Class: Chemicalml::Model::Atom

Inherits:
Node
  • Object
show all
Defined in:
lib/chemicalml/model/atom.rb

Overview

A chemical atom. Carries every attribute CML's <atom> carries that's chemistry-relevant: element symbol, formal charge, isotope, count (multiplicity), hydrogen count, lone pairs, radical electrons, spin multiplicity, 2D/3D coordinates, fractional coordinates. Optional atom_parity for atom-centre chirality.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from Node

#==, #accept, #hash, short_name

Constructor Details

#initialize(element:, id: nil, formal_charge: nil, isotope: nil, count: nil, hydrogen_count: nil, lone_pairs: nil, radical_electrons: nil, spin_multiplicity: nil, title: nil, x2: nil, y2: nil, x3: nil, y3: nil, z3: nil, x_fract: nil, y_fract: nil, z_fract: nil, atom_parity: nil) ⇒ Atom

Returns a new instance of Atom.



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# File 'lib/chemicalml/model/atom.rb', line 19

def initialize(element:, id: nil, formal_charge: nil,
               isotope: nil, count: nil, hydrogen_count: nil,
               lone_pairs: nil, radical_electrons: nil,
               spin_multiplicity: nil, title: nil,
               x2: nil, y2: nil, x3: nil, y3: nil, z3: nil,
               x_fract: nil, y_fract: nil, z_fract: nil,
               atom_parity: nil)
  @element = element
  @id = id
  @formal_charge = formal_charge
  @isotope = isotope
  @count = count
  @hydrogen_count = hydrogen_count
  @lone_pairs = lone_pairs
  @radical_electrons = radical_electrons
  @spin_multiplicity = spin_multiplicity
  @title = title
  @x2 = x2
  @y2 = y2
  @x3 = x3
  @y3 = y3
  @z3 = z3
  @x_fract = x_fract
  @y_fract = y_fract
  @z_fract = z_fract
  @atom_parity = atom_parity
end

Instance Attribute Details

#atom_parity ⇒ Object

Returns the value of attribute atom_parity.



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# File 'lib/chemicalml/model/atom.rb', line 12

def atom_parity
  @atom_parity
end

#count ⇒ Object

Returns the value of attribute count.



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# File 'lib/chemicalml/model/atom.rb', line 12

def count
  @count
end

#element ⇒ Object

Returns the value of attribute element.



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# File 'lib/chemicalml/model/atom.rb', line 12

def element
  @element
end

#formal_charge ⇒ Object

Returns the value of attribute formal_charge.



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# File 'lib/chemicalml/model/atom.rb', line 12

def formal_charge
  @formal_charge
end

#hydrogen_count ⇒ Object

Returns the value of attribute hydrogen_count.



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# File 'lib/chemicalml/model/atom.rb', line 12

def hydrogen_count
  @hydrogen_count
end

#id ⇒ Object

Returns the value of attribute id.



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# File 'lib/chemicalml/model/atom.rb', line 12

def id
  @id
end

#isotope ⇒ Object

Returns the value of attribute isotope.



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# File 'lib/chemicalml/model/atom.rb', line 12

def isotope
  @isotope
end

#lone_pairs ⇒ Object

Returns the value of attribute lone_pairs.



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# File 'lib/chemicalml/model/atom.rb', line 12

def lone_pairs
  @lone_pairs
end

#radical_electrons ⇒ Object

Returns the value of attribute radical_electrons.



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# File 'lib/chemicalml/model/atom.rb', line 12

def radical_electrons
  @radical_electrons
end

#spin_multiplicity ⇒ Object

Returns the value of attribute spin_multiplicity.



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# File 'lib/chemicalml/model/atom.rb', line 12

def spin_multiplicity
  @spin_multiplicity
end

#title ⇒ Object

Returns the value of attribute title.



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# File 'lib/chemicalml/model/atom.rb', line 12

def title
  @title
end

#x2 ⇒ Object

Returns the value of attribute x2.



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# File 'lib/chemicalml/model/atom.rb', line 12

def x2
  @x2
end

#x3 ⇒ Object

Returns the value of attribute x3.



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# File 'lib/chemicalml/model/atom.rb', line 12

def x3
  @x3
end

#x_fract ⇒ Object

Returns the value of attribute x_fract.



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# File 'lib/chemicalml/model/atom.rb', line 12

def x_fract
  @x_fract
end

#y2 ⇒ Object

Returns the value of attribute y2.



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# File 'lib/chemicalml/model/atom.rb', line 12

def y2
  @y2
end

#y3 ⇒ Object

Returns the value of attribute y3.



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# File 'lib/chemicalml/model/atom.rb', line 12

def y3
  @y3
end

#y_fract ⇒ Object

Returns the value of attribute y_fract.



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# File 'lib/chemicalml/model/atom.rb', line 12

def y_fract
  @y_fract
end

#z3 ⇒ Object

Returns the value of attribute z3.



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# File 'lib/chemicalml/model/atom.rb', line 12

def z3
  @z3
end

#z_fract ⇒ Object

Returns the value of attribute z_fract.



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# File 'lib/chemicalml/model/atom.rb', line 12

def z_fract
  @z_fract
end

Instance Method Details

#children ⇒ Object 



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# File 'lib/chemicalml/model/atom.rb', line 47

def children
  [atom_parity].compact
end

#value_attributes ⇒ Object 



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# File 'lib/chemicalml/model/atom.rb', line 51

def value_attributes
  {
    element: element, id: id, formal_charge: formal_charge,
    isotope: isotope, count: count, hydrogen_count: hydrogen_count,
    lone_pairs: lone_pairs, radical_electrons: radical_electrons,
    spin_multiplicity: spin_multiplicity, title: title,
    x2: x2, y2: y2, x3: x3, y3: y3, z3: z3,
    x_fract: x_fract, y_fract: y_fract, z_fract: z_fract,
    atom_parity: atom_parity
  }
end