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)