static PyObject *
__read_next_frame(PyObject *self, PyObject *args)
{
dcdhandle *dcd;
PyObject *temp;
PyArrayObject *x, *y, *z, *uc;
int skip=1;
int rc,numskip;
float* unitcell;
float alpha, beta, gamma;
if (!self) {
/* we were in fact called as a module function, try to retrieve
a matching object from args */
if( !PyArg_ParseTuple(args, "OO!O!O!O!|i", &self, &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc, &skip) )
return NULL;
} else {
/* we were obviously called as an object method so args should
only have the int value. */
if( !PyArg_ParseTuple(args, "O!O!O!O!|i", &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc, &skip) )
return NULL;
}
if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
// Raise exception
PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
return NULL;
}
dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
Py_DECREF(temp);
unitcell = (float*) uc->data;
unitcell[0] = unitcell[2] = unitcell[5] = 0.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
/* Check for EOF here; that way all EOF's encountered later must be errors */
if (dcd->setsread == dcd->nsets) {
// Is this an exception?
PyErr_SetString(PyExc_IOError, "End of file reached for dcd file");
return NULL;
//return MOLFILE_EOF;
}
if (skip > 1) {
if (dcd->first && dcd->nfixed) {
/* We can't just skip it because we need the fixed atom coordinates */
rc = read_dcdstep(dcd->fd, dcd->natoms, (float*)x->data, (float*)y->data, (float*)z->data,
unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error reading first frame from DCD file");
//fprintf(stderr, "read_dcdstep returned %d\n", rc);
return NULL;
//return MOLFILE_ERROR;
}
dcd->setsread++;
temp = Py_BuildValue("i", dcd->setsread);
return temp;
//return rc; /* XXX this needs to be updated */
}
dcd->first = 0;
// Figure out how many steps to skip
numskip = skip - (dcd->setsread % skip) - 1;
/* XXX this needs to be changed */
rc = skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm, numskip);
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error skipping frame from DCD file");
//fprintf(stderr, "read_dcdstep returned %d\n", rc);
return NULL;
//return MOLFILE_ERROR;
}
dcd->setsread+=numskip;
}
rc = read_dcdstep(dcd->fd, dcd->natoms, (float*)x->data, (float*)y->data, (float*)z->data, unitcell,
dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
dcd->setsread++;
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
//fprintf(stderr, "read_dcdstep returned %d\n", rc);
return NULL;
//return MOLFILE_ERROR;
}
if (unitcell[1] >= -1.0 && unitcell[1] <= 1.0 &&
unitcell[3] >= -1.0 && unitcell[3] <= 1.0 &&
unitcell[4] >= -1.0 && unitcell[4] <= 1.0) {
/* This file was generated by Charmm, or by NAMD > 2.5, with the angle */
/* cosines of the periodic cell angles written to the DCD file. */
/* This formulation improves rounding behavior for orthogonal cells */
/* so that the angles end up at precisely 90 degrees, unlike acos(). */
/* (changed in MDAnalysis 0.9.0 to have NAMD ordering of the angles; */
/* see Issue 187) */
alpha = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2;
beta = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2;
gamma = 90.0 - asin(unitcell[1]) * 90.0 / M_PI_2;
} else {
/* This file was likely generated by NAMD 2.5 and the periodic cell */
/* angles are specified in degrees rather than angle cosines. */
alpha = unitcell[4];
beta = unitcell[3];
gamma = unitcell[1];
}
unitcell[4] = alpha;
unitcell[3] = beta;
unitcell[1] = gamma;
// Return the frame read
temp = Py_BuildValue("i", dcd->setsread);
return temp;
}
static int read_next_timestep(void *v, int natoms, molfile_timestep_t *ts) {
dcdhandle *dcd;
int i, j, rc;
float unitcell[6];
unitcell[0] = unitcell[2] = unitcell[5] = 1.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
dcd = (dcdhandle *)v;
/* Check for EOF here; that way all EOF's encountered later must be errors */
if (dcd->setsread == dcd->nsets) return MOLFILE_EOF;
dcd->setsread++;
if (!ts) {
if (dcd->first && dcd->nfixed) {
/* We can't just skip it because we need the fixed atom coordinates */
rc = read_dcdstep(dcd->fd, dcd->natoms, dcd->x, dcd->y, dcd->z,
unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
return rc; /* XXX this needs to be updated */
}
dcd->first = 0;
/* XXX this needs to be changed */
return skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm);
}
rc = read_dcdstep(dcd->fd, dcd->natoms, dcd->x, dcd->y, dcd->z, unitcell,
dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
if (rc < 0) {
print_dcderror("read_dcdstep", rc);
return MOLFILE_ERROR;
}
/* copy timestep data from plugin-local buffers to VMD's buffer */
/* XXX
* This code is still the root of all evil. Just doing this extra copy
* cuts the I/O rate of the DCD reader from 728 MB/sec down to
* 394 MB/sec when reading from a ram filesystem.
