void gmx_fio_rewind(int fio)
{
gmx_fio_check(fio);
if (FIO[fio].xdr) {
xdrclose(FIO[fio].xdr);
/* File is always opened as binary by xdropen */
xdropen(FIO[fio].xdr,FIO[fio].fn,FIO[fio].bRead ? "r" : "w");
}
else
frewind(FIO[fio].fp);
}
bool XtcFileFormat::read(std::istream &input, chemkit::TrajectoryFile *file)
{
// read data into temporary file
QTemporaryFile dataFile;
dataFile.open();
unsigned int dataSize = 0;
for(;;){
char c = input.get();
if(input.eof()){
break;
}
dataFile.write(&c, 1);
dataSize++;
}
dataFile.close();
XDR xdrs;
xdropen(&xdrs, dataFile.fileName().toAscii().constData(), "r");
chemkit::Trajectory *trajectory = new chemkit::Trajectory;
while(xdr_getpos(&xdrs) < dataSize){
// read magic (should be '1995')
int magic = 0;
xdr_int(&xdrs, &magic);
if(magic != 1995){
break;
}
// create new frame
chemkit::TrajectoryFrame *frame = trajectory->addFrame();
// read atom count
int atomCount = 0;
xdr_int(&xdrs, &atomCount);
// read frame number
int frameNumber = 0;
xdr_int(&xdrs, &frameNumber);
// read time
float time = 0;
xdr_float(&xdrs, &time);
// read unit cell
float box[3][3];
for(int i = 0; i < 3; i++){
for(int j = 0; j < 3; j++){
xdr_float(&xdrs, &box[i][j]);
}
}
chemkit::Vector3 x(box[0][0], box[0][1], box[0][2]);
chemkit::Vector3 y(box[1][0], box[1][1], box[1][2]);
chemkit::Vector3 z(box[2][0], box[2][1], box[2][2]);
frame->setUnitCell(new chemkit::UnitCell(x * 10, y * 10, z * 10));
// read coordinates
float coordinateData[3 * atomCount];
float precision = 1000.0f;
xdr3dfcoord(&xdrs, coordinateData, &atomCount, &precision);
chemkit::Coordinates coordinates(atomCount);
for(int i = 0; i < atomCount; i++){
// multiply each coordinate by 10 to convert
// from nanometers to angstroms
chemkit::Point3 position(coordinateData[i*3+0] * 10,
coordinateData[i*3+1] * 10,
coordinateData[i*3+2] * 10);
coordinates.setPosition(i, position);
}
frame->setCoordinates(&coordinates);
}
xdrclose(&xdrs);
if(trajectory->isEmpty()){
delete trajectory;
return false;
}
file->setTrajectory(trajectory);
return true;
}
/*****************************************************************
*
* EXPORTED SECTION
*
*****************************************************************/
int gmx_fio_open(const char *fn,const char *mode)
{
t_fileio *fio=NULL;
int i,nfio=0;
char *bf,newmode[5];
bool bRead;
int xdrid;
if (fn2ftp(fn)==efTPA)
{
strcpy(newmode,mode);
}
else
{
if (mode[0]=='r')
{
strcpy(newmode,"r");
}
else if (mode[0]=='w')
{
strcpy(newmode,"w");
}
else if (mode[0]=='a')
{
strcpy(newmode,"a");
}
else
{
gmx_fatal(FARGS,"DEATH HORROR in gmx_fio_open, mode is '%s'",mode);
}
}
/* Check if it should be opened as a binary file */
if (strncmp(ftp2ftype(fn2ftp(fn)),"ASCII",5))
{
/* Not ascii, add b to file mode */
if ((strchr(newmode,'b')==NULL) && (strchr(newmode,'B')==NULL))
{
strcat(newmode,"b");
}
}
/* Determine whether we have to make a new one */
for(i=0; (i<nFIO); i++)
{
if (!FIO[i].bOpen)
{
fio = &(FIO[i]);
nfio = i;
break;
}
}
if (i == nFIO)
{
nFIO++;
srenew(FIO,nFIO);
fio = &(FIO[nFIO-1]);
nfio = nFIO-1;
}
bRead = (newmode[0]=='r');
fio->fp = NULL;
fio->xdr = NULL;
if (fn)
{
fio->iFTP = fn2ftp(fn);
fio->fn = strdup(fn);
fio->bStdio = FALSE;
/* If this file type is in the list of XDR files, open it like that */
if (in_ftpset(fio->iFTP,asize(ftpXDR),ftpXDR))
{
/* First check whether we have to make a backup,
* only for writing, not for read or append.
*/
if (newmode[0]=='w')
{
#ifndef GMX_FAHCORE
/* only make backups for normal gromacs */
if (gmx_fexist(fn))
{
bf=(char *)backup_fn(fn);
if (rename(fn,bf) == 0)
{
fprintf(stderr,"\nBack Off! I just backed up %s to %s\n",fn,bf);
}
else
{
fprintf(stderr,"Sorry, I couldn't backup %s to %s\n",fn,bf);
}
}
#endif
}
else
{
/* Check whether file exists */
if (!gmx_fexist(fn))
{
gmx_open(fn);
}
}
snew(fio->xdr,1);
xdrid = xdropen(fio->xdr,fn,newmode);
if (xdrid == 0)
{
if(newmode[0]=='r')
gmx_fatal(FARGS,"Cannot open file %s for reading\nCheck permissions if it exists.",fn);
else
gmx_fatal(FARGS,"Cannot open file %s for writing.\nCheck your permissions, disk space and/or quota.",fn);
}
fio->fp = xdr_get_fp(xdrid);
}
else
{
/* If it is not, open it as a regular file */
fio->fp = ffopen(fn,newmode);
}
}
else
{
/* Use stdin/stdout for I/O */
fio->iFTP = efTPA;
fio->fp = bRead ? stdin : stdout;
fio->fn = strdup("STDIO");
fio->bStdio = TRUE;
}
fio->bRead = bRead;
fio->bDouble= (sizeof(real) == sizeof(double));
fio->bDebug = FALSE;
fio->bOpen = TRUE;
return nfio;
}
