void readangleparm(char *filename)
{
int mindex = -1;
int bindex = 0;
int aindex = 0;
int num = 0;
FILE *fp;
char line[MAXCHAR];
if ((fp = fopen(filename, "r")) == NULL) {
printf("\n Cannot open the angle parameter file %s in readangleparm(), exit", filename);
return;
}
for (;;) {
if (fgets(line, MAXCHAR, fp) == NULL)
break;
num++;
if (mindex == -1 && num == 1) {
mindex = 1;
continue;
}
if (mindex == 1 && spaceline(line) == 1) {
mindex = 0;
num = 0;
bindex = -1;
continue;
}
if (bindex == -1 && num == 1) {
bindex = 1;
continue;
}
if (bindex == 1 && spaceline(line) == 1) {
bindex = 0;
aindex = 1;
continue;
}
if (aindex == 1 && spaceline(line) == 1) {
aindex = 0;
break;
}
if (aindex == 1) {
angleparm[angleparmnum].name1[0] = line[0];
angleparm[angleparmnum].name1[1] = line[1];
angleparm[angleparmnum].name2[0] = line[3];
angleparm[angleparmnum].name2[1] = line[4];
angleparm[angleparmnum].name3[0] = line[6];
angleparm[angleparmnum].name3[1] = line[7];
sscanf(&line[8], "%lf%lf", &angleparm[angleparmnum].force,
&angleparm[angleparmnum].angle);
angleparmnum++;
if(angleparmnum >= 10 * MAXATOMTYPE * MAXATOMTYPE) {
fprintf(stdout, "Error, the number of angle parameters (%ld) exceed 10 * MAXATOMTYPE * MAXATOMTYPE,\nincrease MAXATOMTYPE (%d) in define.h\n", angleparmnum, MAXATOMTYPE);
}
}
}
fclose(fp);
}
void rsqmout_coord(char *filename, ATOM * atom) {
/* int i,j; */
int flag;
int number = 0;
int tmpint1, tmpint2;
FILE *fpout;
char tmpchar1[MAXCHAR];
char tmpchar2[MAXCHAR];
char tmpchar3[MAXCHAR];
char tmpchar4[MAXCHAR];
char tmpchar5[MAXCHAR];
char tmpchar6[MAXCHAR];
char tmpchar7[MAXCHAR];
char line[MAXCHAR];
double tmpfloat1;
double tmpfloat2;
double tmpfloat3;
if ((fpout = fopen(filename, "r")) == NULL) {
fprintf(stdout, "Cannot open sqm output file: %s in rsqmout(), exit\n", filename);
exit(1);
}
flag = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpout) == NULL)
break;
sscanf(line, "%s%s%s%s%s%s%s", tmpchar1, tmpchar2, tmpchar3,
tmpchar4, tmpchar5, tmpchar6, tmpchar7);
if (strcmp(tmpchar1, "Final") == 0 && strcmp(tmpchar2, "Structure") == 0) {
flag = 1;
continue;
}
if (flag == 1 && strcmp("QM_NO.", tmpchar2) == 0
&& strcmp("MM_NO.", tmpchar3) == 0
&& strcmp("ATOM", tmpchar4) == 0
&& strcmp("X", tmpchar5) == 0
&& strcmp("Y", tmpchar6) == 0
&& strcmp("Z", tmpchar7) == 0) {
flag = 2;
continue;
}
if (flag == 2 && spaceline(line) == 1) break;
if (flag == 2) {
sscanf(line, "%s%d%d%s%lf%lf%lf", tmpchar1, &tmpint1, &tmpint2, tmpchar2, &tmpfloat1, &tmpfloat2, &tmpfloat3);
atom[number].x = tmpfloat1;
atom[number].y = tmpfloat2;
atom[number].z = tmpfloat3;
number++;
}
}
fclose(fpout);
}
/* MOPAC CRT */
int rmopcrt(char *filename, int *atomnum, ATOM atom[], CONTROLINFO cinfo,
MOLINFO minfo)
{
FILE *fpin;
int index;
int numatom;
int tmpint1, tmpint2, tmpint3;
int overflow_flag = 0;
char line[MAXCHAR];
