def exs(
config,
inp: str,
center: int,
subnr: int,
name: str,
exclude: bool,
rotate: int,
out: click.File,
):
"""Exchange a substrate within a transition metal complex with another
substrate. Use an root mean squared deviation (RMSD) measure to rotate
and shift new substrate to the position of the old substrate.
Calculate the RMSD between two structures using quaternions."""
# setup reference molecular structure
ref = ksr.constructMolecule(geometry=inp[0], out=out)
substrate = ksr.constructMolecule(geometry=inp[1], out=out)
nat = ref.get_number_of_atoms()
# get all covalent bonding partner in reference complex
covBonds = config.context.invoke(bonds, inp=inp[0])
# get covalent bonds in new substrate
newSubBonds = substrate.get_bonds(partner="X")
newSubBonds = np.array(newSubBonds, dtype=object)
from kallisto.rmsd import exchangeSubstructure
exchangeSubstructure(
nat,
center,
subnr,
covBonds,
ref,
substrate,
newSubBonds,
name,
rotate,
exclude,
)
def test_exs_rotate_180_degrees():
# Iridium atom complex
center = 18
# Exchange benzene with pyridine
subnr = 2
# set output name
name = "iridium_pyridine_180_rotated"
# define rotation angle along covalent bond
rotate = 180
# do not constrain bonding atom of substrate
exclude = False
ref = iridiumCatalyst()
refBonds = ref.get_bonds()
refNat = ref.get_number_of_atoms()
exchanger = pyridine_mH()
exchangerBonds = exchanger.get_bonds()
mol = exchangeSubstructure(
refNat,
center,
subnr,
refBonds, # type: ignore
ref,
exchanger,
exchangerBonds, # type: ignore
name,
rotate,
exclude,
) # type: ignore
at = mol.get_atomic_numbers()
assert at[85] == 6
coords = mol.get_positions()
# position of Carbon bonding to Iridium
assert (coords[85, 0] - 0.2001 / Bohr) < epsilon
assert (coords[85, 1] - -2.2076 / Bohr) < epsilon
assert (coords[85, 2] - 2.6787 / Bohr) < epsilon
# position of Nitrogen
assert (coords[90, 0] - 1.3335 / Bohr) < epsilon
assert (coords[90, 1] - -2.8374 / Bohr) < epsilon
assert (coords[90, 2] - 3.0650 / Bohr) < epsilon
constrain = "constrain.inp"
gotFile = os.path.isfile(constrain)
assert gotFile is True
if gotFile:
os.remove(constrain)
name += ".xyz"
gotFile = os.path.isfile(name)
assert gotFile is True
if gotFile:
os.remove(name)
def test_exs():
# Iridium atom complex
center = 18
# Exchange benzene with pyridine
subnr = 2
# set output name
name = "iridium_pyridine"
# define rotation angle along covalent bond
rotate = 0
# do not constrain bonding atom of substrate
exclude = False
ref = iridiumCatalyst()
refBonds = ref.get_bonds()
refNat = ref.get_number_of_atoms()
exchanger = pyridine_mH()
exchangerBonds = exchanger.get_bonds()
mol = exchangeSubstructure(
refNat,
center,
subnr,
refBonds,
ref,
exchanger,
exchangerBonds,
name,
rotate,
exclude,
) # type: ignore
at = mol.get_atomic_numbers()
assert at[85] == 6
coords = mol.get_positions()
# position of Carbon bonding to Iridium
assert np.isclose(coords[85, 0], 0.2001 / Bohr, rtol=1e-04)
assert np.isclose(coords[85, 1], -2.2076 / Bohr, rtol=1e-04)
assert np.isclose(coords[85, 2], 2.6787 / Bohr, rtol=1e-04)
# position of Nitrogen
assert np.isclose(coords[90, 0], -1.0435 / Bohr, rtol=1e-04)
assert np.isclose(coords[90, 1], -2.4569 / Bohr, rtol=1e-04)
assert np.isclose(coords[90, 2], 3.1496 / Bohr, rtol=1e-04)
constrain = "constrain.inp"
gotFile = os.path.isfile(constrain)
assert gotFile is True
if gotFile:
os.remove(constrain)
name += ".xyz"
gotFile = os.path.isfile(name)
assert gotFile is True
if gotFile:
os.remove(name)