Source code for mordred.BondCount

from enum import IntEnum
from itertools import chain

from rdkit import Chem

from ._base import Descriptor
from ._util import parse_enum

__all__ = ("BondCount",)


class BondType(IntEnum):
    __slots__ = ()

    any = 1
    heavy = 2

    single = 3
    double = 4
    triple = 5

    aromatic = 6
    multiple = 7

    @property
    def as_argument(self):
        return self.name


bond_types = (
    (BondType.any, ("", "all bonds", lambda _: True)),
    (BondType.heavy, ("O", "bonds connecting to heavy atom", lambda _: True)),
    (
        BondType.single,
        ("S", "single bonds", lambda b: b.GetBondType() == Chem.BondType.SINGLE),
    ),
    (
        BondType.double,
        ("D", "double bonds", lambda b: b.GetBondType() == Chem.BondType.DOUBLE),
    ),
    (
        BondType.triple,
        ("T", "triple bonds", lambda b: b.GetBondType() == Chem.BondType.TRIPLE),
    ),
    (
        BondType.aromatic,
        (
            "A",
            "aromatic bonds",
            lambda b: b.GetIsAromatic() or b.GetBondType() == Chem.BondType.AROMATIC,
        ),
    ),
    (
        BondType.multiple,
        (
            "M",
            "multiple bonds",
            lambda b: b.GetIsAromatic() or b.GetBondType() != Chem.BondType.SINGLE,
        ),
    ),
)

bond_type_dict = dict(bond_types)


[docs] class BondCount(Descriptor): r"""bond count descriptor. :type type: str :param type: one of bond_types :type kekulize: bool :param kekulize: use kekulized structure """ since = "1.0.0" __slots__ = ("_type", "_bond_name", "_bond_desc", "_check_bond", "kekulize")
[docs] def description(self): return "number of {} in {}kekulized structure".format( self._bond_desc, "" if self.kekulize else "non-" )
bond_types = tuple(b.name for b in BondType) @classmethod def preset(cls, version): return chain( map(lambda t: cls(t, False), BondType), map(lambda t: cls(t, True), [BondType.single, BondType.double]), ) def __str__(self): K = "K" if self.kekulize else "" return "nBonds{}{}".format(K, self._bond_name) @property def explicit_hydrogens(self): return self._type in (BondType.any, BondType.single) def parameters(self): return self._type, self.kekulize def __init__(self, type="any", kekulize=False): self._type = parse_enum(BondType, type) self._bond_name, self._bond_desc, self._check_bond = bond_type_dict[self._type] self.kekulize = kekulize def calculate(self): return sum(1 for b in self.mol.GetBonds() if self._check_bond(b)) rtype = int _extra_docs = ("bond_types",)