char tmpchar[20];
double tmpfloat1, tmpfloat2, tmpfloat3;
if ((fpin = fopen(filename, "r")) == NULL) {
fprintf(stdout, "Cannot open file %s to read in rmopcrt(), exit\n", filename);
exit(1);
}
initial(cinfo.maxatom, atom, minfo.resname);
index = 0;
numatom = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) {
/* printf("\nFinished reading %s file.", cinfo.ifilename); */
break;
}
index++;
if (index < 4)
continue;
sscanf(line, "%s%lf%d%lf%d%lf%d", tmpchar, &tmpfloat1, &tmpint1,
&tmpfloat2, &tmpint2, &tmpfloat3, &tmpint3);
if (spaceline(line) == 1)
break;
if (overflow_flag == 0) {
strcpy(atom[numatom].name, tmpchar);
atom[numatom].x = tmpfloat1;
atom[numatom].y = tmpfloat2;
atom[numatom].z = tmpfloat3;
}
numatom++;
if (numatom >= cinfo.maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
}
fclose(fpin);
*atomnum = numatom;
/* printf("\n atom number is %5d", *atomnum); */
return overflow_flag;
}
/* GCRT */
int rgcrt(char *filename, int *atomnum, ATOM * atom, CONTROLINFO cinfo,
MOLINFO minfo)
{
FILE *fpin;
int i, index;
int nameindex;
int numatom;
int read_charge = 1;
int overflow_flag = 0;
char tmpchar[MAXCHAR];
char line[MAXCHAR];
if ((fpin = fopen(filename, "r")) == NULL) {
fprintf(stdout, "Cannot open the gcrt file %s to read, exit\n", filename);
exit(1);
}
initial(cinfo.maxatom, atom, minfo.resname);
index = 0;
numatom = 0;
nameindex = -1;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) {
break;
}
if (spaceline(line) == 1 || strlen(line) <= 1) {
index++;
continue;
}
if (index == 0 || index == 1) continue;
if (read_charge ==1 && index == 2) {
sscanf(line, "%d%d", &(minfo.icharge), &(minfo.multiplicity));
read_charge = 0;
continue;
}
if (index == 3) {
break;
}
sscanf(line, "%s", tmpchar);
if (nameindex == -1) {
if (tmpchar[0] >= '0' && tmpchar[0] <= '9')
nameindex = 0;
else
nameindex = 1;
}
if (overflow_flag == 0) {
if (nameindex == 0)
sscanf(line, "%d%lf%lf%lf", &atom[numatom].atomicnum,
&atom[numatom].x, &atom[numatom].y,
&atom[numatom].z);
else
sscanf(line, "%s%lf%lf%lf", atom[numatom].name,
&atom[numatom].x, &atom[numatom].y,
&atom[numatom].z);
}
numatom++;
if (numatom >= cinfo.maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
}
*atomnum = numatom;
if (nameindex == 0) {
element(*atomnum, atom);
for (i = 0; i < *atomnum; i++)
strcpy(atom[i].name, atom[i].element);
}
if (nameindex == 1)
atomicnum(*atomnum, atom);
/* printf("\n atom number is %5d", *atomnum); */
fclose(fpin);
return overflow_flag;
}
/* GZMAT */
int rgzmat(char *filename, int *atomnum, ATOM * atom, CONTROLINFO cinfo,
MOLINFO minfo)
{
typedef struct {
char name[30];
} STRNAME;
FILE *fpin;
int i, j, index, index0;
int overflow_flag = 0;
int findindex;
int numatom;
STRNAME *bondstr;
STRNAME *anglestr;
STRNAME *twiststr;
char tmpchar1[10];
char tmpchar2[10];
char line[MAXCHAR];
