def test_load(): filenames = [ "frame0.xtc", "frame0.trr", "frame0.dcd", "frame0.binpos", "traj.h5", 'legacy_msmbuilder_trj0.lh5', 'frame0.nc', six.u('traj.h5') ] num_block = 3 for filename in filenames: t0 = md.load(get_fn(filename), top=nat, discard_overlapping_frames=True) t1 = md.load(get_fn(filename), top=nat, discard_overlapping_frames=False) t2 = md.load([get_fn(filename) for i in xrange(num_block)], top=nat, discard_overlapping_frames=False) t3 = md.load([get_fn(filename) for i in xrange(num_block)], top=nat, discard_overlapping_frames=True) # these don't actually overlap, so discard_overlapping_frames should have no effect # the overlap is between the last frame of one and the first frame of the next. yield lambda: eq(t0.n_frames, t1.n_frames) yield lambda: eq(t0.n_frames * num_block, t2.n_frames) yield lambda: eq(t3.n_frames, t2.n_frames)
def test_load(): filenames = [ "frame0.xtc", "frame0.trr", "frame0.dcd", "frame0.binpos", "traj.h5", "legacy_msmbuilder_trj0.lh5", "frame0.nc", six.u("traj.h5"), "frame0.lammpstrj", "frame0.xyz", ] num_block = 3 for filename in filenames: t0 = md.load(get_fn(filename), top=nat, discard_overlapping_frames=True) t1 = md.load(get_fn(filename), top=nat, discard_overlapping_frames=False) t2 = md.load([get_fn(filename) for i in xrange(num_block)], top=nat, discard_overlapping_frames=False) t3 = md.load([get_fn(filename) for i in xrange(num_block)], top=nat, discard_overlapping_frames=True) # these don't actually overlap, so discard_overlapping_frames should have no effect # the overlap is between the last frame of one and the first frame of the next. yield lambda: eq(t0.n_frames, t1.n_frames) yield lambda: eq(t0.n_frames * num_block, t2.n_frames) yield lambda: eq(t3.n_frames, t2.n_frames)
def topology(self): """Get the topology out from the file Returns ------- topology : mdtraj.Topology A topology object """ if np.all(self._handle.root.AtomID[:] == 0) and (np.all(self._handle.root.AtomNames[:] == b'') or np.all(self._handle.root.eAtomNames[:] == u(''))): return None return _topology_from_arrays( self._handle.root.AtomID[:], self._handle.root.AtomNames[:], self._handle.root.ChainID[:], self._handle.root.ResidueID[:], self._handle.root.ResidueNames[:])