def xtc_coords(filename,idxs=None):
""" Get the coordinates """
try:
import xdrfile.libxdrfile2 as libxdr
except ImportError:
raise ImportError("libxdrfile2 library needed for xtc trajectories!")
file = libxdr.xdrfile_open(filename, "r")
natoms = libxdr.read_xtc_natoms(filename)
nframes, offsets = libxdr.read_xtc_numframes(filename)
box = np.zeros((3,3),dtype=np.float32)
config = np.zeros((natoms,3),dtype=np.float32)
if idxs is not None:
# Seek to read frames specified by idxs.
nframes = len(idxs)
coords = np.zeros((nframes,3,natoms),dtype="float")
for i in xrange(nframes):
libxdr.xdr_seek(file,offsets[idxs[i]],0)
status,step,timestmp,prec = libxdr.read_xtc(file, box, config)
coords[i,:,:] = config.astype("float").T
else:
coords = np.zeros((nframes,3,natoms),dtype=np.float32)
status = libxdr.exdrOK
i = 0
while status == libxdr.exdrOK:
status,step,timestmp,prec = libxdr.read_xtc(file, box, config)
coords[i,:,:] = config.astype("float").T
i += 1
libxdr.xdrfile_close(file)
return coords
def read(self):
assert self.model != None, "# Model uninitialized. call parse before read!"
# read pdb
if self.xtc == None:
data = []
for line in self.fh:
at = line[0:6].strip()
if at == "ATOM" or at == "HETATM":
vv = [float(line[30:38]), float(line[38:46]), float(line[46:54])]
data.append(vv)
if at == "ENDMDL":
self.model.set_coords(np.array(data))
self.time += 1
# return step
return self.time
self.fh.close()
return -1
# read xtc
else:
coords = np.zeros((self.natoms, 3), dtype=np.float32)
box = np.zeros((3, 3), dtype=np.float32)
status, step, time, prec = libxdrfile2.read_xtc(self.xtc, box, coords)
self.model.set_coords(10.0 * coords)
if status:
libxdrfile2.xdrfile_close(self.xtc)
return -1
else:
return time
def next(self):
status = libxdr.read_xtc(self.file, self.box, self.config)[0]
return np.array(self.config, copy=True, dtype=np.float64), status
def _read(self, fp, box, x):
status, step, ftime, prec = libxdrfile2.read_xtc(fp, box, x)
return status, step, ftime
def _read( self, fp, box, x ):
status, step, ftime, prec = libxdrfile2.read_xtc( fp, box, x )
return status, step, ftime
def next(self):
status = libxdr.read_xtc(self.file, self.box, self.config)[0]
return np.array(self.config,copy=True,dtype=np.float64), status
