Source code for mordred.VdwVolumeABC
from math import pi
from ._base import Descriptor
from .BondCount import BondCount
from .RingCount import RingCount
from ._atomic_property import GetAtomicNumber
__all__ = (
"VdwVolumeABC",
)
bondi_radii = {
"H": 1.20,
"C": 1.70, # noqa: S001
"N": 1.55,
"O": 1.52,
"F": 1.47, # noqa: S001
"Cl": 1.75, # noqa: S001
"Br": 1.85, # noqa: S001
"P": 1.80,
"S": 1.80,
"As": 1.85, # noqa: S001
"B": 2.13,
"Si": 2.10,
"Se": 1.90, # noqa: S001
}
atom_contrib = {
GetAtomicNumber(s): 4. / 3. * pi * r ** 3
for s, r in bondi_radii.items()
}
[docs]class VdwVolumeABC(Descriptor):
r"""van der waals volume(ABC) descriptor.
:returns: NaN when any atoms are non-compat_atoms
References
* :doi:`10.1021/jo034808o`
"""
__slots__ = ()
[docs] def description(self):
return "ABC van der waals volume"
compat_atoms = tuple(bondi_radii)
@classmethod
def preset(cls):
yield cls()
def __str__(self):
return "Vabc"
def parameters(self):
return ()
def dependencies(self):
return {
"NRA": RingCount(None, False, False, False, None),
"NRa": RingCount(None, False, False, True, None),
"Nb": BondCount(),
}
def calculate(self, Nb, NRa, NRA):
try:
ac = sum(
atom_contrib[a.GetAtomicNum()]
for a in self.mol.GetAtoms()
)
except KeyError:
self.fail(ValueError("unknown atom type"))
return ac - 5.92 * Nb - 14.7 * NRa - 3.8 * NRA
rtype = float