def test_closest_compared_to_cpptraj(self):
trajin = fn('tz2.ortho.nc')
parm = fn('tz2.ortho.parm7')
traj = pt.iterload(trajin, parm, frame_slice=[
(0, 2),
])
state = pt.load_cpptraj_state('''
parm {}
trajin {} 1 2
autoimage
closest 100 :1-13
createcrd mycrd'''.format(parm, trajin))
state.run()
fi, top = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100,
dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def test_closest():
print('test_closest')
for frame in pt.closest(
traj(0, 100),
n_solvents=10,
restype='iterator')[0]:
pass
def test_closest_compared_to_cpptraj(self):
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
state = pt.load_cpptraj_state('''
autoimage
closest 100 :1-13
createcrd mycrd''', traj)
state.run()
fi, top = pt.closest(traj(autoimage=True), mask=':1-13', n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True), mask=':1-13', n_solvents=100, dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def test_closest(self):
# raise if not has solvent
traj0 = pt.iterload(fn('tz2.nc'),
fn('tz2.parm7'),
frame_slice=[(0, 2)])
self.assertRaises(RuntimeError, lambda: pt.closest(traj0))
traj = pt.iterload(fn('tz2.ortho.nc'),
fn('tz2.ortho.parm7'),
frame_slice=[(0, 2)])
fi, top = pt.closest(traj)
coords = []
for frame in fi:
coords.append(frame.xyz.copy())
assert isinstance(frame, pt.Frame), 'must be Frame'
# make a Trajectory
fi, top = pt.closest(traj)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(np.array(coords), t0.xyz)
# test write to disk
fi, top = pt.closest(traj)
pt.write_traj(outputname('fi.nc'), fi, top=top, overwrite=True)
# load back
t1 = pt.load(outputname('fi.nc'), top=top)
aa_eq(t0.xyz, t1.xyz)
# make sure n_sovent=10 (default)
n_solvents = 0
for mol in top.mols:
if mol.is_solvent():
n_solvents += 1
assert n_solvents == 10, 'must be 10 solvents'
fi, top = pt.closest(traj)
pt.write_traj(outputname('test.pdb'),
next(fi),
top=top,
overwrite=True)
def test_closest_compared_to_cpptraj(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
state = pt.load_cpptraj_state(
'''
autoimage
closest 100 :1-13
createcrd mycrd''', traj)
state.run()
fi, top = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100,
dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def test_closest(self):
# raise if not has solvent
traj0 = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
self.assertRaises(RuntimeError, lambda: pt.closest(traj0))
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
fi, top = pt.closest(traj)
coords = []
for frame in fi:
coords.append(frame.xyz.copy())
assert isinstance(frame, pt.Frame), 'must be Frame'
# make a Trajectory
fi, top = pt.closest(traj)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(np.array(coords), t0.xyz)
# test write to disk
fi, top = pt.closest(traj)
pt.write_traj('output/fi.nc', fi, top=top, overwrite=True)
# load back
t1 = pt.load('output/fi.nc', top=top)
aa_eq(t0.xyz, t1.xyz)
# make sure n_sovent=10 (default)
n_solvents = 0
for mol in top.mols:
if mol.is_solvent():
n_solvents += 1
assert n_solvents == 10, 'must be 10 solvents'
fi, top = pt.closest(traj)
pt.write_traj('output/test.pdb', next(fi), top=top, overwrite=True)
#solvmask is the mask for the atom around which you can keep the closest waters
solvmask = ':504@CHC'
wat2keep = 390
##########################################################
##########################################################
traj = pt.iterload(trajectory, top=topology)
top = pt.load_topology(topology)
stripped_prm = pt.strip(top, mask=stripmask)
stripped_traj = pt.strip(traj, stripmask)
print stripmask, "stripped"
print "selecting closest", wat2keep, "water molecules ..."
closest_traj = pt.closest(stripped_traj,
mask=solvmask,
n_solvents=wat2keep,
dtype='trajectory')
# NOTE: framelist here starts from zero!
framelist = range(start - 1, stop, every)
for frame in framelist:
# NOTE: output files have numbering starting from one!
name = 'closest_%04d.mol2' % (frame + 1)
print " ... writing frame %s" % (name)
pt.save(name,
closest_traj,
options='single',
overwrite=True,
frame_indices=[frame])
def test_closest():
print('test_closest')
for frame in pt.closest(traj(0, 100),
n_solvents=10,
restype='iterator')[0]:
pass
