Class: Rubabel::Atom

Inherits:
Object show all
Includes:
Enumerable
Defined in:
lib/rubabel/atom.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Enumerable

#index_by, #uniq_by

Constructor Details

#initialize(obatom) ⇒ Atom

Returns a new instance of Atom.



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# File 'lib/rubabel/atom.rb', line 35

def initialize(obatom)
  @ob = obatom
end

Instance Attribute Details

#ob ⇒ Object

the OpenBabel::OBAtom object



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# File 'lib/rubabel/atom.rb', line 33

def ob
  @ob
end

Class Method Details

.[](el_sym = :h, id = nil) ⇒ Object

takes an element symbol and creates that atom. If el_sym is set to nil or 0, then an atom of atomic number 0 is used



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

def [](el_sym=:h, id=nil)
  ob_atom = OpenBabel::OBAtom.new
  ob_atom.set_id(id) if id
  ob_atom.set_atomic_num(Rubabel::EL_TO_NUM[el_sym] || 0)
  self.new(ob_atom)
end

Instance Method Details

#add_atom!(other) ⇒ Object

creates a bond and adds it to both atoms



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# File 'lib/rubabel/atom.rb', line 63

def add_atom!(other)
  obbond = OpenBabel::OBBond.new
  obbond.set_begin(self.ob)
  obbond.set_end(other.ob)
  @ob.add_bond(obbond)
  other.ob.add_bond(obbond)
  self
end

#amide_nitrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 263

def amide_nitrogen?() @ob.is_amide_nitrogen end

#anti_clockwise? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 270

def anti_clockwise?() @ob.is_anti_clockwise end

#aromatic? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 251

def aromatic?() @ob.is_aromatic end

#aromatic_noxide? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 266

def aromatic_noxide?() @ob.is_aromatic_noxide end

#atomic_mass ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 110

def atomic_mass
  @ob.get_atomic_mass
end

#atomic_num ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 114

def atomic_num
  @ob.get_atomic_num
end

#atoms ⇒ Object

returns the neighboring atoms. Consider using each_atom.



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# File 'lib/rubabel/atom.rb', line 106

def atoms
  each_atom.map.to_a
end

#axial? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 268

def axial?() @ob.is_axial end

#bonds ⇒ Object

returns the bonds. Consider using each_bond.



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# File 'lib/rubabel/atom.rb', line 89

def bonds
  each_bond.map.to_a
end

#carbon? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 246

def carbon?() @ob.is_carbon end

#carbonyl_carbon? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 296

def carbonyl_carbon?
  each_atom.any?(&:carbonyl_oxygen?)
end

#carbonyl_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 291

def carbonyl_oxygen?
  ats = atoms
  ats.size == 1 && ats.first.el == :c && double_bond?
end

#carboxyl_carbon? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 287

def carboxyl_carbon?
  each_atom.any?(&:carboxyl_oxygen?)
end

#carboxyl_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 259

def carboxyl_oxygen?() @ob.is_carboxyl_oxygen end

#chiral? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 267

def chiral?() @ob.is_chiral end

#chiral_volume? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 274

def chiral_volume?() @ob.has_chiral_volume end

#chirality_specified? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 273

def chirality_specified?() @ob.has_chirality_specified end

#clockwise? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 269

def clockwise?() @ob.is_clockwise end

#connected? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 256

def connected?() @ob.is_connected end

#coords ⇒ Object

# does this carbon hold a primary alcohol

def primary_alcohol_carbon?
end



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# File 'lib/rubabel/atom.rb', line 304

def coords
  Vector[@ob.x, @ob.y, @ob.z]
end

#double_bond? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 279

def double_bond?
  each_bond.any? {|bond| bond.bond_order == 2 }
end

#each_atom(&block) ⇒ Object Also known as: each

iterates through each neighboring atom



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# File 'lib/rubabel/atom.rb', line 94

def each_atom(&block)
  block or return enum_for(__method__)
  iter = @ob.begin_bonds
  _atom = @ob.begin_nbr_atom(iter)
  while _atom
    block.call _atom.upcast
    _atom = @ob.next_nbr_atom(iter)
  end
end

#each_bond(&block) ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 72

def each_bond(&block)
  block or return enum_for(__method__)
  iter = @ob.begin_bonds
  _bond = @ob.begin_bond(iter)
  while _bond
    block.call _bond.upcast
    _bond = @ob.next_bond(iter)
  end
end

#el ⇒ Object

abbreviated name, all lowercase as a Symbol



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# File 'lib/rubabel/atom.rb', line 53

def el
  NUM_TO_EL[atomic_num]
end

#element ⇒ Object

abbreviated name, properly capitalized and as a String



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

def element
  NUM_TO_ELEMENT[atomic_num]
end

#equal?(other) ⇒ Boolean Also known as: ==, eql?

the exact same atom in the same molecule. The equivalency test for molecules is a little pricey, so better to use something like atom.id == other.id if you know you are working within the same molecule.