if ((fpin = fopen(filename, "r")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", filename);
exit(1);
}
bondstr = (STRNAME *) malloc(sizeof(STRNAME) * (cinfo.maxatom +10));
if (bondstr == NULL) {
fprintf(stderr, "memory allocation error for *bondstr in rgzmat()\n");
exit(0);
}
anglestr = (STRNAME *) malloc(sizeof(STRNAME) * (cinfo.maxatom +10));
if (anglestr == NULL) {
fprintf(stderr, "memory allocation error for *anglestr in rgzmat()\n");
exit(0);
}
twiststr = (STRNAME *) malloc(sizeof(STRNAME) * (cinfo.maxatom +10));
if (twiststr == NULL) {
fprintf(stderr, "memory allocation error for *twiststr in rgzmat()\n");
exit(0);
}
initial(cinfo.maxatom, atom, minfo.resname);
index = 0;
index0 = 1;
numatom = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) {
/* printf("\nFinished reading %s file.", cinfo.ifilename); */
break;
}
if (spaceline(line) == 1) {
index++;
continue;
}
if (index >= 2)
index++;
if (index <= 3)
continue;
if (index >= 4) {
if (spaceline(line) == 1 || strncmp(line, "Vari", 4) == 0
|| strncmp(line, "vari", 4) == 0)
index0 = -1;
if (strncmp(line, "Const", 5) == 0
|| strncmp(line, "const", 5) == 0)
index0 = -1;
}
if (index == 4) {
if (overflow_flag == 0)
sscanf(line, "%s", atom[numatom].name);
numatom++;
if (numatom >= cinfo.maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
continue;
}
if (index == 5) {
if (overflow_flag == 0)
sscanf(line, "%s%d%s", atom[numatom].name,
&atom[numatom].bondatom, bondstr[numatom].name);
numatom++;
if (numatom >= cinfo.maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
continue;
}
if (index == 6) {
if (overflow_flag == 0)
sscanf(line, "%s%d%s%d%s", atom[numatom].name,
&atom[numatom].bondatom, bondstr[numatom].name,
&atom[numatom].angleatom, anglestr[numatom].name);
numatom++;
if (numatom >= cinfo.maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
continue;
}
if (index0 != -1) {
if (overflow_flag == 0)
sscanf(line, "%s%d%s%d%s%d%s", atom[numatom].name,
&atom[numatom].bondatom, bondstr[numatom].name,
&atom[numatom].angleatom, anglestr[numatom].name,
&atom[numatom].twistatom, twiststr[numatom].name);
numatom++;
if (numatom >= cinfo.maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
continue;
}
if (index0 == -1) {
sscanf(line, "%s%s", tmpchar1, tmpchar2);
for (i = 1; i < numatom; i++) {
findindex = 1;
for (j = 0; j < strlen(bondstr[i].name); j++)
if (bondstr[i].name[j] != tmpchar1[j]) {
findindex = 0;
break;
}
if (findindex == 1) {
strcpy(bondstr[i].name, tmpchar2);
break;
}
}
for (i = 2; i < numatom; i++) {
findindex = 1;
for (j = 0; j < strlen(anglestr[i].name); j++)
if (anglestr[i].name[j] != tmpchar1[j]) {
findindex = 0;
break;
}
if (findindex == 1) {
strcpy(anglestr[i].name, tmpchar2);
break;
}
}
for (i = 3; i < numatom; i++) {
findindex = 1;
for (j = 0; j < strlen(twiststr[i].name); j++)
if (twiststr[i].name[j] != tmpchar1[j]) {
