/* Read in the next atom info into the given storage areas; this assumes
that file has already been moved to the beginning of the atom records.
Returns the serial number of the atom. If there is an error, returns -1.*/
static int get_psf_atom(FILE *f, char *name, char *atype, char *resname,
char *segname, int *resid, float *q, float *m, int charmmext) {
char inbuf[PSF_RECORD_LENGTH+2];
int num;
if (inbuf != fgets(inbuf, PSF_RECORD_LENGTH+1, f)) {
return(-1); /* failed to read in an atom */
}
if (strlen(inbuf) < 50) {
fprintf(stderr, "Line too short in psf file: \n%s\n", inbuf);
return -1;
}
num = atoi(inbuf); /* atom index */
if (charmmext == 1) {
/* CHARMM PSF format is (if CMAP,CHEQ are also included):
* '(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)'
*/
strnwscpy(segname, inbuf+11, 7);
strnwscpy(resname, inbuf+29, 7);
strnwscpy(name, inbuf+38, 7);
strnwscpy(atype, inbuf+47, 4);
*resid = atoi(inbuf+20);
*q = (float) atof(inbuf+52);
*m = (float) atof(inbuf+68);
} else {
strnwscpy(segname, inbuf+9, 4);
strnwscpy(resname, inbuf+19, 4);
strnwscpy(name, inbuf+24, 4);
strnwscpy(atype, inbuf+29, 4);
*resid = atoi(inbuf+13);
*q = (float) atof(inbuf+34);
*m = (float) atof(inbuf+50);
}
#if 0
/* if this is a Charmm31 PSF file, there may be two extra */
/* columns containing polarizable force field data. */
if (psf->charmmcheq) {
/* do something to read in these columns here */
}
#endif
return num;
}
/* Read in the next atom info into the given storage areas; this assumes
that file has already been moved to the beginning of the atom records.
Returns the serial number of the atom. If there is an error, returns -1.*/
static int get_psf_atom(FILE *f, char *name, char *atype, char *resname,
char *segname, int *resid, float *q, float *m,
int namdfmt, int charmmext, int charmmdrude) {
char inbuf[PSF_RECORD_LENGTH+2];
int num;
if (inbuf != fgets(inbuf, PSF_RECORD_LENGTH+1, f)) {
return(-1); /* failed to read in an atom */
}
if (strlen(inbuf) < 50) {
fprintf(stderr, "Line too short in psf file: \n%s\n", inbuf);
return -1;
}
num = atoi(inbuf); /* atom index */
if (namdfmt == 1) {
/* XXX We should add field width limits here so that */
/* a PSF file with crazy wide fields cannot overwrite */
/* destination buffers. */
int cnt;
cnt = sscanf(inbuf, "%d %s %d %s %s %s %f %f",
&num, segname, resid, resname, name, atype, q, m);
if (cnt != 8) {
printf("psfplugin) Failed to parse atom line in NAMD PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
} else if (charmmdrude == 1) {
/* CHARMM PSF format is (if DRUDE and CHEQ are enabled):
* '(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)'
*/
strnwscpy(segname, inbuf+11, 7);
strnwscpy(resname, inbuf+29, 7);
strnwscpy(name, inbuf+38, 7);
strnwscpy(atype, inbuf+47, 4);
*resid = atoi(inbuf+20);
*q = (float) atof(inbuf+52);
*m = (float) atof(inbuf+68);
// data we don't currently read:
// *imove = atoi(inbuf+84);
// *alphadp = atof(inbuf+92);
// *tholei = atof(inbuf+108);
} else if (charmmext == 1) {
/* CHARMM PSF format is (if CMAP and CHEQ are also enabled):
* '(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)'
*/
strnwscpy(segname, inbuf+11, 7);
strnwscpy(resname, inbuf+29, 7);
strnwscpy(name, inbuf+38, 7);
strnwscpy(atype, inbuf+47, 4);
*resid = atoi(inbuf+20);
*q = (float) atof(inbuf+52);
*m = (float) atof(inbuf+68);
} else {
/* CHARMM PSF format is
* '(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8)'
*/
strnwscpy(segname, inbuf+9, 4);
strnwscpy(resname, inbuf+19, 4);
strnwscpy(name, inbuf+24, 4);
strnwscpy(atype, inbuf+29, 4);
*resid = atoi(inbuf+13);
*q = (float) atof(inbuf+34);
*m = (float) atof(inbuf+50);
}
#if 0
/* if this is a Charmm31 PSF file, there may be two extra */
/* columns containing polarizable force field data. */
if (psf->charmmcheq) {
/* do something to read in these columns here */
}
#endif
return num;
}
/* Read in the next atom info into the given storage areas; this assumes
that file has already been moved to the beginning of the atom records.
