def test_modify():
Mol = Molecule()
assert Mol.getUndo() == None
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.newAtom('C', (0.5, 0.5, 0.5), fmt='crystal')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 1
Mol.mult(2, 1, 1)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 2
Mol.mult(1, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.crop()
assert Mol.nat == 1
Mol.mult(2, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((7, 0, 0), (0, 7, 0), (0, 0, 7)))
Mol.wrap()
assert Mol.nat == 8
assert list(map(len, Mol.getBonds(1.1))) == [24, 0, 0, 0, 0, 0, 0, 0]
assert Mol.getUndo() == 'wrap atoms'
Mol.undo()
assert list(map(len, Mol.getBonds(1.1))) == [0, 4, 4, 4, 4, 4, 4, 0]
Mol.wrap()
Mol.reshape(((14, 7, 0), (0, 7, 0), (0, 0, 7)))
assert list(map(len, Mol.getBonds(1.1))) == [38, 0, 10, 0, 0, 0, 0, 0]
assert vec_equal(Mol.getVec(), ((14, 7, 0), (0, 7, 0), (0, 0, 7)))
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert atom_equal(Mol.getAtom(1, fmt="crystal"), ('C', (0.1, 0.5, 0.5)))
Mol.align(1, 'x')
assert vec_equal(Mol.getVec(), ((0, -5, 0), (5, 0, 0), (0, 0, 5)))
Mol.undo()
Mol.align(1, 'y')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.align(1, 'z')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 0, 5), (0, -5, 0)))
Mol.undo()
try:
Mol.align(0, 1)
except ValueError:
assert True
except:
assert False, "Wrong error"
else:
assert False, "Error missing"
def test_scripting():
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.newAtom('C', (0, 0, 0))
Mol.newAtom('O', (1, 1, 0))
Mol.newAtom('B', (2, 2, 0))
Mol.newAtom('U', (0, 2, 0))
Mol.evalScript("def g all tU\n"
"shi g 1-3 2")
assert atom_equal(Mol.getAtom(3), ('U', (2, 0, 0)))
Mol.undo()
Mol.evalScript("rot 3 90 2-0 1")
assert atom_equal(Mol.getAtom(3), ('U', (1, 1, np.sqrt(2))))
Mol.undo()
Mol.evalScript("rot 3 90 2-0\n"
"mir 3 (1,0,0) (0,0,1,'angstrom') (1,0,0)")
assert atom_equal(Mol.getAtom(3), ('U', (1, -1, np.sqrt(2))))
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.setCellDim(15)
Mol.newAtom('C1', (0, 0, 0))
Mol.newAtom('C1', (1, 0, 0))
Mol.newAtom('C1', (1, 0, 0))
Mol.newAtom('C2', (0, 0, 3))
Mol.newAtom('C2', (1, 0, 3))
Mol.newAtom('C2', (1, 0, 3))
Mol.evalScript("rot [2, 5] 60 (0, 0, 1)")
Mol.evalScript("rot 3-5 90 (1, 0, 0) 3")
assert len(Mol.getBonds(1.1)[0]) == 6
Mol.evalScript("sel all tC2\npar sel sel 0-2")
atoms = Mol.getAtoms()
assert vec_equal(atoms[0][1], atoms[3][1]-(0,0,3))
assert vec_equal(atoms[1][1], atoms[4][1]-(0,0,3))
assert vec_equal(atoms[2][1], atoms[5][1]-(0,0,3))
Mol.evalScript("rot sel 45 (1, 0, 0) 3")
Mol.evalScript("pshift 0-2 (0,0,1) sel")
assert atom_equal(Mol.getAtom(0), ['C1', (0, np.sqrt(2)/2, -np.sqrt(2)/2)])
assert atom_equal(Mol.getAtom(1), ['C1', (1, np.sqrt(2)/2, -np.sqrt(2)/2)])
assert atom_equal(Mol.getAtom(2), ['C1', (0.5, (np.sqrt(3)+np.sqrt(2))/2, -np.sqrt(2)/2)])
