def test_xtc_dcd():
pdb_filename = get("native.pdb", just_filename=True)
xtc_filename = get('RUN00_frame0.xtc', just_filename=True)
dcd_filename = get('RUN00_frame0.dcd', just_filename=True)
r_xtc = Trajectory.load_from_xtc(xtc_filename, pdb_filename)
r_dcd = Trajectory.load_from_dcd(dcd_filename, pdb_filename)
x_xtc = r_xtc["XYZList"]
x_dcd = r_dcd["XYZList"]
eq(x_xtc, x_dcd, decimal=4)
def _load_traj(self, file_list):
"""
Load a set of xtc or dcd files as a single trajectory
Note that the ordering of `file_list` is relevant, as the trajectories
are catted together.
Returns
-------
traj : msmbuilder.Trajectory
"""
if self.input_traj_ext == '.xtc':
traj = Trajectory.load_from_xtc(file_list, PDBFilename=self.conf_filename,
discard_overlapping_frames=True)
elif self.input_traj_ext == '.dcd':
traj = Trajectory.load_from_dcd(file_list, PDBFilename=self.conf_filename)
else:
raise ValueError()
return traj
def _load_traj(self, file_list):
"""
Load a set of xtc or dcd files as a single trajectory
Note that the ordering of `file_list` is relevant, as the trajectories
are catted together.
Returns
-------
traj : msmbuilder.Trajectory
"""
if self.input_traj_ext == '.xtc':
traj = Trajectory.load_from_xtc(file_list, Conf=self.conf,
discard_overlapping_frames=True)
elif self.input_traj_ext == '.dcd':
traj = Trajectory.load_from_dcd(file_list, Conf=self.conf,
discard_overlapping_frames=True)
else:
raise ValueError()
# return the number of files loaded, which in this case is all or
# nothing, since an error is raised if the Trajectory.load_from_<ext>
# doesn't work
return traj, len(file_list)
