x;
atom[i].y = y;
atom[i].z = z;
}
if(format == 1) wpdb(ofilename, atomnum, atom);
if(format == 2) wac(ofilename, atomnum, atom, bondnum, bond, cinfo, minfo);
if(format == 3) wmol2(ofilename, atomnum, atom, bondnum, bond, arom, cinfo, minfo);
if(format == 4) wmdl(ofilename, atomnum, atom, bondnum, bond, cinfo);
if(format == 5) wrst(ofilename, atomnum, atom);
}
return 0;
}