* For a physical disk filesystem, the I/O rate goes from
* 187 MB/sec down to 122 MB/sec. Clearly this extra copy has to go.
*/
{
int natoms = dcd->natoms;
float *nts = ts->coords;
const float *bufx = dcd->x;
const float *bufy = dcd->y;
const float *bufz = dcd->z;
for (i=0, j=0; i<natoms; i++, j+=3) {
nts[j ] = bufx[i];
nts[j + 1] = bufy[i];
nts[j + 2] = bufz[i];
}
}
ts->A = unitcell[0];
ts->B = unitcell[2];
ts->C = unitcell[5];
if (unitcell[1] >= -1.0 && unitcell[1] <= 1.0 &&
unitcell[3] >= -1.0 && unitcell[3] <= 1.0 &&
unitcell[4] >= -1.0 && unitcell[4] <= 1.0) {
/* This file was generated by CHARMM, or by NAMD > 2.5, with the angle */
/* cosines of the periodic cell angles written to the DCD file. */
/* This formulation improves rounding behavior for orthogonal cells */
/* so that the angles end up at precisely 90 degrees, unlike acos(). */
ts->alpha = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2; /* cosBC */
ts->beta = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2; /* cosAC */
ts->gamma = 90.0 - asin(unitcell[1]) * 90.0 / M_PI_2; /* cosAB */
} else {
/* This file was likely generated by NAMD 2.5 and the periodic cell */
/* angles are specified in degrees rather than angle cosines. */
ts->alpha = unitcell[4]; /* angle between B and C */
ts->beta = unitcell[3]; /* angle between A and C */
ts->gamma = unitcell[1]; /* angle between A and B */
}
return MOLFILE_SUCCESS;
}
static PyObject *
__read_timeseries(PyObject *self, PyObject *args)
{
PyObject *temp = NULL;
PyArrayObject *coord = NULL;
PyListObject *atoms = NULL;
int lowerb = 0, upperb = 0, range=0;
float *tempX = NULL, *tempY = NULL, *tempZ = NULL;
int rc;
int i, j, index;
int n_atoms = 0, n_frames = 0;
/* Stop = -1 is incorrect and causes an error, look for a fix of this in line
469 */
int start = 0, stop = -1, step = 1, numskip = 0, remaining_frames=0;
dcdhandle *dcd = NULL;
int *atomlist = NULL;
npy_intp dimensions[3];
float unitcell[6];
const char* format = "afc";
if (!self) {
/* we were in fact called as a module function, try to retrieve
a matching object from args */
if( !PyArg_ParseTuple(args, "OO!|iiis", &self, &PyList_Type, &atoms, &start, &stop, &step, &format) )
return NULL;
} else {
/* we were obviously called as an object method so args should
only have the int value. */
if( !PyArg_ParseTuple(args, "O!|iiis", &PyList_Type, &atoms, &start, &stop, &step, &format) )
return NULL;
}
if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
// Raise exception
PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
return NULL;
}
dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
Py_DECREF(temp);
n_frames = ((stop-start) / step);
if ((stop-start) % step > 0) { n_frames++; }
//n_frames = dcd->nsets / skip;
n_atoms = PyList_Size((PyObject*)atoms);
if (n_atoms == 0) {
PyErr_SetString(PyExc_Exception, "No atoms passed into _read_timeseries function");
return NULL;
}
atomlist = (int*)malloc(sizeof(int)*n_atoms);
memset(atomlist, 0, sizeof(int)*n_atoms);
// Get the atom indexes
for (i=0;i<n_atoms;i++) {
temp = PyList_GetItem((PyObject*)atoms, i); // Borrowed Reference
if (temp==NULL) goto error;
// Make sure temp is an integer
/* TODO: this is not the proper check but [OB] cannot figure out how
to check if this is a numpy.int64 or similar; PyInt_Check would fail
on those (Issue 18)
*/
if (!PyArray_IsAnyScalar((PyObject*)temp)) {
PyErr_SetString(PyExc_ValueError, "Atom number is not an integer");
goto error;
}
atomlist[i] = PyInt_AsLong(temp);
}
lowerb = atomlist[0]; upperb = atomlist[n_atoms-1];
range = upperb-lowerb+1;
// Figure out the format string
if (strncasecmp(format, "afc", 3) == 0) {
dimensions[0] = n_atoms; dimensions[1] = n_frames; dimensions[2] = 3;
} else if (strncasecmp(format, "acf", 3) == 0) {
dimensions[0] = n_atoms; dimensions[1] = 3; dimensions[2] = n_frames;
} else if (strncasecmp(format, "fac", 3) == 0) {
dimensions[0] = n_frames; dimensions[1] = n_atoms; dimensions[2] = 3;
} else if (strncasecmp(format, "fca", 3) == 0) {
dimensions[0] = n_frames; dimensions[1] = 3; dimensions[2] = n_atoms;
} else if (strncasecmp(format, "caf", 3) == 0) {
dimensions[0] = 3; dimensions[1] = n_atoms; dimensions[2] = n_frames;
} else if (strncasecmp(format, "cfa", 3) == 0) {
