Source code for mordred.BCUT

import numpy as np

from ._base import Descriptor
from ._util import to_ordinal
from ._atomic_property import AtomicProperty, get_properties

__all__ = ("BCUT",)


class BCUTBase(Descriptor):
    __slots__ = ()
    explicit_hydrogens = False
    require_connected = True


class Burden(BCUTBase):
    __slots__ = ()

    def parameters(self):
        return ()

    def calculate(self):
        N = self.mol.GetNumAtoms()

        mat = 0.001 * np.ones((N, N))

        for bond in self.mol.GetBonds():
            a = bond.GetBeginAtom()
            b = bond.GetEndAtom()
            i = a.GetIdx()
            j = b.GetIdx()

            try:
                w = bond.GetBondTypeAsDouble() / 10.0
            except RuntimeError:
                self.fail(ValueError("unknown bond type"))

            if a.GetDegree() == 1 or b.GetDegree() == 1:
                w += 0.01

            mat[i, j] = w
            mat[j, i] = w

        return mat


class BurdenEigenValues(BCUTBase):
    __slots__ = ("_prop",)

    def parameters(self):
        return self._prop,

    def __init__(self, prop):
        self._prop = prop

    def dependencies(self):
        return {
            "burden": Burden(),
            "ps": self._prop,
        }

    def calculate(self, burden, ps):
        bmat = burden.copy()

        np.fill_diagonal(bmat, ps)
        ev = np.linalg.eig(bmat)[0]

        if np.iscomplexobj(ev):
            ev = ev.real

        return np.sort(ev)[-1::-1]


[docs]class BCUT(BCUTBase): r"""BCUT descriptor. :type prop: :py:class:`str` or :py:class:`function` :param prop: :ref:`atomic_properties` :type nth: int :param nth: n-th eigen value. 0 is highest, -1 is lowest. :returns: NaN when * any atomic properties are NaN * :math:`\left| nth \right| > A` """ __slots__ = ("_prop", "_nth",)
[docs] def description(self): return "{} {} eigenvalue of Burden matrix weighted by {}".format( to_ordinal(np.abs(self._nth) if self._nth < 0 else 1 + self._nth), "lowest" if self._nth < 0 else "heighest", self._prop.get_long(), )
@classmethod def preset(cls): return ( cls(a, n) for a in get_properties(valence=True, charge=True) for n in [0, -1] ) def __str__(self): if self._nth < 0: return "BCUT{}-{}l".format(self._prop.as_argument, np.abs(self._nth)) else: return "BCUT{}-{}h".format(self._prop.as_argument, self._nth + 1) def parameters(self): return self._prop, self._nth def __init__(self, prop="m", nth=0): self._prop = AtomicProperty(self.explicit_hydrogens, prop) self._nth = nth def dependencies(self): return {"bev": BurdenEigenValues(self._prop)} def calculate(self, bev): try: return bev[self._nth] except IndexError: self.fail(ValueError("nth greater then atom count")) rtype = float