Returns the serial number of the atom. If there is an error, returns -1.*/
static int get_psf_atom(FILE *f, char *name, char *atype, char *resname,
char *segname, int *resid, char *insertion, float *q, float *m,
int namdfmt, int charmmext, int charmmdrude) {
char inbuf[PSF_RECORD_LENGTH+2];
int num;
if (inbuf != fgets(inbuf, PSF_RECORD_LENGTH+1, f)) {
return(-1); /* failed to read in an atom */
}
if (strlen(inbuf) < 50) {
fprintf(stderr, "Line too short in psf file: \n%s\n", inbuf);
return -1;
}
num = atoi(inbuf); /* atom index */
if (namdfmt == 1) {
int cnt, rcnt;
char residstr[8], trash;
cnt = sscanf(inbuf, "%d %7s %7s %7s %7s %7s %f %f",
&num, segname, residstr, resname, name, atype, q, m);
insertion[0] = ' '; insertion[1] = '\0';
rcnt = sscanf(residstr, "%d%c%c", resid, insertion, &trash);
if (cnt != 8 || rcnt < 1 || rcnt > 2) {
printf("psfplugin) Failed to parse atom line in NAMD PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
} else if (charmmdrude == 1 || charmmext == 1) {
int xplorshift;
/* CHARMM PSF format is (if DRUDE or (?) CHEQ are enabled):
* '(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)'
*/
if ( inbuf[10] != ' ' ||
inbuf[19] != ' ' ||
inbuf[28] != ' ' ||
inbuf[37] != ' ' ||
inbuf[46] != ' ' ) {
printf("psfplugin) Failed to parse atom line in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
strnwscpy(segname, inbuf+11, 7);
strnwscpy(resname, inbuf+29, 7);
strnwscpy(name, inbuf+38, 7);
xplorshift = 0;
strnwscpy(atype, inbuf+47, 4);
if ( ! isdigit(atype[0]) ) {
strnwscpy(atype, inbuf+47, 6);
xplorshift = 2;
}
if ( inbuf[51+xplorshift] != ' ' ) {
printf("psfplugin) Failed to parse atom line in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
insertion[0] = ' '; insertion[1] = '\0';
sscanf(inbuf+20, "%d%c", resid, insertion);
*q = (float) atof(inbuf+52+xplorshift);
*m = (float) atof(inbuf+66+xplorshift);
// data we don't currently read:
// if (charmmdrude == 1) {
// *imove = atoi(inbuf+80+xplorshift);
// *alphadp = atof(inbuf+88+xplorshift);
// *tholei = atof(inbuf+102+xplorshift);
// }
} else {
/* CHARMM PSF format is
* '(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8)'
*/
const char *rdbuf = inbuf;
char intbuf[16];
intbuf[0] = '\0';
rdbuf += strnwscpy_shift(intbuf, rdbuf, 8, 10);
if ( rdbuf[8] != ' ' ) {
printf("psfplugin) Failed to parse atom index in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
rdbuf += strnwscpy_shift(segname, rdbuf+9, 4, 7);
if ( rdbuf[13] != ' ' ) {
printf("psfplugin) Failed to parse segname in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
intbuf[0] = '\0';
rdbuf += strnwscpy_shift(intbuf, rdbuf+14, 4, 8);
insertion[0] = ' '; insertion[1] = '\0';
sscanf(intbuf, "%d%c", resid, insertion);
if ( rdbuf[18] != ' ' ) {
printf("psfplugin) Failed to parse resid in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
rdbuf += strnwscpy_shift(resname, rdbuf+19, 4, 7);
if ( rdbuf[23] != ' ' ) {
printf("psfplugin) Failed to parse resname in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
rdbuf += strnwscpy_shift(name, rdbuf+24, 4, 7);
if ( rdbuf[28] != ' ' ) {
printf("psfplugin) Failed to parse atom name in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
rdbuf += strnwscpy_shift(atype, rdbuf+29, 4, 7);
if ( rdbuf[33] != ' ' ) {
printf("psfplugin) Failed to parse atom type in PSF file:\n");
printf("psfplugin) '%s'\n", inbuf);
return -1;
}
*q = (float) atof(rdbuf+34);
*m = (float) atof(rdbuf+48);
}
#if 0
/* if this is a Charmm31 PSF file, there may be two extra */
/* columns containing polarizable force field data. */
if (psf->charmmcheq) {
/* do something to read in these columns here */
}
#endif
return num;
}