findindex = 0;
break;
}
if (findindex == 1) {
strcpy(twiststr[i].name, tmpchar2);
break;
}
}
}
}
atom[1].bondatom--;
atom[2].bondatom--;
atom[2].angleatom--;
for (i = 3; i < numatom; i++) {
atom[i].bondatom--;
atom[i].angleatom--;
atom[i].twistatom--;
}
for (i = 1; i < numatom; i++)
atom[i].bond = atof(bondstr[i].name);
for (i = 2; i < numatom; i++)
atom[i].angle = atof(anglestr[i].name);
for (i = 3; i < numatom; i++)
atom[i].twist = atof(twiststr[i].name);
*atomnum = numatom;
/* printf("\n atom number is %5d", *atomnum); */
fclose(fpin);
free(bondstr);
free(anglestr);
free(twiststr);
return overflow_flag;
}
void readfrcmod(char *filename)
{
int mindex = 0;
int bindex = 0;
int aindex = 0;
int tindex = 0;
int iindex = 0;
int vindex = 0;
FILE *fp;
char line[MAXCHAR];
if ((fp = fopen(filename, "r")) == NULL) {
printf("\n Cannot open file %s, exit", filename);
return;
}
for (;;) {
if (fgets(line, MAXCHAR, fp) == NULL)
break;
if (strncmp("MASS", &line[0], 4) == 0) {
mindex = 1;
continue;
}
if (strncmp("BOND", &line[0], 4) == 0) {
bindex = 1;
continue;
}
if (strncmp("ANGL", &line[0], 4) == 0) {
aindex = 1;
continue;
}
if (strncmp("DIHE", &line[0], 4) == 0) {
tindex = 1;
continue;
}
if (strncmp("IMPR", &line[0], 4) == 0) {
iindex = 1;
continue;
}
if (strncmp("NONB", &line[0], 4) == 0) {
vindex = 1;
continue;
}
if (mindex == 1 && spaceline(line) == 1)
mindex = 0;
if (bindex == 1 && spaceline(line) == 1)
bindex = 0;
if (aindex == 1 && spaceline(line) == 1)
aindex = 0;
if (tindex == 1 && spaceline(line) == 1)
tindex = 0;
if (iindex == 1 && spaceline(line) == 1)
iindex = 0;
if (vindex == 1 && spaceline(line) == 1)
vindex = 0;
if (mindex == 1) {
sscanf(line, "%s", atomtype[atomtypenum].name);
strcpy(atomtype[atomtypenum].parm, line);
atomtypenum++;
if (atomtypenum >= maxatomtype) {
maxatomtype += MAX_FF_ATOMTYPE;
atomtype =
(ATOMTYPE *) realloc(atomtype,
sizeof(ATOMTYPE) * maxatomtype);
if (atomtype == NULL) {
fprintf(stderr,
"memory allocation error for *atomtype\n");
exit(0);
}
}
}
if (bindex == 1) {
bondparm[bondparmnum].name1[0] = line[0];
bondparm[bondparmnum].name1[1] = line[1];
bondparm[bondparmnum].name2[0] = line[3];
bondparm[bondparmnum].name2[1] = line[4];
strcpy(bondparm[bondparmnum].parm, line);
bondparmnum++;
if (bondparmnum >= maxbondparm) {
maxbondparm += MAX_FF_BOND;
bondparm =
(BOND_FF *) realloc(bondparm,
sizeof(BOND_FF) * maxbondparm);
if (bondparm == NULL) {
fprintf(stderr,
"memory allocation error for *bondparm\n");
exit(0);
}
}
}
if (aindex == 1) {
angleparm[angleparmnum].name1[0] = line[0];
angleparm[angleparmnum].name1[1] = line[1];
angleparm[angleparmnum].name2[0] = line[3];
angleparm[angleparmnum].name2[1] = line[4];
angleparm[angleparmnum].name3[0] = line[6];
angleparm[angleparmnum].name3[1] = line[7];
strcpy(angleparm[angleparmnum].parm, line);
angleparmnum++;
