def get_frames_num(filepath, file_type, ext=None):
if file_type == 'coor':
if ext is None:
traj = mdtraj_load(filepath)
else:
ext2 = ext.lower()
if ext2 == 'pdb':
traj = mdtraj_load_pdb(filepath)
else:
raise ValueError('Extension "' + ext2 + '" not implemented.')
numframes = traj.n_frames
elif file_type == 'traj':
if ext is None:
trajfile = mdtraj_open(filepath)
else:
ext2 = ext.lower()
if ext2 == 'dcd':
trajfile = DCDTrajectoryFile(filepath)
elif ext2 == 'xtc':
trajfile = XTCTrajectoryFile(filepath)
else:
raise ValueError('Extension "' + ext + '" not implemented.')
numframes = mdtraj_get_frames_num(trajfile)
trajfile.close()
return numframes
def get_atoms_num(filepath, file_type, ext=None):
if file_type == 'coor':
if ext is None:
traj = mdtraj_load(filepath)
else:
ext2 = ext.lower()
if ext2 == 'pdb':
traj = mdtraj_load_pdb(filepath)
else:
raise ValueError('Extension "' + ext2 + '" not implemented.')
numatoms = traj.n_atoms
elif file_type == 'traj':
if ext is None:
trajfile = mdtraj_open(filepath)
else:
ext2 = ext.lower()
if ext2 == 'dcd':
trajfile = DCDTrajectoryFile(filepath)
elif ext2 == 'xtc':
trajfile = XTCTrajectoryFile(filepath)
else:
raise ValueError('Extension "' + ext + '" not implemented.')
res = trajfile.read(1)
xyz = res[0]
numatoms = xyz.shape[1]
trajfile.close()
return numatoms
def test_write_2():
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
box_lengths = 25 * np.ones((500, 3), dtype=np.float32)
box_angles = 90 * np.ones((500, 3), dtype=np.float32)
box_lengths[0, 0] = 10.0
f = DCDTrajectoryFile(temp, "w")
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(temp)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
yield lambda: eq(xyz, xyz2)
yield lambda: eq(box_lengths, box_lengths2)
yield lambda: eq(box_angles, box_angles2)
def test_write_2():
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
box_lengths = 25 * np.ones((500, 3), dtype=np.float32)
box_angles = 90 * np.ones((500, 3), dtype=np.float32)
box_lengths[0, 0] = 10.0
f = DCDTrajectoryFile(temp, 'w')
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(temp)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
yield lambda: eq(xyz, xyz2)
yield lambda: eq(box_lengths, box_lengths2)
yield lambda: eq(box_angles, box_angles2)
def test_write_2(tmpdir):
fn = '{}/x.dcd'.format(tmpdir)
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
box_lengths = 25 * np.ones((500, 3), dtype=np.float32)
box_angles = 90 * np.ones((500, 3), dtype=np.float32)
box_lengths[0, 0] = 10.0
f = DCDTrajectoryFile(fn, 'w')
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(fn)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
assert eq(xyz, xyz2)
assert eq(box_lengths, box_lengths2)
assert eq(box_angles, box_angles2)
def test_write_2(tmpdir):
fn = '{}/x.dcd'.format(tmpdir)
xyz = np.array(np.random.randn(500, 10, 3), dtype=np.float32)
box_lengths = 25 * np.ones((500, 3), dtype=np.float32)
box_angles = 90 * np.ones((500, 3), dtype=np.float32)
box_lengths[0, 0] = 10.0
f = DCDTrajectoryFile(fn, 'w')
f.write(xyz, box_lengths, box_angles)
f.close()
f = DCDTrajectoryFile(fn)
xyz2, box_lengths2, box_angles2 = f.read()
f.close()
assert eq(xyz, xyz2)
assert eq(box_lengths, box_lengths2)
assert eq(box_angles, box_angles2)
def read_onefile(self):
""" Read all snapshots from one dump file
The keyword filetype is used for different MD engines
It has four choices:
'lammps' (default)
'lammpscenter' (lammps molecular dump with known atom type of each molecule center)
moltypes is a dict mapping center atomic type to molecular type
moltypes is also used to select the center atom
such as moltypes = {3: 1, 5: 2}
'gsd' (HOOMD-blue standard output for static properties)
'gsd_dcd' (HOOMD-blue outputs for static and dynamic properties)
"""
#------------------lammps atomic trajectory---------------------------------
if self.filetype == 'lammps':
f = open(self.filename, 'r')
positions = self.read_lammps(f)
