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);
}
int
gmx_fio_close(int fio)
{
int rc = 0;
gmx_fio_check(fio);
if (in_ftpset(FIO[fio].iFTP,asize(ftpXDR),ftpXDR)) {
rc = !xdrclose(FIO[fio].xdr); /* xdrclose returns 1 if happy, negate it */
sfree(FIO[fio].xdr);
}
else {
/* Don't close stdin and stdout! */
if (!FIO[fio].bStdio)
rc = fclose(FIO[fio].fp); /* fclose returns 0 if happy */
}
sfree(FIO[fio].fn);
FIO[fio].bOpen = FALSE;
do_read = do_dummy;
do_write = do_dummy;
return rc;
}
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;
}
