Shapes

All shapes that molassembler can classify from positions and treat permutationally. These are shapes from 2 vertices (line, bent) up to 12 vertices (icosahedron, cuboctahedron).

Shapes are classified into molecules by determining the nearest shape with a matching number of vertices.

Shape submodule

class scine_molassembler.shapes.Shape

Enumeration of recognizable polyhedral shapes

>>> all_shapes = shapes.Shape.__members__.values() # Full list of shapes
>>> shapes.Shape.SquareAntiprism in all_shapes
True
>>> shapes.Shape.__members__["TrigonalPrism"] # String lookup by enum name
<Shape.TrigonalPrism: 13>
>>> str(shapes.Shape.TrigonalPrism) # displayable string
'trigonal prism'

Members:

Line

Bent

EquilateralTriangle

VacantTetrahedron

T

Tetrahedron

Square

Seesaw

TrigonalPyramid

SquarePyramid

TrigonalBipyramid

Pentagon

Octahedron

TrigonalPrism

PentagonalPyramid

Hexagon

PentagonalBipyramid

CappedOctahedron

CappedTrigonalPrism

SquareAntiprism

Cube

TrigonalDodecahedron

HexagonalBipyramid

TricappedTrigonalPrism

CappedSquareAntiprism

HeptagonalBipyramid

BicappedSquareAntiprism

EdgeContractedIcosahedron

Icosahedron

Cuboctahedron

Bent = <Shape.Bent: 1>

BicappedSquareAntiprism = <Shape.BicappedSquareAntiprism: 26>

CappedOctahedron = <Shape.CappedOctahedron: 17>

CappedSquareAntiprism = <Shape.CappedSquareAntiprism: 24>

CappedTrigonalPrism = <Shape.CappedTrigonalPrism: 18>

Cube = <Shape.Cube: 20>

Cuboctahedron = <Shape.Cuboctahedron: 29>

EdgeContractedIcosahedron = <Shape.EdgeContractedIcosahedron: 27>

EquilateralTriangle = <Shape.EquilateralTriangle: 2>

HeptagonalBipyramid = <Shape.HeptagonalBipyramid: 25>

Hexagon = <Shape.Hexagon: 15>

HexagonalBipyramid = <Shape.HexagonalBipyramid: 22>

Icosahedron = <Shape.Icosahedron: 28>

Line = <Shape.Line: 0>

Octahedron = <Shape.Octahedron: 12>

Pentagon = <Shape.Pentagon: 11>

PentagonalBipyramid = <Shape.PentagonalBipyramid: 16>

PentagonalPyramid = <Shape.PentagonalPyramid: 14>

Seesaw = <Shape.Seesaw: 7>

Square = <Shape.Square: 6>

SquareAntiprism = <Shape.SquareAntiprism: 19>

SquarePyramid = <Shape.SquarePyramid: 9>

T = <Shape.T: 4>

Tetrahedron = <Shape.Tetrahedron: 5>

TricappedTrigonalPrism = <Shape.TricappedTrigonalPrism: 23>

TrigonalBipyramid = <Shape.TrigonalBipyramid: 10>

TrigonalDodecahedron = <Shape.TrigonalDodecahedron: 21>

TrigonalPrism = <Shape.TrigonalPrism: 13>

TrigonalPyramid = <Shape.TrigonalPyramid: 8>

VacantTetrahedron = <Shape.VacantTetrahedron: 3>

__init__(self: scine_molassembler.shapes.Shape, value: int) → None

name()

__str__(*args, **kwargs) Overloaded function.

1. __str__(self: scine_molassembler.shapes.Shape) -> str

2. __str__(self: handle) -> str

property value

scine_molassembler.shapes.coordinates(shape: scine_molassembler.shapes.Shape) → numpy.ndarray[numpy.float64[3, n]]

Idealized spherical coordinates of the shape

scine_molassembler.shapes.name_from_str(name_str: str) → scine_molassembler.shapes.Shape

Fetch a shape name from its string representation. Case and whitespace-sensitive.

>>> s = shapes.Shape.CappedSquareAntiprism
>>> str(s)
'capped square antiprism'
>>> shapes.name_from_str(str(s)) == s
True

scine_molassembler.shapes.size(shape: scine_molassembler.shapes.Shape) → int

Number of vertices of a shape. Does not include a centroid.

>>> shapes.size(shapes.Shape.Line)
2
>>> shapes.size(shapes.Shape.Octahedron)
6
>>> shapes.size(shapes.Shape.Cuboctahedron)
12