if (angleparmnum >= maxangleparm) {
maxangleparm += MAX_FF_ANGLE;
angleparm =
(ANGLE *) realloc(angleparm,
sizeof(ANGLE) * maxangleparm);
if (angleparm == NULL) {
fprintf(stderr,
"memory allocation error for *angleparm\n");
exit(0);
}
}
}
if (tindex == 1) {
torsionparm[torsionparmnum].name1[0] = line[0];
torsionparm[torsionparmnum].name1[1] = line[1];
torsionparm[torsionparmnum].name2[0] = line[3];
torsionparm[torsionparmnum].name2[1] = line[4];
torsionparm[torsionparmnum].name3[0] = line[6];
torsionparm[torsionparmnum].name3[1] = line[7];
torsionparm[torsionparmnum].name4[0] = line[9];
torsionparm[torsionparmnum].name4[1] = line[10];
strcpy(torsionparm[torsionparmnum].parm, line);
torsionparmnum++;
if (torsionparmnum >= maxtorsionparm) {
maxtorsionparm += MAX_FF_TORSION;
torsionparm =
(TORSION *) realloc(torsionparm,
sizeof(TORSION) * maxtorsionparm);
if (torsionparm == NULL) {
fprintf(stderr,
"memory allocation error for *torsionparm\n");
exit(0);
}
}
}
if (iindex == 1) {
improperparm[improperparmnum].name1[0] = line[0];
improperparm[improperparmnum].name1[1] = line[1];
improperparm[improperparmnum].name2[0] = line[3];
improperparm[improperparmnum].name2[1] = line[4];
improperparm[improperparmnum].name3[0] = line[6];
improperparm[improperparmnum].name3[1] = line[7];
improperparm[improperparmnum].name4[0] = line[9];
improperparm[improperparmnum].name4[1] = line[10];
strcpy(improperparm[improperparmnum].parm, line);
improperparmnum++;
if (improperparmnum >= maximproperparm) {
maximproperparm += MAX_FF_IMPROPER;
improperparm =
(IMPROPER *) realloc(improperparm,
sizeof(IMPROPER) *
maximproperparm);
if (improperparm == NULL) {
fprintf(stderr,
"memory allocation error for *improperparm\n");
exit(0);
}
}
}
if (vindex == 1) {
sscanf(line, "%s", vdwparm[vdwparmnum].name);
strcpy(vdwparm[vdwparmnum].parm, line);
vdwparmnum++;
if (vdwparmnum >= maxvdwparm) {
maxvdwparm += MAX_FF_VDW;
vdwparm =
(VDW *) realloc(vdwparm, sizeof(VDW) * maxvdwparm);
if (vdwparm == NULL) {
fprintf(stderr,
"memory allocation error for *vdwparm\n");
exit(0);
}
}
}
}
fclose(fp);
}
void join(char *filename1, char *filename2)
{
FILE *fp1, *fp2;
char line[MAXCHAR];
int mindex = 0;
int bindex = 0;
int aindex = 0;
int tindex = 0;
int iindex = 0;
int vindex = 0;
if ((fp1 = fopen(filename1, "r")) == NULL) {
printf("\n Cannot open file %s, exit", filename1);
return;
}
if ((fp2 = fopen(filename2, "w")) == NULL) {
printf("\n Cannot open file %s, exit", filename2);
return;
}
for (;;) {
if (fgets(line, MAXCHAR, fp1) == NULL)
break;
if (vindex == 1 && strncmp(line, "MOD", 3) == 0)
vindex = 2;
if (spaceline(line) == 1) {
if (mindex == 0)
mindex = 1;
if (mindex == 2 && bindex == 0)
bindex = 1;
if (bindex == 2 && aindex == 0)
aindex = 1;
if (aindex == 2 && tindex == 0)
tindex = 1;
if (tindex == 2 && iindex == 0)
iindex = 1;
