Source code for mordred.TopologicalIndex

from __future__ import division

from ._base import Descriptor
from ._graph_matrix import Radius as CRadius
from ._graph_matrix import Diameter as CDiameter

__all__ = ("Diameter", "Radius", "TopologicalShapeIndex", "PetitjeanIndex")


class TopologicalIndexBase(Descriptor):
    __slots__ = ()
    explicit_hydrogens = False

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

    def parameters(self):
        return ()

    rtype = int


class Radius(TopologicalIndexBase):
    r"""radius descriptor."""

    since = "1.0.0"
    __slots__ = ()

    def description(self):
        return "topological radius"

    def __str__(self):
        return "Radius"

    def dependencies(self):
        return {"R": CRadius(self.explicit_hydrogens)}

    def calculate(self, R):
        return int(R)


class Diameter(TopologicalIndexBase):
    r"""diameter descriptor."""

    since = "1.0.0"
    __slots__ = ()

    def description(self):
        return "topological diameter"

    def __str__(self):
        return "Diameter"

    def dependencies(self):
        return {"D": CDiameter(self.explicit_hydrogens)}

    def calculate(self, D):
        return int(D)


class TopologicalShapeIndex(TopologicalIndexBase):
    r"""topological shape index descriptor.

    .. math::

        I_{\rm topo} = \frac{D - R}{R}

    where
    :math:`R` is graph radius,
    :math:`D` is graph diameter.

    :returns: NaN when :math:`R = 0`
    """

    since = "1.0.0"
    __slots__ = ()

    def description(self):
        return "topological shape index"

    def __str__(self):
        return "TopoShapeIndex"

    def dependencies(self):
        return {
            "D": CDiameter(self.explicit_hydrogens),
            "R": CRadius(self.explicit_hydrogens),
        }

    def calculate(self, R, D):
        with self.rethrow_zerodiv():
            return (D - R) / R

    rtype = float


class PetitjeanIndex(TopologicalShapeIndex):
    r"""Petitjean index descriptor.

    .. math::

        I_{\rm Petitjean} = \frac{D - R}{D}

    where
    :math:`R` is graph radius,
    :math:`D` is graph diameter.

    :returns: NaN when :math:`D = 0`
    """

    since = "1.0.0"
    __slots__ = ()

    def description(self):
        return "Petitjean index"

    def __str__(self):
        return "PetitjeanIndex"

    def calculate(self, R, D):
        with self.rethrow_zerodiv():
            return (D - R) / D