Source code for mordred.GeometricalIndex

from __future__ import division

from ._base import Descriptor
from ._graph_matrix import Radius3D as CRadius3D
from ._graph_matrix import Diameter3D as CDiameter3D

__all__ = ("Diameter3D", "Radius3D", "GeometricalShapeIndex", "PetitjeanIndex3D",)


class GeometricalIndexBase(Descriptor):
    __slots__ = ()
    explicit_hydrogens = True
    require_3D = True

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

    def parameters(self):
        return ()

    rtype = float


[docs]class Radius3D(GeometricalIndexBase): r"""geometric radius descriptor.""" __slots__ = ()
[docs] def description(self): return "geometric radius"
def __str__(self): return "GeomRadius" def dependencies(self): return {"R": CRadius3D(self.explicit_hydrogens)} def calculate(self, R): return R
[docs]class Diameter3D(GeometricalIndexBase): r"""geometric diameter descriptor.""" __slots__ = ()
[docs] def description(self): return "geometric diameter"
def __str__(self): return "GeomDiameter" def dependencies(self): return {"D": CDiameter3D(self.explicit_hydrogens)} def calculate(self, D): return D
[docs]class GeometricalShapeIndex(GeometricalIndexBase): r"""geometrical shape index descriptor. .. math:: I_{\rm topo} = \frac{D - R}{R} where :math:`R` is geometric radius, :math:`D` is geometric diameter. :returns: NaN when :math:`R = 0` """ __slots__ = ()
[docs] def description(self): return "geometrical shape index"
def __str__(self): return "GeomShapeIndex" def dependencies(self): return { "D": CDiameter3D(self.explicit_hydrogens), "R": CRadius3D(self.explicit_hydrogens), } def calculate(self, R, D): with self.rethrow_zerodiv(): return (D - R) / (R)
[docs]class PetitjeanIndex3D(GeometricalShapeIndex): r"""geometric Petitjean index descriptor. .. math:: I_{\rm Petitjean} = \frac{D - R}{D} where :math:`R` is geometric radius, :math:`D` is geometric diameter. :returns: NaN when :math:`D = 0` """ __slots__ = ()
[docs] def description(self): return "geometric Petitjean index"
def __str__(self): return "GeomPetitjeanIndex" def calculate(self, R, D): with self.rethrow_zerodiv(): return (D - R) / (D)