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);
}
static PyObject* rdparm(PyObject *self, PyObject *args) {
char *filename;
if (!PyArg_ParseTuple(args, "s", &filename))
return NULL;
std::string fname(filename);
std::string error_message;
// The data we are parsing from the prmtop
ParmDataMap parmData;
ParmStringMap parmComments, unkParmData;
ParmFormatMap parmFormats;
std::vector<std::string> flagList;
std::string version;
ExitStatus retval;
Py_BEGIN_ALLOW_THREADS
retval = readparm(fname, flagList, parmData, parmComments,
unkParmData, parmFormats, version);
Py_END_ALLOW_THREADS
if (retval == NOOPEN) {
error_message = "Could not open " + fname + " for reading";
PyErr_SetString(PyExc_IOError, error_message.c_str());
return NULL;
}
if (retval == NOVERSION) {
error_message = "Could not find %VERSION in " + fname;
PyErr_SetString(PyExc_TypeError, error_message.c_str());
return NULL;
}
if (retval == EMPTY) {
error_message = fname + " was empty";
PyErr_SetString(PyExc_ValueError, error_message.c_str());
return NULL;
}
if (retval == ERR) {
error_message = "Prmtop parsing error parsing " + fname;
PyErr_SetString(PyExc_RuntimeError, error_message.c_str());
return NULL;
}
// If we got here, the parsing must have been OK. Create the parm_data,
// formats, and comments dicts to pass back to Python
PyObject *parm_data = PyDict_New();
PyObject *comments = PyDict_New();
PyObject *formats = PyDict_New();
PyObject *unknown_flags = PyList_New((Py_ssize_t) unkParmData.size());
PyObject *flag_list = PyList_New((Py_ssize_t) flagList.size());
Py_ssize_t unkFlagNum = 0;
for (size_t i = 0; i < flagList.size(); i++) {
std::string flag = flagList[i];
Py_ssize_t listSize;
PyObject *list;
if (parmFormats[flag].dataType == UNKNOWN)
listSize = (Py_ssize_t) unkParmData[flag].size();
else
listSize = (Py_ssize_t) parmData[flag].size();
list = PyList_New(listSize);
// Now see what type this is and fill the list up accordingly
switch (parmFormats[flag].dataType) {
case INTEGER:
for (Py_ssize_t j = 0; j < listSize; j++) {
long val = (long) parmData[flag][(size_t)j].i;
PyList_SET_ITEM(list, j, PyInt_FromLong(val));
}
break;
case FLOAT:
for (Py_ssize_t j = 0; j < listSize; j++) {
double val = parmData[flag][(size_t)j].f;
PyList_SET_ITEM(list, j, PyFloat_FromDouble(val));
}
break;
case HOLLERITH:
for (Py_ssize_t j = 0; j < listSize; j++) {
PyList_SET_ITEM(list, j,
PyString_FromString(parmData[flag][(size_t)j].c));
}
break;
case UNKNOWN:
for (Py_ssize_t j = 0; j < listSize; j++) {
std::string line = unkParmData[flag][(size_t) j];
PyList_SET_ITEM(list, j, PyString_FromString(line.c_str()));
}
// Add this to the list of unknown flags
PyList_SET_ITEM(unknown_flags, unkFlagNum++,
PyString_FromString(flag.c_str()));
break;
default:
// Should not be here
PyErr_SetString(PyExc_RuntimeError, "This should be unreachable");
return NULL;
}
SetItem_PyDict_AndDecref(parm_data, flag.c_str(), list);
// Now comments
if (parmComments.count(flag) == 0) {
SetItem_PyDict_AndDecref(comments, flag.c_str(), PyList_New(0));
} else {
int ncom = parmComments[flag].size();
PyObject *commentList = PyList_New(ncom);
for (Py_ssize_t j = 0; j < ncom; j++) {
std::string line = parmComments[flag][(size_t)j];
PyList_SET_ITEM(commentList, j,
PyString_FromString(line.c_str()));
}
SetItem_PyDict_AndDecref(comments, flag.c_str(), commentList);
}
// Now formats
PyObject *fmt = PyString_FromString(parmFormats[flag].fmt.c_str());
SetItem_PyDict_AndDecref(formats, flag.c_str(), fmt);
// Now flag list
PyList_SET_ITEM(flag_list, (Py_ssize_t)i,
PyString_FromString(flag.c_str()));
}
PyObject *ret = PyTuple_New(6);
PyTuple_SET_ITEM(ret, 0, parm_data);
PyTuple_SET_ITEM(ret, 1, comments);
PyTuple_SET_ITEM(ret, 2, formats);
PyTuple_SET_ITEM(ret, 3, unknown_flags);
PyTuple_SET_ITEM(ret, 4, flag_list);
PyTuple_SET_ITEM(ret, 5, PyString_FromString(version.c_str()));
return ret;
}
