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