struct Chem::Spatial::CoordinatesProxy

• Chem::Spatial::CoordinatesProxy
• Struct
• Value
• Object

Included Modules

• Enumerable(Chem::Spatial::Vector)
• Iterable(Chem::Spatial::Vector)

Defined in:

Constructors

• .new(atoms : AtomCollection, lattice : Lattice | Nil = nil)

Instance Method Summary

• #==(rhs : Enumerable(Vector)) : Bool
• #bounds : Bounds
• #center : Vector
• #center_along(vec : Vector) : self

  Translates coordinates so that the center is at the middle of vec.

• #center_at(vec : Vector) : self

  Translates coordinates so that the center is at vec.

• #center_at_cell : self

  Translates coordinates so that they are centered at the primary unit cell.

• #center_at_origin : self

  Translates coordinates so that the center is at the origin.

• #com : Vector

  Returns the center of mass.

• #each(fractional : Bool = false) : Iterator(Vector)

  Must return an Iterator over the elements in this collection.

• #each(fractional : Bool = false, &block : Vector -> )

  Must yield this collection's elements to the block.

• #each_with_atom(fractional : Bool = false, &block : Vector, Atom -> )
• #map(fractional : Bool = false, &block : Vector -> Vector) : Array(Vector)

  Returns an Array with the results of running the block against each element of the collection.

• #map!(fractional : Bool = false, &block : Vector -> Vector) : self
• #map_with_atom(fractional : Bool = false, &block : Vector, Atom -> Vector) : Array(Vector)
• #map_with_atom!(fractional : Bool = false, &block : Vector, Atom -> Vector) : self
• #to_a(fractional : Bool = false) : Array(Vector)

  Returns an Array with all the elements in the collection.

• #to_cartesian! : self
• #to_fractional! : self
• #transform(transform : AffineTransform) : Array(Vector)
• #transform!(transform : AffineTransform) : self
• #translate(by offset : Vector) : Array(Vector)
• #translate!(by offset : Vector) : self
• #wrap(around center : Vector | Nil = nil) : self
• #wrap(lattice : Lattice, around center : Vector | Nil = nil) : self

Constructor Detail

Instance Method Detail

structure = Structure.read "path/to/file"
structure.coords.center # => [1.5 2.0 3.2]
structure.coords.center_along Vector[0, 10, 0]
structure.coords.center # => [1.5 5.0 3.2]

structure = Structure.read "path/to/file"
structure.coords.center # => [1.0 2.0 3.0]
structure.coords.center_at Vector[10, 20, 30]
structure.coords.center # => [10 20 30]

structure = Structure.read "path/to/file"
structure.lattice       # => [[1.0 0.0 0.0] [0.0 25.0 0.0] [0.0 0.0 213]]
structure.coords.center # => [1.0 2.0 3.0]
structure.coords.center_at_cell
structure.coords.center # => [0.5 12.5 106.5]

structure = Structure.read "path/to/non_periodic_file"
structure.coords.center_at_cell # raises NotPeriodicError

structure = Structure.read "path/to/file"
structure.coords.center # => [1.0 2.0 3.0]
structure.coords.center_at_origin
structure.coords.center # => [0.0 0.0 0.0]

structure = Chem::Structure.build do
  atom :O, Vector[1, 2, 3]
  atom :H, Vector[4, 5, 6]
  atom :H, Vector[7, 8, 9]
end
structure.coords.center # => [4.0 5.0 6.0]
structure.coords.com    # => [1.5035248 2.5035248 3.5035248]

[1, 2, 3].map { |i| i * 10 } # => [10, 20, 30]

(1..5).to_a # => [1, 2, 3, 4, 5]