while positions.any():
self.Positions.append(positions)
positions = self.read_lammps(f)
f.close()
self.SnapshotNumber = len(self.TimeStep)
print('--------LAMMPS Atomic Dump Reading Over---------')
#------------------lammps molecular trajectory---------------------------------
if self.filetype == 'lammpscenter':
f = open(self.filename, 'r')
positions = self.read_centertype(f)
while positions.any():
self.Positions.append(positions)
positions = self.read_centertype(f)
f.close()
self.SnapshotNumber = len(self.TimeStep)
print('--------LAMMPS Molecule Center Dump Reading Over---------')
#------------------hoomd-blue gsd trajectory---------------------------------
if self.filetype == 'gsd':
import gsd.hoomd
import gsd
f = gsd.hoomd.open(self.filename, mode='rb')
self.read_gsd(f)
print('---------GSD file reading over-----------')
#------------------hoomd-blue gsd with dcd trajectory---------------------------------
if self.filetype == 'gsd_dcd':
import gsd.hoomd
import gsd, os
from mdtraj.formats import DCDTrajectoryFile
gsd_filename = self.filename
gsd_filepath = os.path.dirname(gsd_filename)
dcd_filename = gsd_filepath + '/' + os.path.basename(
gsd_filename)[:-3] + 'dcd'
f_gsd = gsd.hoomd.open(gsd_filename, mode='rb')
f_dcd = DCDTrajectoryFile(dcd_filename, 'r')
self.read_gsd_dcd(f_gsd, f_dcd)
f_dcd.close()
print('---------GSD & DCD file reading over-----------')
def test_write_closed(get_fn):
fn_dcd = get_fn('frame0.dcd')
with pytest.raises(IOError):
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10, 3, 3))
def test_read_closed(get_fn):
fn_dcd = get_fn('frame0.dcd')
with pytest.raises(IOError):
f = DCDTrajectoryFile(fn_dcd)
f.close()
f.read()
def test_write_closed():
f = DCDTrajectoryFile(fn_dcd, "w")
f.close()
f.write(np.random.randn(10, 3, 3))
def test_read_closed():
f = DCDTrajectoryFile(fn_dcd)
f.close()
f.read()
def test_write_closed():
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10, 3, 3))
def test_read_closed():
f = DCDTrajectoryFile(fn_dcd)
f.close()
f.read()
class Dcd(TrjHandler):
'''
Read and write cell and positions from/to DCD file.
Velocities, step and time are ignored.
Currently mstools use mdtraj to support DCD file.
Therefore, appending is not supported.
'''
def __init__(self, file, mode='r'):
super().__init__()
try:
from mdtraj.formats import DCDTrajectoryFile
except:
raise ImportError('Currently mstools use mdtraj to parse DCD format. Cannot import mdtraj')
if mode == 'r':
self._dcd = DCDTrajectoryFile(file, mode='r')
elif mode == 'w':
self._dcd = DCDTrajectoryFile(file, mode='w')
else:
raise Exception('Appending not supported for DCD')
def close(self):
try:
self._dcd.close()
except:
pass
def get_info(self):
self.n_frame = len(self._dcd)
if self.n_frame == 0:
raise Exception('Empty DCD file')
positions, lengths, angles = self._dcd.read(1)
_, self.n_atom, _ = positions.shape
return self.n_atom, self.n_frame
def read_frame(self, i_frame, frame):
self._dcd.seek(i_frame)
positions, box_lengths, box_angles = self._dcd.read(1)
angle = box_angles[0]
angle[np.abs(angle - 90) < 1E-4] = 90 # in case precision issue
frame.positions = positions[0] / 10 # convert A to nm
frame.cell.set_box([box_lengths[0] / 10, angle]) # convert A to nm
def write_frame(self, frame, subset=None, **kwargs):
'''
Write a frame into the opened DCD file
Parameters
----------
frame : Frame
subset : list of int, optional
kwargs : dict
Ignored
'''
if subset is None:
positions = frame.positions
else:
positions = frame.positions[subset]
self._dcd.write(positions * 10, frame.cell.lengths * 10, frame.cell.angles) # convert nm to A
def test_write_closed(get_fn):
fn_dcd = get_fn('frame0.dcd')
with pytest.raises(IOError):
f = DCDTrajectoryFile(fn_dcd, 'w')
f.close()
f.write(np.random.randn(10, 3, 3))
def test_read_closed(get_fn):
fn_dcd = get_fn('frame0.dcd')
with pytest.raises(IOError):
f = DCDTrajectoryFile(fn_dcd)
f.close()
f.read()
