def stm(config, inp: str, origin: int, partner: int, out: click.File):
"""Calculate sterimol descriptors using kallisto van der Waals radii."""
# setup molecular structure
mol = ksr.constructMolecule(geometry=inp, out=out)
# calculate Sterimol descriptors: L, bmin, bmax
from kallisto.sterics import getClassicalSterimol
L, bmin, bmax = getClassicalSterimol(mol, origin, partner)
if config.verbose:
# print values in Bohr
verbosePrinter(
config.verbose,
"L, Bmin, Bmax / au: {:5.2f} {:5.2f} {:5.2f}".format(
L, bmin, bmax),
out,
)
# print values in Angstrom
from kallisto.units import Bohr
verbosePrinter(
config.verbose,
"L, Bmin, Bmax / A: {:5.2f} {:5.2f} {:5.2f}".format(
L * Bohr, bmin * Bohr, bmax * Bohr),
out,
)
return L, bmin, bmax
def test_stm():
mol = toluene()
origin = 6
partner = 5
L, bmin, bmax = getClassicalSterimol(mol, origin, partner)
assert np.isclose(L, 12.714385)
assert np.isclose(bmin, 3.539068)
assert np.isclose(bmax, 6.640342)
def test_stm():
mol = toluene()
origin = 6
partner = 5
L, bmin, bmax = getClassicalSterimol(mol, origin, partner)
assert (L - 12.714385) < epsilon
assert (bmin - 3.539068) < epsilon
assert (bmax - 6.640342) < epsilon
def stm(config, inp: str, origin: int, partner: int, out: click.File):
"""Calculate sterimol descriptors using kallisto van der Waals radii."""
# setup molecular structure
mol = ksr.constructMolecule(geometry=inp, out=out)
# calculate Sterimol descriptors: L, bmin, bmax
from kallisto.sterics import getClassicalSterimol
L, bmin, bmax = getClassicalSterimol(mol, origin, partner)
# print origin and partner
silentPrinter(
config.silent,
"Calculated for atom {0} (origin) and atom {1} (partner)".format(
origin, partner
),
out,
)
# descriptors in Bohr
silentPrinter(
config.silent,
"L, Bmin, Bmax / au: {:8.6f} {:8.6f} {:8.6f}".format(L, bmin, bmax),
out,
)
# descriptors in Angstrom
from kallisto.units import Bohr
silentPrinter(
config.silent,
"L, Bmin, Bmax / A: {:8.6f} {:8.6f} {:8.6f}".format(
L * Bohr, bmin * Bohr, bmax * Bohr
),
out,
)
return L, bmin, bmax