if (iindex == 2 && vindex == 0)
vindex = 1;
if (vindex == 2)
vindex = 3;
}
if (vindex == 2 && strncmp(line, "END", 3) == 0)
vindex = 3;
if (mindex == 1) {
for (i = 0; i < atomtypenum; i++)
if (atomtypeindex[i] == 0)
fprintf(fp2, "%s", atomtype[i].parm);
fprintf(fp2, "\n");
mindex = 2;
continue;
}
if (bindex == 1) {
for (i = 0; i < bondparmnum; i++)
if (bondparmindex[i] == 0)
fprintf(fp2, "%s", bondparm[i].parm);
fprintf(fp2, "\n");
bindex = 2;
continue;
}
if (aindex == 1) {
for (i = 0; i < angleparmnum; i++)
if (angleparmindex[i] == 0)
fprintf(fp2, "%s", angleparm[i].parm);
fprintf(fp2, "\n");
aindex = 2;
continue;
}
if (tindex == 1) {
for (i = 0; i < torsionparmnum; i++)
if (torsionparmindex[i] == 0)
fprintf(fp2, "%s", torsionparm[i].parm);
fprintf(fp2, "\n");
tindex = 2;
continue;
}
if (iindex == 1) {
for (i = 0; i < improperparmnum; i++)
if (improperparmindex[i] == 0)
fprintf(fp2, "%s", improperparm[i].parm);
fprintf(fp2, "\n");
iindex = 2;
continue;
}
if (vindex == 3) {
for (i = 0; i < vdwparmnum; i++)
if (vdwparmindex[i] == 0)
fprintf(fp2, "%s", vdwparm[i].parm);
fprintf(fp2, "\n");
vindex = -1;
continue;
}
fprintf(fp2, "%s", line);
}
fclose(fp1);
fclose(fp2);
}
void check(char *filename)
{
int mindex = -1;
int bindex = 0;
int aindex = 0;
int tindex = 0;
int iindex = 0;
int vindex = 0;
int num = 0;
FILE *fp;
char line[MAXCHAR];
char tmpchar[5];
if ((fp = fopen(filename, "r")) == NULL) {
printf("\n Cannot open file %s, exit", filename);
return;
}
for (;;) {
if (fgets(line, MAXCHAR, fp) == NULL)
break;
num++;
if (mindex == -1 && num == 1) {
mindex = 1;
continue;
}
if (mindex == 1 && spaceline(line) == 1) {
mindex = 0;
num = 0;
bindex = -1;
continue;
}
if (bindex == -1 && num == 1) {
bindex = 1;
continue;
}
if (bindex == 1 && spaceline(line) == 1) {
bindex = 0;
aindex = 1;
continue;
}
if (aindex == 1 && spaceline(line) == 1) {
aindex = 0;
tindex = 1;
continue;
}
if (tindex == 1 && spaceline(line) == 1) {
tindex = 0;
iindex = 1;
continue;
}
if (iindex == 1 && spaceline(line) == 1) {
iindex = 0;
vindex = -1;
num = 0;
continue;
}
if (vindex == -1 && num == 2) {
vindex = 1;
continue;
}
if (vindex == 2 && spaceline(line) == 1) {
vindex = 0;
continue;
}
if (vindex == 1)
if (strncmp(line, "MOD4", 4) == 0) {
vindex = 2;
continue;
} else
vindex = 3;
if (mindex == 1) {
tmpchar[0] = '\0';
sscanf(line, "%s", tmpchar);
for (i = 0; i < atomtypenum; i++)
if (strcmp(tmpchar, atomtype[i].name) == 0)
atomtypeindex[i] = 1;
}
if (bindex == 1)
for (i = 0; i < bondparmnum; i++)
if ((bondparm[i].name1[0] == line[0]
&& bondparm[i].name1[1] == line[1]
&& bondparm[i].name2[0] == line[3]
&& bondparm[i].name2[1] == line[4])
|| (bondparm[i].name2[0] == line[0]
&& bondparm[i].name2[1] == line[1]
&& bondparm[i].name1[0] == line[3]
&& bondparm[i].name1[1] == line[4]))
bondparmindex[i] = 1;
if (aindex == 1)
for (i = 0; i < angleparmnum; i++)
