Class: Alumina::Atom

Inherits:
Object show all
Includes:
HIN::Writer::Atom
Defined in:
lib/alumina/atom.rb

Overview

An atom as part of a Molecule.

Constant Summary collapse

BOND_TYPES = 
[ :single, :double, :triple, :aromatic ]

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from HIN::Writer::Atom

#to_hin

Constructor Details

#initialize(id, element, x, y, z) ⇒ Atom

Initializes a new atom. After initializing it you can define its bonds strucrure using the bind method. Atoms are added to Molecules with the @<<@ method.

checked here.

Parameters:

  • id (Fixnum) —

    A unique identifier for this atom. Uniqueness is not

  • element (Element) —

    The atom’s type.

  • x (Float) —

    The atom’s x-coordinate in the molecule.

  • y (Float) —

    The atom’s y-coordinate in the molecule.

  • z (Float) —

    The atom’s z-coordinate in the molecule.



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# File 'lib/alumina/atom.rb', line 42

def initialize(id, element, x, y, z)
  @id = id
  @element = element
  @x = x
  @y = y
  @z = z
  @bonds = Hash.new
end

Instance Attribute Details

#bonds ⇒ Hash<Atom, Symbol>

the bond type.

Returns:

  • (Hash<Atom, Symbol>) —

    The atoms this atom is bonded to, along with



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# File 'lib/alumina/atom.rb', line 24

def bonds
  @bonds
end

#element ⇒ Element

Returns The atomic type.

Returns:



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# File 'lib/alumina/atom.rb', line 15

def element
  @element
end

#id ⇒ Fixnum

Returns The unique numerical identifier assigned to the atom.

Returns:

  • (Fixnum) —

    The unique numerical identifier assigned to the atom.



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# File 'lib/alumina/atom.rb', line 11

def id
  @id
end

#ignored1 ⇒ Object 



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# File 'lib/alumina/atom.rb', line 29

def ignored1
  @ignored1
end

#ignored2 ⇒ Object 



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# File 'lib/alumina/atom.rb', line 29

def ignored2
  @ignored2
end

#label ⇒ String?

Returns The optional label given to the atom.

Returns:

  • (String, nil) —

    The optional label given to the atom.



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# File 'lib/alumina/atom.rb', line 13

def label
  @label
end

#partial_charge ⇒ Fixnum

Returns The partial charge.

Returns:

  • (Fixnum) —

    The partial charge.



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# File 'lib/alumina/atom.rb', line 26

def partial_charge
  @partial_charge
end

#x ⇒ Float

Returns The atom’s x-coordinate in the molecule.

Returns:

  • (Float) —

    The atom’s x-coordinate in the molecule.



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# File 'lib/alumina/atom.rb', line 17

def x
  @x
end

#y ⇒ Float

Returns The atom’s y-coordinate in the molecule.

Returns:

  • (Float) —

    The atom’s y-coordinate in the molecule.



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# File 'lib/alumina/atom.rb', line 19

def y
  @y
end

#z ⇒ Float

Returns The atom’s z-coordinate in the molecule.

Returns:

  • (Float) —

    The atom’s z-coordinate in the molecule.



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# File 'lib/alumina/atom.rb', line 21

def z
  @z
end

Class Method Details

.bind(atom1, atom2, type) ⇒ Object

Binds two atoms together.

Parameters:

  • atom1 (Atom) —

    An atom to bind.

  • atom2 (Atom) —

    An atom to bind.

  • The (Symbol) —

    bond type. (See BOND_TYPES.)

Raises:

  • (ArgumentError) —

    If an invalid bond type is given.



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# File 'lib/alumina/atom.rb', line 58

def self.bind(atom1, atom2, type)
  raise ArgumentError, "Invalid bond type #{type.inspect}" unless BOND_TYPES.include?(type)
  
  atom1.bonds[atom2] = type
  atom2.bonds[atom1] = type
end

Instance Method Details

#bond_count ⇒ Fixnum

Returns The number of atoms bound to this atom.

Returns:

  • (Fixnum) —

    The number of atoms bound to this atom.



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# File 'lib/alumina/atom.rb', line 67

def bond_count
  bonds.size
end

#dup ⇒ Atom

Creates a duplicate of this atom with no bonds.

Returns:

  • (Atom) —

    A duplicate of this atom.



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# File 'lib/alumina/atom.rb', line 75

def dup
  atom = Atom.new(id, element, x, y, z)
  atom.label = label
  atom.partial_charge = partial_charge
  atom.ignored1 = ignored1
  atom.ignored2 = ignored2
  return atom
end

#inspect ⇒ Object 



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# File 'lib/alumina/atom.rb', line 85

def inspect
  if label then
    "#<Atom ##{id} #{label} (#{element.symbol})>"
  else
    "#<Atom ##{id} #{element.symbol}>"
  end
end