def XTCwrite(coords, box, filename, time=None, step=None):
numFrames = coords.shape[2]
if np.size(box,
1) != numFrames: # Box should have as many frames as trajectory
box = np.tile(box, (1, numFrames))
nframes = np.size(coords, 2)
if np.size(time) != nframes:
time = np.zeros(nframes)
if np.size(step) != nframes:
step = np.zeros(nframes, dtype=int)
if os.path.isfile(filename):
os.unlink(filename)
lib = xtc_lib()
bbox = (ct.c_float * 3)()
natoms = ct.c_int(coords.shape[0])
cstep = ct.c_int()
# print(coords.shape)
for f in range(coords.shape[2]):
cstep = ct.c_int(step[f])
ctime = ct.c_float(time[f]) # TODO FIXME
# print ( step )
# print ( time )
bbox[0] = box[0, f] * 0.1
bbox[1] = box[1, f] * 0.1
bbox[2] = box[2, f] * 0.1
data = coords[:, :, f].astype(np.float32) * 0.1 # Convert from A to nm
pos = data.ctypes.data_as(ct.POINTER(ct.c_float))
lib['libxtc'].xtc_write(ct.c_char_p(filename.encode("ascii")), natoms,
cstep, ctime, pos, bbox)
def XTCwrite(mol, filename):
coords = mol.coords
box = mol.box
time = mol.time
step = mol.step
numFrames = mol.numFrames
if np.size(box, 1) != numFrames: # Box should have as many frames as trajectory
box = np.tile(box, (1, numFrames))
nframes = np.size(coords, 2)
if np.size(time) != nframes:
time = np.zeros(nframes)
if np.size(step) != nframes:
step = np.zeros(nframes, dtype=int)
if os.path.isfile(filename):
os.unlink(filename)
box = box.astype(np.float32) * 0.1
step = step.astype(np.int32)
time = time.astype(np.float32)
coords = coords.astype(np.float32) * 0.1 # Convert from A to nm
if not box.flags['C_CONTIGUOUS']:
box = np.ascontiguousarray(box)
if not step.flags['C_CONTIGUOUS']:
step = np.ascontiguousarray(step)
if not time.flags['C_CONTIGUOUS']:
time = np.ascontiguousarray(time)
if not coords.flags['C_CONTIGUOUS']:
coords = np.ascontiguousarray(coords)
lib = xtc_lib()
natoms = ct.c_int(coords.shape[0])
nframes = ct.c_int(coords.shape[2])
cstep = step.ctypes.data_as(ct.POINTER(ct.c_int))
ctime = time.ctypes.data_as(ct.POINTER(ct.c_float))
cbox = box.ctypes.data_as(ct.POINTER(ct.c_float))
ccoords = coords.ctypes.data_as(ct.POINTER(ct.c_float))
lib['libxtc'].xtc_write(
ct.c_char_p(filename.encode("ascii")),
natoms,
nframes,
cstep,
ctime,
ccoords,
cbox)
def XTCwrite(mol, filename):
coords = mol.coords
box = mol.box
time = mol.time
step = mol.step
numFrames = mol.numFrames
if np.size(box, 1) != numFrames: # Box should have as many frames as trajectory
box = np.tile(box, (1, numFrames))
nframes = np.size(coords, 2)
if np.size(time) != nframes:
time = np.zeros(nframes)
if np.size(step) != nframes:
step = np.zeros(nframes, dtype=int)
if os.path.isfile(filename):
os.unlink(filename)
lib = xtc_lib()
bbox = (ct.c_float * 3)()
natoms = ct.c_int(coords.shape[0])
cstep = ct.c_int()
# print(coords.shape)
for f in range(coords.shape[2]):
cstep = ct.c_int(step[f])
ctime = ct.c_float(time[f]) # TODO FIXME
# print ( step )
# print ( time )
bbox[0] = box[0, f] * 0.1
bbox[1] = box[1, f] * 0.1
bbox[2] = box[2, f] * 0.1
data = coords[:, :, f].astype(np.float32) * 0.1 # Convert from A to nm
pos = data.ctypes.data_as(ct.POINTER(ct.c_float))
lib['libxtc'].xtc_write(
ct.c_char_p(filename.encode("ascii")),
natoms,
cstep,
ctime,
pos,
bbox)
def XTCread(filename, frame=None, topoloc=None):
""" Reads XTC file
Parameters
----------
filename : str
Path of xtc file.
frame : list
A list of integer frames which we want to read from the file. If None will read all.