dimensions[0] = 3; dimensions[1] = n_frames; dimensions[2] = n_atoms;
}
coord = (PyArrayObject*) PyArray_SimpleNew(3, dimensions, NPY_DOUBLE);
if (coord == NULL) goto error;
// Reset trajectory
rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
dcd->setsread = 0;
dcd->first = 1;
// Jump to starting frame
jump_to_frame(dcd, start);
// Now read through trajectory and get the atom pos
tempX = (float*)malloc(sizeof(float)*range);
tempY = (float*)malloc(sizeof(float)*range);
tempZ = (float*)malloc(sizeof(float)*range);
if ((tempX == NULL) | (tempY == NULL) || (tempZ == NULL)) {
PyErr_SetString(PyExc_MemoryError, "Can't allocate temporary space for coordinate arrays");
goto error;
}
remaining_frames = stop-start;
for (i=0;i<n_frames;i++) {
if (step > 1 && i>0) {
// Check if we have fixed atoms
// XXX not done
/* Figure out how many steps to step over, if step = n, np array
slicing treats this as skip over n-1, read the nth. */
numskip = step -1;
/* If the number to skip is greater than the number of frames left
to be jumped over, just take one more step to reflect np slicing
if there is a remainder, guaranteed to have at least one more
frame.
*/
if(remaining_frames < numskip){
numskip = 1;
}
rc = skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm, numskip);
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error skipping frame from DCD file");
goto error;
}
}
// on first iteration, numskip == 0, first set is always read.
dcd->setsread += numskip;
//now read from subset
rc = read_dcdsubset(dcd->fd, dcd->natoms, lowerb, upperb, tempX, tempY, tempZ,
unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
dcd->setsread++;
remaining_frames = stop - dcd->setsread;
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
goto error;
}
// Copy into Numeric array only those atoms we are interested in
for (j=0;j<n_atoms;j++) {
index = atomlist[j]-lowerb;
/*
* coord[a][b][c] = *(float*)(coord->data + a*coord->strides[0] + b*coord->strides[1] + c*coord->strides[2])
*/
if (strncasecmp(format, "afc", 3) == 0) {
*(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
*(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
*(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "acf", 3) == 0) {
*(double*)(coord->data + j*coord->strides[0] + 0*coord->strides[1] + i*coord->strides[2]) = tempX[index];
*(double*)(coord->data + j*coord->strides[0] + 1*coord->strides[1] + i*coord->strides[2]) = tempY[index];
*(double*)(coord->data + j*coord->strides[0] + 2*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "fac", 3) == 0) {
*(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
*(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
*(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "fca", 3) == 0) {
*(double*)(coord->data + i*coord->strides[0] + 0*coord->strides[1] + j*coord->strides[2]) = tempX[index];
*(double*)(coord->data + i*coord->strides[0] + 1*coord->strides[1] + j*coord->strides[2]) = tempY[index];
*(double*)(coord->data + i*coord->strides[0] + 2*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "caf", 3) == 0) {
*(double*)(coord->data + 0*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempX[index];
*(double*)(coord->data + 1*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempY[index];
*(double*)(coord->data + 2*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "cfa", 3) == 0) {
*(double*)(coord->data + 0*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempX[index];
*(double*)(coord->data + 1*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempY[index];
*(double*)(coord->data + 2*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
}
}
// Check if we've been interupted by the user
if (PyErr_CheckSignals() == 1) goto error;
}
// Reset trajectory
rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
dcd->setsread = 0;
dcd->first = 1;
free(atomlist);
free(tempX);
free(tempY);
free(tempZ);
return PyArray_Return(coord);
error:
// Reset trajectory
rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
dcd->setsread = 0;
dcd->first = 1;
Py_XDECREF(coord);
if (atomlist != NULL) free(atomlist);
if (tempX != NULL) free(tempX);
if (tempY != NULL) free(tempY);
if (tempZ != NULL) free(tempZ);
return NULL;
}
