def test_0(self):
atm = AtomMask("@CA")
assert atm.n_atoms == 0
top = pt.load_topology("./data/Tc5b.top")
top.set_integer_mask(atm)
assert atm.n_atoms == 20
top2 = top._modify_state_by_mask(atm)
assert top2.n_atoms == 20
for atom in top2:
assert atom.name == 'CA'
atm.invert_mask()
top3 = top._modify_state_by_mask(atm)
assert top3.n_atoms == top.n_atoms - 20
def test_0(self):
atm = AtomMask("@CA")
assert atm.n_atoms == 0
top = pt.load_topology(fn('Tc5b.top'))
top._set_integer_mask(atm)
assert atm.n_atoms == 20
top2 = top._modify_state_by_mask(atm)
assert top2.n_atoms == 20
for atom in top2:
assert atom.name == 'CA'
atm.invert_mask()
top3 = top._modify_state_by_mask(atm)
assert top3.n_atoms == top.n_atoms - 20
def test_6_speed(self):
import numpy as np
from pytraj import AtomMask
# test constructor from list/array/python array
top = pt.load_topology(fn('DOPC.parm7'))
indices = top.select(":WAT")
atm1 = AtomMask(indices)
atm2 = AtomMask(list(indices))
atm3 = AtomMask(np.asarray(indices))
# use max_atoms
atm4 = AtomMask(np.asarray(indices), 1000)
import numpy as np
assert np.all(atm1.indices == atm2.indices)
assert np.all(atm3.indices == atm4.indices)
def test_4(self):
from array import array
atm = AtomMask()
indices = array('i', range(100))
atm.add_selected_indices(indices)
assert_almost_equal(indices, atm.selected_indices())
assert_almost_equal(indices, atm.indices)
# test list
atm2 = AtomMask(list(indices))
assert_almost_equal(indices, atm2.indices)
# test range
r100 = range(100)
atm3 = AtomMask(range(100))
assert_almost_equal(indices, atm3.indices)
def test_4(self):
from array import array
atm = AtomMask()
indices = array('i', range(100))
atm.add_selected_indices(indices)
assert_almost_equal(indices, atm.selected_indices())
assert_almost_equal(indices, atm.indices)
# test list
atm2 = AtomMask(list(indices))
assert_almost_equal(indices, atm2.indices)
# test range
range(100)
atm3 = AtomMask(range(100))
assert_almost_equal(indices, atm3.indices)
def test_rmsd_with_mask(self):
TRAJ = pt.iterload(filename=tc5b_trajin, top=tc5b_top)
cpptraj_rmsd = np.loadtxt(fn("rmsd_to_firstFrame_CA_allres.Tc5b.dat"),
skiprows=1).transpose()[1]
f0 = TRAJ[0]
arr0 = np.zeros(TRAJ.n_frames)
arr1 = np.zeros(TRAJ.n_frames)
mask = "@CA"
atm = AtomMask(mask)
TRAJ.top._set_integer_mask(atm)
for i, frame in enumerate(TRAJ):
arr0[i] = frame.rmsd(f0, mask=mask, top=TRAJ.top)
arr1[i] = frame.rmsd(f0, atommask=atm)
arr2 = pt.rmsd(TRAJ, mask=mask, ref=f0)
arr3 = pt.rmsd(TRAJ, mask=mask, ref=0)
aa_eq(arr0, cpptraj_rmsd, decimal=3)
aa_eq(arr1, cpptraj_rmsd, decimal=3)
aa_eq(arr2, cpptraj_rmsd, decimal=3)
aa_eq(arr3, cpptraj_rmsd, decimal=3)
def test_3_indexing(self):
top = pt.load_topology(fn('Tc5b.top'))
atm = AtomMask("@CA")
top._set_integer_mask(atm)
def test_1(self):
atm = AtomMask(10)
assert atm.n_atoms == 1
def test_3_indexing(self):
top = pt.load_topology("./data/Tc5b.top")
atm = AtomMask("@CA")
top.set_integer_mask(atm)