Source code for mordred.ABCIndex

r"""ABC Index descriptor.

References
    * http://match.pmf.kg.ac.rs/electronic_versions/Match75/n1/match75n1_233-242.pdf

"""

import numpy as np

from ._base import Descriptor
from ._graph_matrix import DistanceMatrix

__all__ = ("ABCIndex", "ABCGGIndex",)


class ABCIndexBase(Descriptor):
    __slots__ = ()

    @classmethod
    def preset(cls):
        yield cls()

    explicit_hydrogens = False

    def parameters(self):
        return ()

    def __str__(self):
        return self.__class__.__name__[:-5]

    rtype = float


[docs]class ABCIndex(ABCIndexBase): r"""atom-bond connectivity index descriptor. References: * :doi:`10.2298/FIL1204733D` """ __slots__ = ()
[docs] def description(self): return "atom-bond connectivity index"
@staticmethod def _each_bond(bond): du = bond.GetBeginAtom().GetDegree() dv = bond.GetEndAtom().GetDegree() return np.sqrt((du + dv - 2.0) / (du * dv)) def calculate(self): return np.float( np.sum( self._each_bond(bond) for bond in self.mol.GetBonds() ), )
[docs]class ABCGGIndex(ABCIndexBase): r"""Graovac-Ghorbani atom-bond connectivity index descriptor. References: * Furtula, B. Atom-bond connectivity index versus Graovac-Ghorbani analog. MATCH Commun. Math. Comput. Chem 75, 233-242 (2016). """ # noqa: E501 __slots__ = ()
[docs] def description(self): return "Graovac-Ghorbani atom-bond connectivity index"
def dependencies(self): return {"D": DistanceMatrix(self.explicit_hydrogens)} @staticmethod def _each_bond(bond, D): u = bond.GetBeginAtomIdx() v = bond.GetEndAtomIdx() nu = np.sum(D[u, :] < D[v, :]) nv = np.sum(D[v, :] < D[u, :]) return np.sqrt((nu + nv - 2.0) / (nu * nv)) def calculate(self, D): return np.float( np.sum( self._each_bond(bond, D) for bond in self.mol.GetBonds() ), )