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):
        yield cls()

    def parameters(self):
        return ()

    rtype = int


[docs]class Radius(TopologicalIndexBase): r"""radius descriptor.""" __slots__ = ()
[docs] 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)
[docs]class Diameter(TopologicalIndexBase): r"""diameter descriptor.""" __slots__ = ()
[docs] 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)
[docs]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` """ __slots__ = ()
[docs] 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
[docs]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` """ __slots__ = ()
[docs] def description(self): return "Petitjean index"
def __str__(self): return "PetitjeanIndex" def calculate(self, R, D): with self.rethrow_zerodiv(): return (D - R) / D