rdkit.Chem.rdShapeAlign module

Module containing PubChem shape alignment functionality.

class rdkit.Chem.rdShapeAlign.ShapeInput

Bases: object

property alpha_vector

(self) -> list[float]

property atom_type_vector

(self) -> list[int]

property coord

(self) -> list[float]

property inertialRot

Rotation applied to put the shape into its principal axes frame of reference.

property shift

Translation of centre of shape coordinates to origin.

property sof

(self) -> float

property sov

(self) -> float

property volumeAtomIndexVector

(self) -> list[int]

class rdkit.Chem.rdShapeAlign.ShapeInputOptions(self)

Bases: object

Shape Input Options

property atomRadii

Non-standard radii to use for the atoms specified by their indices in the molecule. A list of tuples of [int, float].

property atomSubset

If not empty, use just these atoms in the molecule to form the ShapeInput object.

property customFeatures

Custom features for the shape.

property dummyRadius

If using dummy atoms in the alignment, what radius to use for them. Default=2.16 (the radius of Xe).

property includeDummies

Whether to use dummy atoms in the alignment. Default=False.

property normalize

Whether to normalise the shape by putting into its inertial frame. Default=True.

property notColorAtoms

Any atoms mentioned here by index should not be used in a color feature.

property useColors

Whether to use colors (pharmacophore features) in the score. Default=True.