static void *open_dcd_read(const char *path, const char *filetype,
int *natoms) {
dcdhandle *dcd;
fio_fd fd;
int rc;
struct stat stbuf;
if (!path) return NULL;
/* See if the file exists, and get its size */
memset(&stbuf, 0, sizeof(struct stat));
if (stat(path, &stbuf)) {
printf("dcdplugin) Could not access file '%s'.\n", path);
return NULL;
}
if (fio_open(path, FIO_READ, &fd) < 0) {
printf("dcdplugin) Could not open file '%s' for reading.\n", path);
return NULL;
}
dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
memset(dcd, 0, sizeof(dcdhandle));
dcd->fd = fd;
if ((rc = read_dcdheader(dcd->fd, &dcd->natoms, &dcd->nsets, &dcd->istart,
&dcd->nsavc, &dcd->delta, &dcd->nfixed, &dcd->freeind,
&dcd->fixedcoords, &dcd->reverse, &dcd->charmm))) {
print_dcderror("read_dcdheader", rc);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
/*
* Check that the file is big enough to really hold the number of sets
* it claims to have. Then we'll use nsets to keep track of where EOF
* should be.
*/
{
fio_size_t ndims, firstframesize, framesize, extrablocksize;
fio_size_t trjsize, filesize, curpos;
int newnsets;
extrablocksize = dcd->charmm & DCD_HAS_EXTRA_BLOCK ? 48 + 8 : 0;
ndims = dcd->charmm & DCD_HAS_4DIMS ? 4 : 3;
firstframesize = (dcd->natoms+2) * ndims * sizeof(float) + extrablocksize;
framesize = (dcd->natoms-dcd->nfixed+2) * ndims * sizeof(float)
+ extrablocksize;
/*
* It's safe to use ftell, even though ftell returns a long, because the
* header size is < 4GB.
*/
curpos = fio_ftell(dcd->fd); /* save current offset (end of header) */
#if defined(_MSC_VER) && defined(FASTIO_NATIVEWIN32)
/* the stat() call is not 64-bit savvy on Windows */
/* so we have to use the fastio fseek/ftell routines for this */
/* until we add a portable filesize routine for this purpose */
fio_fseek(dcd->fd, 0, FIO_SEEK_END); /* seek to end of file */
filesize = fio_ftell(dcd->fd);
fio_fseek(dcd->fd, curpos, FIO_SEEK_SET); /* return to end of header */
#else
filesize = stbuf.st_size; /* this works ok on Unix machines */
#endif
trjsize = filesize - curpos - firstframesize;
if (trjsize < 0) {
printf("dcdplugin) file '%s' appears to contain no timesteps.\n", path);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
newnsets = trjsize / framesize + 1;
if (dcd->nsets > 0 && newnsets != dcd->nsets) {
printf("dcdplugin) Warning: DCD header claims %d frames, file size indicates there are actually %d frames\n", dcd->nsets, newnsets);
}
dcd->nsets = newnsets;
dcd->setsread = 0;
}
dcd->first = 1;
dcd->x = (float *)malloc(dcd->natoms * sizeof(float));
dcd->y = (float *)malloc(dcd->natoms * sizeof(float));
dcd->z = (float *)malloc(dcd->natoms * sizeof(float));
if (!dcd->x || !dcd->y || !dcd->z) {
printf("dcdplugin) Unable to allocate space for %d atoms.\n", dcd->natoms);
if (dcd->x)
free(dcd->x);
if (dcd->y)
free(dcd->y);
if (dcd->z)
free(dcd->z);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
*natoms = dcd->natoms;
return dcd;
}
static PyObject *
__read_dcd_header(PyObject *self, PyObject *args)
{
/* At this point we assume the file has been checked for existence and opened, and the DCD class
* contains a reference to the file (which can be used to retrieve the file descriptor)
*/
PyObject *temp;
fio_fd fd;
int rc;
char *remarks = NULL;
int len_remarks = 0;
dcdhandle *dcd = NULL;
if (! self) {
/* we were in fact called as a module function, try to retrieve
a matching object from args */
if( !PyArg_ParseTuple(args, "O", &self) )
return NULL;
} else {
/* we were obviously called as an object method so args should
only have the int value. */
if( !PyArg_ParseTuple(args, "") )
return NULL;
}
// Get the file object from the class
if (!PyObject_HasAttrString(self, "dcdfile")) {
// Raise exception
PyErr_SetString(PyExc_AttributeError, "dcdfile is not an attribute");
return NULL;
}
if ((temp = PyObject_GetAttrString(self, "dcdfile")) == NULL) { // This gives me a New Reference
// Raise exception
PyErr_SetString(PyExc_AttributeError, "dcdfile is not an attribute");
return NULL;
}
