def test_with_statement(self):
try:
with DCDReader(DCD) as trj:
N = trj.n_frames
frames = [ts.frame for ts in trj]
except:
raise AssertionError("with_statement not working for DCDReader")
assert_equal(
N,
98,
err_msg="with_statement: DCDReader reads wrong number of frames")
assert_array_equal(
frames,
np.arange(0, N),
err_msg="with_statement: DCDReader does not read all frames")
from MDAnalysis.coordinates.DCD import DCDReader
from MDAnalysis.coordinates.XYZ import XYZReader
from MDAnalysis.analysis.rms import RMSD
from MDAnalysis.core.universe import Universe, AtomGroup, Atom
from MDAnalysis.tests.datafiles import PSF, DCD
from MDAnalysis.coordinates.PDB import PDBReader
dcd = DCDReader('/home/jinho93/slab/LAO/grimes/opt/test/lao.dcd')
xyz = XYZReader('/home/jinho93/slab/LAO/grimes/opt/test/lao.xyz')
Universe(xyz)
for ts in dcd.trajectory:
print(ts.forces)
#print(f"Frame: {ts.frame:5d}, Time: {ts.time:8.3f} ps {dir(ts)}")