Module: Chem::Atom

Included in:
GSpanAtom, MDL::MDLAtom, MDL::RxnAtom, SkeletonAtom, SmilesAtom, Sybyl::SybylAtom, TINKER::TinkerAtom, XYZ::XyzAtom
Defined in:
lib/chem/model.rb,
lib/chem/db/mdl.rb,
lib/chem/db/sybyl.rb,
lib/chem/db/vector.rb,
lib/chem/utils/prop.rb

Overview

Atom module is top level abstract module for atom in molecule. It will be mixed-in to other concrete class.

Constant Summary collapse

MDLAtomLineFormat = 
"%10.4f%10.4f%10.4f %2s%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d"

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#charge ⇒ Object

charge



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# File 'lib/chem/model.rb', line 34

def charge
  @charge
end

#color ⇒ Object

r, g, b 


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# File 'lib/chem/model.rb', line 19

def color
  @color
end

#element ⇒ Object

atomic symbol (Symbol object)



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# File 'lib/chem/model.rb', line 22

def element
  @element
end

#mass ⇒ Object

Returns atomic mass



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# File 'lib/chem/model.rb', line 37

def mass
  @mass
end

#v_pos ⇒ Object

position vector for visualization



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# File 'lib/chem/db/vector.rb', line 20

def v_pos
  @v_pos
end

#visible ⇒ Object

true if visible (for visualization)



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# File 'lib/chem/model.rb', line 17

def visible
  @visible
end

#x ⇒ Object

x-axis position



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# File 'lib/chem/model.rb', line 25

def x
  @x
end

#y ⇒ Object

y-axis position



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# File 'lib/chem/model.rb', line 28

def y
  @y
end

#z ⇒ Object

z-axis position



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# File 'lib/chem/model.rb', line 31

def z
  @z
end

Instance Method Details

#atomic_number ⇒ Object

Returns Atomic Number. If unknown return 100.



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# File 'lib/chem/model.rb', line 41

def atomic_number
  Number2Element.index(element) ? Number2Element.index(element) : 100
end

#electro_negativity ⇒ Object

Returns electro negativity see chem/data/electronegativity.rb



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# File 'lib/chem/utils/prop.rb', line 11

def electro_negativity
  ElectroNegativity[self.element]
end

#natural_bond_order ⇒ Object

Returns Natural Bond Order of this atom :C => 4, :H => 1… see chem/data/character.rb



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# File 'lib/chem/utils/prop.rb', line 18

def natural_bond_order
  NaturalBondOrder[self.element]
end

#to_mdl(mapping = 0) ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 33

def to_mdl mapping = 0
  MDLAtomLineFormat % [x, y, z, element, 0, 0, 0, 0, 0, 0, 0, 0, 0, mapping, 0, 0]
end

#to_sybyl ⇒ Object 



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# File 'lib/chem/db/sybyl.rb', line 14

def to_sybyl
  "      1 C1         -3.262565   -0.588014   -0.082185 C.3       1 <1>        -0.020001 "
  "%7d" % [1]
end

#weight ⇒ Object

Returns Atomic weight see chem/data/atomic_weight.rb



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# File 'lib/chem/utils/prop.rb', line 24

def weight
  AtomicWeight[self.element]
end