def test_frame_indices(self):
traj = pt.iterload(fn("tz2.truncoct.nc"), fn("tz2.truncoct.parm7"))
traj2 = pt.iterload(fn("tz2.truncoct.nc"),
fn("tz2.truncoct.parm7"),
frame_slice=(2, 8))
txt = '''
reference {} 2 2
rmsd :2-11 refindex 0 perres perresout center.agr range 1 perrescenter
'''.format(fn('tz2.truncoct.nc'))
state = pt.load_batch(traj2, txt)
with tempfolder():
state.run()
frame_indices = range(2, 8)
rmsd0 = pt.rmsd(traj, ref=1, mask=':2-11', frame_indices=frame_indices)
rmsdperres = pt.rmsd_perres(traj,
ref=1,
mask=':2-11',
perres_mask='*',
resrange='1',
perres_center=True,
frame_indices=frame_indices)
aa_eq(rmsd0, state.data[2])
aa_eq(rmsdperres[1], state.data[3].values)
def test_frame_indices(self):
traj = pt.iterload("data/tz2.truncoct.nc", "data/tz2.truncoct.parm7")
traj2 = pt.iterload("data/tz2.truncoct.nc",
"data/tz2.truncoct.parm7",
frame_slice=(2, 8))
txt = '''
reference ./data/tz2.truncoct.nc 2 2
rmsd :2-11 refindex 0 perres perresout center.agr range 1 perrescenter
'''
state = pt.load_batch(traj2, txt)
state.run()
frame_indices = range(2, 8)
rmsd0 = pt.rmsd(traj, ref=1, mask=':2-11', frame_indices=frame_indices)
rmsdperres = pt.rmsd_perres(traj,
ref=1,
mask=':2-11',
perres_mask='*',
resrange='1',
perres_center=True,
frame_indices=frame_indices)
aa_eq(rmsd0, state.data[2])
aa_eq(rmsdperres[1], state.data[3].values)
def test_frame_indices(self):
traj = pt.iterload("data/tz2.truncoct.nc", "data/tz2.truncoct.parm7")
traj2 = pt.iterload("data/tz2.truncoct.nc",
"data/tz2.truncoct.parm7",
frame_slice=(2, 8))
txt = '''
reference ./data/tz2.truncoct.nc 2 2
rmsd :2-11 refindex 0 perres perresout center.agr range 1 perrescenter
'''
state = pt.load_batch(traj2, txt)
state.run()
frame_indices = range(2, 8)
rmsd0 = pt.rmsd(traj, ref=1, mask=':2-11', frame_indices=frame_indices)
rmsdperres = pt.rmsd_perres(traj,
ref=1,
mask=':2-11',
perres_mask='*',
resrange='1',
perres_center=True,
frame_indices=frame_indices)
aa_eq(rmsd0, state.data[2])
aa_eq(rmsdperres[1], state.data[3].values)
def test_noreference(self):
from pytraj.datafiles import load_cpptraj_output, tz2_ortho_trajin
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
cout = load_cpptraj_output(tz2_ortho_trajin + """
rmsd first @CA perres range 2-7""")
d = pt.rmsd_perres(traj,
ref=0,
mask='@CA',
resrange='2-7',
dtype='ndarray')
aa_eq(cout[1:].values, d)
def test_noreference(self):
from pytraj.datafiles import load_cpptraj_output, tz2_ortho_trajin
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
cout = load_cpptraj_output(tz2_ortho_trajin + """
rmsd first @CA perres range 2-7""")
d = pt.rmsd_perres(traj,
ref=0,
mask='@CA',
resrange='2-7',
dtype='ndarray')
aa_eq(cout[1:].values, d)
def test_reference(self):
traj = pt.iterload("./data/tz2.truncoct.nc", "data/tz2.truncoct.parm7")
txt = '''
reference data/tz2.truncoct.nc 2 2
rmsd :2-11 refindex 0 perres perresout center.agr range 1 perrescenter
'''
state = pt.load_batch(traj, txt).run()
# state.data has 3 datasets: ref, rmsd, rmsd perres
# cpptraj use 2nd reference
rmsd0 = pt.rmsd(traj, ref=1, mask=':2-11')
rmsdperres = pt.rmsd_perres(traj,
ref=1,
mask=':2-11',
perres_mask='*',
resrange='1',
perres_center=True)
aa_eq(rmsd0, state.data[2])
aa_eq(rmsdperres[1], state.data[3].values)
def test_reference(self):
traj = pt.iterload("./data/tz2.truncoct.nc", "data/tz2.truncoct.parm7")
txt = '''
reference data/tz2.truncoct.nc 2 2
rmsd :2-11 refindex 0 perres perresout center.agr range 1 perrescenter
'''
state = pt.load_batch(traj, txt).run()
# state.data has 3 datasets: ref, rmsd, rmsd perres
# cpptraj use 2nd reference
rmsd0 = pt.rmsd(traj, ref=1, mask=':2-11')
rmsdperres = pt.rmsd_perres(traj,
ref=1,
mask=':2-11',
perres_mask='*',
resrange='1',
perres_center=True)
aa_eq(rmsd0, state.data[2])
aa_eq(rmsdperres[1], state.data[3].values)
def test_reference(self):
traj = pt.iterload(fn("tz2.truncoct.nc"), fn("tz2.truncoct.parm7"))
txt = '''
reference {} 2 2
rmsd :2-11 refindex 0 perres perresout center.agr range 1 perrescenter
'''.format(fn('tz2.truncoct.nc'))
with tempfolder():
state = pt.load_batch(traj, txt).run()
# state.data has 3 datasets: ref, rmsd, rmsd perres
# cpptraj use 2nd reference
rmsd0 = pt.rmsd(traj, ref=1, mask=':2-11')
rmsdperres = pt.rmsd_perres(traj,
ref=1,
mask=':2-11',
perres_mask='*',
resrange='1',
perres_center=True)
aa_eq(rmsd0, state.data[2])
aa_eq(rmsdperres[1], state.data[3].values)