def test_center(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
pt.load(fn("tz2.center_mass.nc"), traj.top)
fa = traj[:]
fa2 = traj[:].copy()
pt.center(fa, mask=':1', mass=True)
aa_eq(fa.xyz, fa.xyz, decimal=5)
# raise if center not in 'origin', 'box'
with pytest.raises(ValueError):
pt.center(fa, center='oh')
# center to point
pt.center(fa, ':1', center=[0, 1, 2], mass=True)
aa_eq(pt.center_of_mass(fa, ':1')[0], [0, 1, 2])
pt.center(fa, ':1', center=[0, 1, 2], mass=False)
aa_eq(pt.center_of_geometry(fa, ':1')[0], [0, 1, 2])
fa2.center(':1', center=[0, 1, 2], mass=False)
aa_eq(pt.center_of_geometry(fa2, ':1')[0], [0, 1, 2])
# on_disk
traj_on_disk = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
pt.center(traj_on_disk, ':1', center=[0, 1, 2], mass=True)
aa_eq(pt.center_of_mass(traj_on_disk, ':1')[0], [0, 1, 2])
def test_0(self):
import numpy as np
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj2 = traj[:]
d1 = pt.calc_center_of_mass(traj, dtype='dataset')
d2 = pt.calc_center_of_mass(traj2, dtype='dataset')
for frame in traj:
pass
saved_d0 = np.loadtxt(fn('vec.out'), skiprows=1, usecols=(1, 2, 3))
aa_eq(d1.to_ndarray().flatten(), saved_d0.flatten())
aa_eq(d2.to_ndarray().flatten(), saved_d0.flatten())
aa_eq(pt.center_of_geometry(traj, dtype='ndarray'),
pt.center_of_geometry(traj2, dtype='ndarray'))
def test_0(self):
import numpy as np
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
traj2 = traj[:]
d1 = pt.calc_center_of_mass(traj, dtype='dataset')
d2 = pt.calc_center_of_mass(traj2, dtype='dataset')
for frame in traj:
pass
saved_d0 = np.loadtxt("./data/vec.out", skiprows=1, usecols=(1, 2, 3))
aa_eq(d1.to_ndarray().flatten(), saved_d0.flatten())
aa_eq(d2.to_ndarray().flatten(), saved_d0.flatten())
aa_eq(
pt.center_of_geometry(traj,
dtype='ndarray'),
pt.center_of_geometry(traj2,
dtype='ndarray'))
import pytraj as pt
# use load method to load all frames to memory
traj = pt.load("../tests/data/Tc5b.x", "../tests/data/Tc5b.top")
# compute center of geometry for residue 1, use all atoms
mask0 = ':1'
cog_0 = pt.center_of_geometry(traj, mask=mask0)
# should be ndarray, shape=(n_frames, 3)
print(cog_0)
# compute center of geometry for residue 1, exclude H atoms
mask1 = ':1&!:1@H='
print(set(atom.name for atom in traj.top[mask1].atoms)
) # should get {'OD1', 'CA', 'ND2', 'CB', 'O', 'C', 'N', 'CG'
cog_1 = pt.center_of_geometry(traj, mask=mask1)
print(cog_1)
# compute center of geometry for residue 1, 3, 5 and use all atoms
mask2 = ':1,3,5'
print(set(atom.name for atom in traj.top[mask2].atoms))
cog_2 = pt.center_of_geometry(traj, mask=mask2)
print(cog_2)
# compute center of geometry for residue 1, 3, 5 and use only CA atoms
mask3 = ':1,3,5@CA'
print(set(atom.name for atom in traj.top[mask3].atoms)) # should get {'@CA'}
cog_3 = pt.center_of_geometry(traj, mask=mask3)
print(cog_3)