def test_real_box(self):
traj = pt.load(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
trajiter = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
saved_box = Box(
[3.94559740E+01, 4.68215170E+01, 4.04695410E+01, 90., 90., 90.])
aa_eq(traj.top.box.values, saved_box.values)
for frame in traj:
assert frame.box.type == 'ortho'
aa_eq(
frame.box.values,
[35.2627796623, 41.8455476799, 36.168629529, 90.0, 90.0, 90.0],
decimal=1)
arr0 = traj.unitcells
arr1 = trajiter.unitcells
for b0, b1, frame in zip(arr0, arr1, trajiter):
box = frame.box
# FIXME:
# python3)
b2 = box.values
aa_eq(b0, b1)
aa_eq(b0, b2)
# test assign Box with list/tuple
b = Box(saved_box.values)
b2 = Box((t for t in saved_box.values))
aa_eq(b.values, saved_box.values, decimal=7)
aa_eq(b2.values, saved_box.values, decimal=7)
# assign frame.box with list/tuple
frame.box = b.values
b3 = frame.box
aa_eq(b3.values, saved_box.values, decimal=7)
def test_1(self):
box = Box()
box.type = 'truncoct'
box.set_nobox()
dummy = 100.
box.data[0] = dummy
assert box.data[0] == dummy
assert box.values[0] == dummy
def test_2(self):
import numpy as np
box = Box()
arr0 = np.arange(6).astype(np.float64)
box.data[:] = arr0
for idx, x in enumerate(arr0):
assert box.data[idx] == x
# set Box for Frame
f1 = Frame()
f1.box = box
aa_eq(f1.box.values, box.values, decimal=7)
def test_2(self):
import numpy as np
box = Box()
arr0 = np.arange(6).astype(np.float64)
box.data[:] = arr0
for idx, x in enumerate(arr0):
assert box.data[idx] == x
# set Box for Frame
f1 = Frame()
f1.box = box
aa_eq(f1.box.values, box.values, decimal=7)
def test_convert_to_dict_and_rebuild(self):
'''test_convert_to_dict_and_rebuild
'''
top = self.traj.top
d = top.to_dict()
new_top = pt.Topology()
MOLNUM = 0
for idx, (aname, atype, charge, mass, resid, resname,
mol_number) in enumerate(
zip(d['atom_name'], d['atom_type'], d['atom_charge'], d[
'atom_mass'], d['resid'], d['resname'], d[
'mol_number'])):
atom = pt.core.Atom(
name=aname, type=atype, charge=charge, mass=mass, resid=resid)
atom.set_mol(mol_number)
residue = pt.core.Residue(resname, resid)
new_top.add_atom(atom, residue)
if idx == 0:
new_top.start_new_mol()
if mol_number > MOLNUM:
new_top.start_new_mol()
MOLNUM += 1
new_top.add_bonds(d['bond_index'])
new_top.add_dihedrals(d['dihedral_index'])
new_top.box = Box(top.box.values)
assert_equal_topology(top, new_top, self.traj)
def test_1(self):
box = Box()
box.type = 'truncoct'
box.set_nobox()
dummy = 100.
box.data[0] = dummy
assert box.data[0] == dummy
assert box.values[0] == dummy
def test_box_constructor_with_type(self):
# TODO: assertion
Box('rhombic')
Box('ortho')
def test_from_matrix_3x3(self):
from pytraj.math import Matrix_3x3
mat = Matrix_3x3()
Box(mat)