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 = Shape.__members__.values() # Full list of shapes
>>> Shape.SquareAntiprism in all_shapes
True
>>> Shape.__members__["TrigonalPrism"] # String lookup
Shape.TrigonalPrism
>>> str(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¶

BicappedSquareAntiprism = Shape.BicappedSquareAntiprism¶

CappedOctahedron = Shape.CappedOctahedron¶

CappedSquareAntiprism = Shape.CappedSquareAntiprism¶

CappedTrigonalPrism = Shape.CappedTrigonalPrism¶

Cube = Shape.Cube¶

Cuboctahedron = Shape.Cuboctahedron¶

EdgeContractedIcosahedron = Shape.EdgeContractedIcosahedron¶

EquilateralTriangle = Shape.EquilateralTriangle¶

HeptagonalBipyramid = Shape.HeptagonalBipyramid¶

Hexagon = Shape.Hexagon¶

HexagonalBipyramid = Shape.HexagonalBipyramid¶

Icosahedron = Shape.Icosahedron¶

Line = Shape.Line¶

Octahedron = Shape.Octahedron¶

Pentagon = Shape.Pentagon¶

PentagonalBipyramid = Shape.PentagonalBipyramid¶

PentagonalPyramid = Shape.PentagonalPyramid¶

Seesaw = Shape.Seesaw¶

Square = Shape.Square¶

SquareAntiprism = Shape.SquareAntiprism¶

SquarePyramid = Shape.SquarePyramid¶

T = Shape.T¶

Tetrahedron = Shape.Tetrahedron¶

TricappedTrigonalPrism = Shape.TricappedTrigonalPrism¶

TrigonalBipyramid = Shape.TrigonalBipyramid¶

TrigonalDodecahedron = Shape.TrigonalDodecahedron¶

TrigonalPrism = Shape.TrigonalPrism¶

TrigonalPyramid = Shape.TrigonalPyramid¶

VacantTetrahedron = Shape.VacantTetrahedron¶

property name¶

handle) -> str

Type: (self

scine_molassembler.shapes.coordinates(shape: scine_molassembler.shapes.Shape) → numpy.ndarray[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

>>> s = Shape.CappedSquareAntiprism
>>> str(s)
"capped square antiprism"
>>> name_from_str(str(s))
Shape.CappedSquareAntiprism

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

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

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