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.

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