Returns
-------
coords : nd.array
box : nd.array
boxangles : nd.array
step : nd.array
time : nd.array
"""
givenframes = frame
class __xtc(ct.Structure):
_fields_ = [("box", (ct.c_float * 3)),
("natoms", ct.c_int),
("step", ct.c_ulong),
("time", ct.c_double),
("pos", ct.POINTER(ct.c_float))]
lib = xtc_lib()
nframes = pack_ulong_buffer([0])
natoms = pack_int_buffer([0])
deltastep = pack_int_buffer([0])
deltat = pack_double_buffer([0])
lib['libxtc'].xtc_read.restype = ct.POINTER(__xtc)
lib['libxtc'].xtc_read_frame.restype = ct.POINTER(__xtc)
coords = None
if givenframes is None: # Read the whole XTC file at once
retval = lib['libxtc'].xtc_read(
ct.c_char_p(filename.encode("ascii")),
natoms,
nframes, deltat, deltastep)
if not retval:
raise IOError('XTC file {} possibly corrupt.'.format(filename))
nframes = nframes[0]
frames = range(nframes)
coords = np.zeros((natoms[0], 3, nframes), dtype=np.float32)
else:
if not isinstance(givenframes, list) and not isinstance(givenframes, np.ndarray):
givenframes = [givenframes]
nframes = len(givenframes)
frames = givenframes
step = np.zeros(nframes, dtype=np.uint64)
time = np.zeros(nframes, dtype=np.float32)
box = np.zeros((3, nframes), dtype=np.float32)
boxangles = np.zeros((3, nframes), dtype=np.float32)
for i, f in enumerate(frames):
if givenframes is not None: # If frames were given, read specific frame
retval = lib['libxtc'].xtc_read_frame(
ct.c_char_p(filename.encode("ascii")),
natoms,
ct.c_int(f))
if not retval:
raise IOError('XTC file {} possibly corrupt.'.format(filename))
if coords is None:
coords = np.zeros((natoms[0], 3, nframes), dtype=np.float32)
fidx = 0
else:
fidx = f
step[i] = retval[fidx].step
time[i] = retval[fidx].time
box[:, i] = retval[fidx].box
coords[:, :, i] = np.ctypeslib.as_array(retval[fidx].pos, shape=(natoms[0], 3))
if givenframes is not None:
lib['libc'].free(retval[0].pos)
lib['libc'].free(retval)
if givenframes is None:
for f in range(len(frames)):
lib['libc'].free(retval[f].pos)
lib['libc'].free(retval)
if np.size(coords, 2) == 0:
raise NameError('Malformed XTC file. No frames read from: {}'.format(filename))
if np.size(coords, 0) == 0:
raise NameError('Malformed XTC file. No atoms read from: {}'.format(filename))
coords *= 10. # Convert from nm to Angstrom
box *= 10. # Convert from nm to Angstrom
nframes = coords.shape[2]
if len(step) != nframes or np.sum(step) == 0:
step = np.arange(nframes)
if len(time) != nframes or np.sum(time) == 0:
logger.warning('No time information read from {}. Defaulting to 0.1ns framestep.'.format(filename))
time = np.arange(nframes) * 1E5 # Default is 0.1ns in femtoseconds = 100.000 fs
return None, Trajectory(coords=coords, box=box, boxangles=boxangles, step=step, time=time)
def XTCread(filename, frames=None):
class __xtc(ct.Structure):
_fields_ = [("box", (ct.c_float * 3)), ("natoms", ct.c_int),
("step", ct.c_ulong), ("time", ct.c_double),
("pos", ct.POINTER(ct.c_float))]
lib = xtc_lib()
nframes = pack_ulong_buffer([0])
natoms = pack_int_buffer([0])
deltastep = pack_int_buffer([0])
deltat = pack_double_buffer([0])
lib['libxtc'].xtc_read.restype = ct.POINTER(__xtc)
lib['libxtc'].xtc_read_frame.restype = ct.POINTER(__xtc)
if frames is None:
retval = lib['libxtc'].xtc_read(ct.c_char_p(filename.encode("ascii")),
natoms, nframes, deltat, deltastep)
if not retval:
raise IOError('XTC file {} possibly corrupt.'.format(filename))
frames = range(nframes[0])
t = Trajectory()
t.natoms = natoms[0]
t.nframes = len(frames)
t.coords = np.zeros((natoms[0], 3, t.nframes), dtype=np.float32)
t.step = np.zeros(t.nframes, dtype=np.uint64)
t.time = np.zeros(t.nframes, dtype=np.float32)
t.box = np.zeros((3, t.nframes), dtype=np.float32)
for i, f in enumerate(frames):
if f >= nframes[0] or f < 0:
raise RuntimeError(
'Frame index out of range in XTCread with given frames')
t.step[i] = retval[f].step
t.time[i] = retval[f].time
t.box[0, i] = retval[f].box[0]
t.box[1, i] = retval[f].box[1]
t.box[2, i] = retval[f].box[2]
# print( t.coords[:,:,f].shape)
# print ( t.box[:,f] )
# t.step[i] = deltastep[0] * i
t.coords[:, :, i] = np.ctypeslib.as_array(retval[f].pos,
shape=(natoms[0], 3))
for f in range(len(frames)):
lib['libc'].free(retval[f].pos)
lib['libc'].free(retval)
else:
if not isinstance(frames, list) and not isinstance(frames, np.ndarray):
frames = [frames]
t = Trajectory()
t.natoms = 0
t.nframes = len(frames)
t.coords = None
t.step = None
t.time = None
t.box = None
nframes = len(frames)
i = 0
for f in frames:
retval = lib['libxtc'].xtc_read_frame(
ct.c_char_p(filename.encode("ascii")), natoms, ct.c_int(f))
if t.coords is None:
t.natoms = natoms[0]
t.coords = np.zeros((natoms[0], 3, nframes), dtype=np.float32)
t.step = np.zeros(nframes, dtype=np.uint64)
t.time = np.zeros(nframes, dtype=np.float32)
t.box = np.zeros((3, nframes), dtype=np.float32)
t.step[i] = retval[0].step
t.time[i] = retval[0].time
t.box[0, i] = retval[0].box[0]
t.box[1, i] = retval[0].box[1]
t.box[2, i] = retval[0].box[2]
t.coords[:, :, i] = np.ctypeslib.as_array(retval[0].pos,
shape=(natoms[0], 3))
i += 1
lib['libc'].free(retval[0].pos)
lib['libc'].free(retval)
if np.size(t.coords, 2) == 0:
raise NameError(
'Malformed XTC file. No frames read from: {}'.format(filename))
if np.size(t.coords, 0) == 0:
raise NameError(
'Malformed XTC file. No atoms read from: {}'.format(filename))
# print( t.step )
# print( t.time )
# print( t.coords[:,:,0] )
# print(t.coords.shape)
t.coords *= 10. # Convert from nm to Angstrom
t.box *= 10. # Convert from nm to Angstrom
return t
def XTCread(filename, frame=None, topoloc=None):
""" Reads XTC file
Parameters
----------
filename : str
Path of xtc file.
frame : list
A list of integer frames which we want to read from the file. If None will read all.
Returns
-------
coords : nd.array
box : nd.array
boxangles : nd.array
step : nd.array
time : nd.array
"""
givenframes = frame
class __xtc(ct.Structure):
_fields_ = [("box", (ct.c_float * 3)),
("natoms", ct.c_int),
("step", ct.c_ulong),
("time", ct.c_double),
("pos", ct.POINTER(ct.c_float))]
lib = xtc_lib()
nframes = pack_ulong_buffer([0])
natoms = pack_int_buffer([0])
deltastep = pack_int_buffer([0])
deltat = pack_double_buffer([0])
lib['libxtc'].xtc_read.restype = ct.POINTER(__xtc)
lib['libxtc'].xtc_read_frame.restype = ct.POINTER(__xtc)
coords = None
if givenframes is None: # Read the whole XTC file at once
retval = lib['libxtc'].xtc_read(
ct.c_char_p(filename.encode("ascii")),
natoms,
nframes, deltat, deltastep)
if not retval:
raise IOError('XTC file {} possibly corrupt.'.format(filename))
nframes = nframes[0]
frames = range(nframes)
coords = np.zeros((natoms[0], 3, nframes), dtype=np.float32)
else:
if not isinstance(givenframes, list) and not isinstance(givenframes, np.ndarray):
givenframes = [givenframes]
nframes = len(givenframes)
frames = givenframes
step = np.zeros(nframes, dtype=np.uint64)
time = np.zeros(nframes, dtype=np.float32)
box = np.zeros((3, nframes), dtype=np.float32)
boxangles = np.zeros((3, nframes), dtype=np.float32)
for i, f in enumerate(frames):
if givenframes is not None: # If frames were given, read specific frame
retval = lib['libxtc'].xtc_read_frame(
ct.c_char_p(filename.encode("ascii")),
natoms,
ct.c_int(f))
if not retval:
raise IOError('XTC file {} possibly corrupt.'.format(filename))
if coords is None:
coords = np.zeros((natoms[0], 3, nframes), dtype=np.float32)
fidx = 0
else:
fidx = f
step[i] = retval[fidx].step
time[i] = retval[fidx].time
box[:, i] = retval[fidx].box
coords[:, :, i] = np.ctypeslib.as_array(retval[fidx].pos, shape=(natoms[0], 3))
if givenframes is not None:
lib['libc'].free(retval[0].pos)
lib['libc'].free(retval)
if givenframes is None:
for f in range(len(frames)):
lib['libc'].free(retval[f].pos)
lib['libc'].free(retval)
if np.size(coords, 2) == 0:
raise NameError('Malformed XTC file. No frames read from: {}'.format(filename))
if np.size(coords, 0) == 0:
raise NameError('Malformed XTC file. No atoms read from: {}'.format(filename))
coords *= 10. # Convert from nm to Angstrom
box *= 10. # Convert from nm to Angstrom
nframes = coords.shape[2]
if len(step) != nframes or np.sum(step) == 0:
step = np.arange(nframes)
if len(time) != nframes or np.sum(time) == 0:
logger.warning('No time information read from {}. Defaulting to 0.1ns framestep.'.format(filename))
time = np.arange(nframes) * 1E5 # Default is 0.1ns in femtoseconds = 100.000 fs
return None, Trajectory(coords=coords, box=box, boxangles=boxangles, step=step, time=time)