if ((angleparm[i].name1[0] == line[0]
&& angleparm[i].name1[1] == line[1]
&& angleparm[i].name2[0] == line[3]
&& angleparm[i].name2[1] == line[4]
&& angleparm[i].name3[0] == line[6]
&& angleparm[i].name3[1] == line[7])
|| (angleparm[i].name3[0] == line[0]
&& angleparm[i].name3[1] == line[1]
&& angleparm[i].name2[0] == line[3]
&& angleparm[i].name2[1] == line[4]
&& angleparm[i].name1[0] == line[6]
&& angleparm[i].name1[1] == line[7]))
angleparmindex[i] = 1;
if (tindex == 1)
for (i = 0; i < torsionparmnum; i++)
if ((torsionparm[i].name1[0] == line[0]
&& torsionparm[i].name1[1] == line[1]
&& torsionparm[i].name2[0] == line[3]
&& torsionparm[i].name2[1] == line[4]
&& torsionparm[i].name3[0] == line[6]
&& torsionparm[i].name3[1] == line[7]
&& torsionparm[i].name4[0] == line[9]
&& torsionparm[i].name4[1] == line[10])
|| (torsionparm[i].name4[0] == line[0]
&& torsionparm[i].name4[1] == line[1]
&& torsionparm[i].name3[0] == line[3]
&& torsionparm[i].name3[1] == line[4]
&& torsionparm[i].name2[0] == line[6]
&& torsionparm[i].name2[1] == line[7]
&& torsionparm[i].name1[0] == line[9]
&& torsionparm[i].name1[1] == line[10]))
torsionparmindex[i] = 1;
if (iindex == 1)
if ((improperparm[i].name1[0] == line[0]
&& improperparm[i].name1[1] == line[1]
&& improperparm[i].name2[0] == line[3]
&& improperparm[i].name2[1] == line[4]
&& improperparm[i].name3[0] == line[6]
&& improperparm[i].name3[1] == line[7]
&& improperparm[i].name4[0] == line[9]
&& improperparm[i].name4[1] == line[10])
|| (improperparm[i].name4[0] == line[0]
&& improperparm[i].name4[1] == line[1]
&& improperparm[i].name3[0] == line[3]
&& improperparm[i].name3[1] == line[4]
&& improperparm[i].name2[0] == line[6]
&& improperparm[i].name2[1] == line[7]
&& improperparm[i].name1[0] == line[9]
&& improperparm[i].name1[1] == line[10]))
improperparmindex[i] = 1;
if (vindex == 3) {
printf
("\nThis program does not support vdw equivalent describations");
printf
("\nPlease list the equivalented vdw parameters explicitly");
exit(0);
}
if (vindex == 2) {
tmpchar[0] = '\0';
sscanf(line, "%s", tmpchar);
if (strcmp(vdwparm[i].name, tmpchar) == 0)
vdwparmindex[i] = 1;
}
}
fclose(fp);
}
/* GCRT */
int rgcrt(char *filename, int *atomnum, ATOM * atom, CONTROLINFO cinfo,
MOLINFO minfo)
{
FILE *fpin;
int i, index;
int nameindex;
int numatom;
int overflow_flag = 0;
char tmpchar[10];
char line[MAXCHAR];
if ((fpin = fopen(filename, "r")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", filename);
exit(1);
}
initial(cinfo.maxatom, atom, minfo.resname);
index = 0;
numatom = 0;
nameindex = -1;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) {
/* printf("\nFinished reading %s file.", cinfo.ifilename); */
break;
}
if (spaceline(line) == 1) {
index++;
continue;
}
if (index >= 2)
index++;
if (index <= 3)
continue;
if (index > 4 && spaceline(line) == 1)