if (!PyFile_CheckExact(temp)) {
// Raise exception
PyErr_SetString(PyExc_TypeError, "dcdfile does not refer to a file object");
goto error;
}
fd = fileno(PyFile_AsFile(temp));
// No longer need the reference to temp
Py_DECREF(temp);
dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
memset(dcd, 0, sizeof(dcdhandle));
dcd->fd = fd;
if ((rc = read_dcdheader(dcd->fd, &dcd->natoms, &dcd->nsets, &dcd->istart,
&dcd->nsavc, &dcd->delta, &dcd->nfixed, &dcd->freeind,
&dcd->fixedcoords, &dcd->reverse, &dcd->charmm, &remarks, &len_remarks))) {
// Raise exception
PyErr_SetString(PyExc_IOError, "Cannot read DCD header");
goto error;
}
/*
* Check that the file is big enough to really hold all the frames it claims to have
*/
{
off_t ndims, firstframesize, framesize, extrablocksize;
off_t filesize;
struct stat stbuf;
extrablocksize = dcd->charmm & DCD_HAS_EXTRA_BLOCK ? 48 + 8 : 0;
ndims = dcd->charmm & DCD_HAS_4DIMS ? 4 : 3;
firstframesize = (dcd->natoms+2) * ndims * sizeof(float) + extrablocksize;
framesize = (dcd->natoms-dcd->nfixed+2) * ndims * sizeof(float)
+ extrablocksize;
// Get filesize from file descriptor
memset(&stbuf, 0, sizeof(struct stat));
if (fstat(dcd->fd, &stbuf)) {
PyErr_SetString(PyExc_IOError, "Could not stat file");
goto error;
}
// Size of header
dcd->header_size = fio_ftell(dcd->fd);
/*
* It's safe to use ftell, even though ftell returns a long, because the
* header size is < 4GB.
*/
filesize = stbuf.st_size - fio_ftell(dcd->fd) - firstframesize;
if (filesize < 0) {
PyErr_SetString(PyExc_IOError, "DCD file appears to contain no timesteps");
goto error;
}
dcd->nsets = filesize / framesize + 1;
dcd->setsread = 0;
}
// We are at the first frame
dcd->first = 1;
temp = Py_BuildValue("s#", remarks, len_remarks);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "remarks", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute remarks");
goto error;
}
Py_DECREF(temp);
temp = Py_BuildValue("i", dcd->natoms);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "n_atoms", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute n_atoms");
goto error;
}
Py_DECREF(temp);
temp = Py_BuildValue("i", dcd->nsets);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "n_frames", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute n_frames");
goto error;
}
Py_DECREF(temp);
temp = Py_BuildValue("i", dcd->nfixed);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "fixed", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute fixed");
goto error;
}
Py_DECREF(temp);
temp = Py_BuildValue("i", dcd->istart);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "start_timestep", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute fixed");
goto error;
}
Py_DECREF(temp);
temp = Py_BuildValue("i", dcd->nsavc);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "skip_timestep", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute fixed");
goto error;
}
Py_DECREF(temp);
temp = Py_BuildValue("d", dcd->delta);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "delta", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute fixed");
goto error;
}
Py_DECREF(temp);
temp = PyCObject_FromVoidPtr(dcd, NULL);
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "_dcd_C_ptr", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute _dcd_C_ptr");
goto error;
}
if ((dcd->charmm & DCD_IS_CHARMM) && (dcd->charmm & DCD_HAS_EXTRA_BLOCK)) {
dcd->with_unitcell = 1;
temp = Py_True;
} else {
temp = Py_False;
}
Py_INCREF(temp);
if (PyObject_SetAttrString(self, "periodic", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute periodic");
goto error;
}
Py_DECREF(temp);
// For debugging purposes
temp = PyBuffer_FromMemory(dcd, sizeof(dcdhandle));
if (temp == NULL) goto error;
if (PyObject_SetAttrString(self, "_dcd_C_str", temp) == -1) {
PyErr_SetString(PyExc_AttributeError, "Could not create attribute _dcd_C_str");
goto error;
}
Py_DECREF(temp);
Py_INCREF(Py_None);
return Py_None;
error:
Py_XDECREF(temp);
if (dcd != NULL) free(dcd);
if (remarks != NULL) free(remarks);
return NULL;
}
