def test_read_write_precision(get_fn):
import random
for t in [
md.load(get_fn('4waters.pdb')), # no unit cell
md.load(get_fn('native2.pdb')), # unitcell
md.load(get_fn('frame0.pdb'))
]: # multiframe
with GroTrajectoryFile(temp, 'w') as f:
f.write(t.xyz,
t.topology,
unitcell_vectors=t.unitcell_vectors,
precision=random.randint(4, 10))
with GroTrajectoryFile(temp) as f:
xyz, time, unitcell = f.read()
top = f.topology
eq(xyz, t.xyz, decimal=3)
eq(list(top.atoms), list(t.top.atoms))
if t.unitcell_vectors is not None:
eq(unitcell, t.unitcell_vectors)
# Test out the automatic saver and loader with different precisions
t = md.load(get_fn('native2.pdb'))
t.save(temp, precision=5)
eq(t.xyz, md.load(temp).xyz, decimal=3)
def test_read_write():
t = md.load(get_fn('4waters.pdb'))
with GroTrajectoryFile(temp, 'w') as f:
f.write(t.xyz, t.topology)
with GroTrajectoryFile(temp) as f:
xyz, time, unitcell = f.read()
top = f.topology
eq(xyz, t.xyz, decimal=3)
eq(list(top.atoms), list(t.top.atoms))
def test_read_write(get_fn):
for t in [md.load(get_fn('4waters.pdb')), # no unit cell
md.load(get_fn('native2.pdb')), # unitcell
md.load(get_fn('frame0.pdb'))]: # multiframe
with GroTrajectoryFile(temp, 'w') as f:
f.write(t.xyz, t.topology, unitcell_vectors=t.unitcell_vectors)
with GroTrajectoryFile(temp) as f:
xyz, time, unitcell = f.read()
top = f.topology
eq(xyz, t.xyz, decimal=3)
eq(list(top.atoms), list(t.top.atoms))
if t.unitcell_vectors is not None:
eq(unitcell, t.unitcell_vectors)
def test_load():
tref = md.load(get_fn('4waters.pdb'))
with GroTrajectoryFile(temp, 'w') as f:
f.write(tref.xyz, tref.topology)
t = md.load(temp)
eq(t.xyz, tref.xyz, decimal=3)
eq(list(t.top.atoms), list(tref.top.atoms))
def test_load(get_fn):
for tref in [
md.load(get_fn('4waters.pdb')), # no unit cell
md.load(get_fn('native2.pdb'))
]: # unit cell
with GroTrajectoryFile(temp, 'w') as f:
f.write(tref.xyz,
tref.topology,
unitcell_vectors=tref.unitcell_vectors)
t = md.load(temp)
eq(t.xyz, tref.xyz, decimal=3)
eq(list(t.top.atoms), list(tref.top.atoms))
eq(t.unitcell_vectors, tref.unitcell_vectors)
def test_load(get_fn):
for tref in [md.load(get_fn('4waters.pdb')), # no unit cell
md.load(get_fn('native2.pdb'))]: # unit cell
with GroTrajectoryFile(temp, 'w') as f:
f.write(tref.xyz, tref.topology, unitcell_vectors=tref.unitcell_vectors)
t = md.load(temp)
eq(t.xyz, tref.xyz, decimal=3)
eq(list(t.top.atoms), list(tref.top.atoms))
eq(t.unitcell_vectors, tref.unitcell_vectors)
#if there are 2 residues with same renum but different resname
t = md.load(get_fn('two_residues_same_resnum.gro'))
eq(t.n_residues, 2)