break;
sscanf(line, "%s", tmpchar);
if (nameindex == -1) {
if (tmpchar[0] >= '0' && tmpchar[0] <= '9')
nameindex = 0;
else
nameindex = 1;
}
if (overflow_flag == 0) {
if (nameindex == 0)
sscanf(line, "%d%lf%lf%lf", &atom[numatom].atomicnum,
&atom[numatom].x, &atom[numatom].y,
&atom[numatom].z);
else
sscanf(line, "%s%lf%lf%lf", atom[numatom].name,
&atom[numatom].x, &atom[numatom].y,
&atom[numatom].z);
}
numatom++;
if (numatom >= cinfo.maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
}
*atomnum = numatom;
if (nameindex == 0) {
element(*atomnum, atom);
for (i = 0; i < *atomnum; i++)
strcpy(atom[i].name, atom[i].element);
}
if (nameindex == 1)
atomicnum(*atomnum, atom);
/* printf("\n atom number is %5d", *atomnum); */
fclose(fpin);
return overflow_flag;
}
/* MOPAC OUTPUT */
int rsqmout(char *filename, int *atomnum, ATOM * atom, CONTROLINFO *cinfo,
MOLINFO *minfo)
{
/* int i,j; */
int flag;
int number = 0;
int tmpint1, tmpint2;
int overflow_flag = 0;
FILE *fpout;
char tmpchar1[MAXCHAR];
char tmpchar2[MAXCHAR];
char tmpchar3[MAXCHAR];
char tmpchar4[MAXCHAR];
char tmpchar5[MAXCHAR];
char tmpchar6[MAXCHAR];
char tmpchar7[MAXCHAR];
char line[MAXCHAR];
double tmpfloat1;
double tmpfloat2;
double tmpfloat3;
if ((fpout = fopen(filename, "r")) == NULL) {
fprintf(stdout, "Cannot open sqm output file: %s in rsqmout(), exit\n", filename);
exit(1);
}
initial((*cinfo).maxatom, atom, (*minfo).resname);
flag = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpout) == NULL)
break;
sscanf(line, "%s%s%s%s%s%s%s", tmpchar1, tmpchar2, tmpchar3,
tmpchar4, tmpchar5, tmpchar6, tmpchar7);
if (strcmp(tmpchar1, "Total") == 0
&& strcmp(tmpchar2, "Mulliken") == 0
&& strcmp(tmpchar3, "Charge") == 0
&& strcmp(tmpchar4, "=") == 0) {
sscanf(line, "%s%s%s%s%lf", tmpchar1, tmpchar2, tmpchar3,
tmpchar4, &(*minfo).dcharge);
(*minfo).icharge = (int) (*minfo).dcharge;
continue;
}
if (strcmp(tmpchar1, "Final") == 0 && strcmp(tmpchar2, "Structure") == 0) {
flag = 1;
continue;
}
if (flag == 1 && strcmp("QM_NO.", tmpchar2) == 0
&& strcmp("MM_NO.", tmpchar3) == 0
&& strcmp("ATOM", tmpchar4) == 0
&& strcmp("X", tmpchar5) == 0
&& strcmp("Y", tmpchar6) == 0
&& strcmp("Z", tmpchar7) == 0) {
flag = 2;
continue;
}
if (flag == 2 && spaceline(line) == 1) {
flag = 3;
*atomnum = number;
break;
}
if (flag == 2) {
if (overflow_flag == 0) {
sscanf(line, "%s%d%d%s%lf%lf%lf", tmpchar1, &tmpint1, &tmpint2, tmpchar2, &tmpfloat1,
&tmpfloat2, &tmpfloat3);
strcpy(atom[number].name, tmpchar2);
atom[number].x = tmpfloat1;
atom[number].y = tmpfloat2;
atom[number].z = tmpfloat3;
strcpy(atom[number].aa, (*minfo).resname);
}
number++;
if (number >= (*cinfo).maxatom && overflow_flag == 0) {
printf
("\nInfo: the atom number exceeds the MAXATOM, reallocate memory automatically");
overflow_flag = 1;
}
}
}
fclose(fpout);
return overflow_flag;
}