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 __init__(self, file_name):
self.file_name = str(file_name)
self.xdr_fp = libxdrfile2.xdrfile_open(self.file_name, "rb")
self.numatoms = self._read_natoms(self.file_name)
self.update()
# allocate coordinate array of the right size and type
self.x = np.zeros((self.numatoms, libxdrfile2.DIM), dtype=np.float32)
# allocate unit cell box
self.box = np.zeros((libxdrfile2.DIM, libxdrfile2.DIM), dtype=np.float32)
def xtc_nframes(filename):
""" 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)
return nframes, natoms
def __init__( self, file_name ):
self.file_name = str( file_name )
self.xdr_fp = libxdrfile2.xdrfile_open( self.file_name, 'rb' )
self.numatoms = self._read_natoms( self.file_name )
self.update()
# allocate coordinate array of the right size and type
self.x = np.zeros(
( self.numatoms, libxdrfile2.DIM ), dtype=np.float32
)
# allocate unit cell box
self.box = np.zeros(
( libxdrfile2.DIM, libxdrfile2.DIM ), dtype=np.float32
)
def __init__(self, filename, **kwargs):
raise NotImplementedError
try:
import xdrfile.libxdrfile2 as libxdr
except ImportError:
raise ImportError("libxdrfile2 library needed for xtc trajectories!")
self.filename = filename
self.velocities = False
self.file = libxdr.xdrfile_open(filename, 'r')
self.natoms = libxdr.read_xtc_natoms(self.filename)
self.nframes, self.offsets = libxdr.read_xtc_numframes(self.filename)
self.box = np.zeros((3,3),dtype=np.float32)
self.config = np.zeros((self.natoms,3),dtype=np.float32)
def __init__(self, filename, **kwargs):
raise NotImplementedError
try:
import xdrfile.libxdrfile2 as libxdr
except ImportError:
raise ImportError(
"libxdrfile2 library needed for xtc trajectories!")
self.filename = filename
self.velocities = False
self.file = libxdr.xdrfile_open(filename, 'r')
self.natoms = libxdr.read_xtc_natoms(self.filename)
self.nframes, self.offsets = libxdr.read_xtc_numframes(self.filename)
self.box = np.zeros((3, 3), dtype=np.float32)
self.config = np.zeros((self.natoms, 3), dtype=np.float32)
def set_xtc(self, xtcfile):
if xtcfile != None:
natoms = libxdrfile2.read_xtc_natoms(xtcfile)
assert natoms == self.natoms
self.xtc = libxdrfile2.xdrfile_open(xtcfile, "r")