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 190

def equal?(other)
  other.respond_to?(:mol) && mol.equal?(other.mol) && id == other.id 
end

#exact_mass ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 118

def exact_mass
  @ob.get_exact_mass
end

#formal_charge ⇒ Object Also known as: charge 



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# File 'lib/rubabel/atom.rb', line 122

def formal_charge
  @ob.get_formal_charge
end

#formal_charge=(val) ⇒ Object Also known as: charge= 



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# File 'lib/rubabel/atom.rb', line 127

def formal_charge=(val)
  @ob.set_formal_charge(val)
end

#get_bond(atom) ⇒ Object

retrieves the bond



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# File 'lib/rubabel/atom.rb', line 84

def get_bond(atom)
  @ob.get_bond(atom.ob).andand.upcast
end

#hbond_acceptor? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 275

def hbond_acceptor?() @ob.is_hbond_acceptor end

#hbond_donor? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 276

def hbond_donor?() @ob.is_hbond_donor end

#hbond_donor_h? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 277

def hbond_donor_h?() @ob.is_hbond_donor_h end

#heavy_valence ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 132

def heavy_valence
  @ob.get_heavy_valence
end

#hetero_valence ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 136

def hetero_valence
  @ob.get_hetero_valence
end

#heteroatom? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 254

def heteroatom?() @ob.is_heteroatom end

#hyb ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 140

def hyb
  @ob.get_hybridization
end

#hydrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 245

def hydrogen?() @ob.is_hydrogen end

#id ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 39

def id
  @ob.get_id
end

#id=(val) ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 43

def id=(val)
  @ob.set_id(val)
end

#idx ⇒ Object

index of the atom (begins with 1)



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# File 'lib/rubabel/atom.rb', line 48

def idx
  @ob.get_idx
end

#implicit_valence ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 144

def implicit_valence
  @ob.get_implicit_valence
end

#in_ring? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 252

def in_ring?() @ob.is_in_ring end

#in_ring_size? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 253

def in_ring_size?() @ob.is_in_ring_size end

#inspect ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 308

def inspect
  "<#{type} id:#{id}>"
end

#inspect_internals ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 312

def inspect_internals
  "<" << @ob.methods.grep(/get_/).map do |mthd| 
    begin
      "#{mthd.to_s.sub(/get_/,'')}=#{@ob.send(mthd)}" 
    rescue ArgumentError
      nil
    end
  end.compact.join(" ") << ">"
end

#isotope ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 148

def isotope
  @ob.get_isotope
end

#mol ⇒ Object

returns the molecule that is parent of this atom



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# File 'lib/rubabel/atom.rb', line 28

def mol
  @ob.get_parent.andand.upcast
end

#negative_stereo? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 272

def negative_stereo?() @ob.is_negative_stereo end

#nitro_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 262

def nitro_oxygen?() @ob.is_nitro_oxygen end

#nitrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 247

def nitrogen?() @ob.is_nitrogen end

#non_polar_hydrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 265

def non_polar_hydrogen?() @ob.is_non_polar_hydrogen end

#not_c_or_h? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 255

def not_c_or_h?() @ob.is_not_cor_h end

#one_four? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 258

def one_four?() @ob.is_one_four end

#one_three? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 257

def one_three?() @ob.is_one_three end

#oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 248

def oxygen?() @ob.is_oxygen end

#partial_charge ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 152

def partial_charge
  @ob.get_partial_charge
end

#phosphate_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 260

def phosphate_oxygen?() @ob.is_phosphate_oxygen end

#phosphorus? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 250

def phosphorus?() @ob.is_phosphorus end

#polar_hydrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 264

def polar_hydrogen?() @ob.is_polar_hydrogen end

#positive_stereo? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 271

def positive_stereo?() @ob.is_positive_stereo end

#remove_an_h!(add_charge = true) ⇒ Object

permanently removes a hydrogen by properly incrementing the spin_multiplicity (and deleting a hydrogen if one is explicitly attached to the atom). If called with cnt=2 a carbene or nitrene can be made (giving a spin_multiplicity of 3). Makes no effort to ensure that the proper number of hydrogens already exist to be deleted, just alters the spin_multiplicity and deletes the right number of hydrogens if they are available to be deleted. Adds one charge to the atom.



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# File 'lib/rubabel/atom.rb', line 163

def remove_an_h!(add_charge=true)
  new_spin = 
    case @ob.get_spin_multiplicity
    when 0 then 2
    when 2 then 3
    end
  @ob.set_spin_multiplicity(new_spin)
  atoms.each do |atom|
    if atom.atomic_num == 1
      self.mol.delete_atom(atom)
      break
    end
  end
  # add the charge
  (self.charge = charge + 1) if add_charge
  self
end

#single_bond? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 283

def single_bond?
  each_bond.any? {|bond| bond.bond_order == 1 }
end

#spin ⇒ Object

end



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# File 'lib/rubabel/atom.rb', line 229

def spin
  @ob.get_spin_multiplicity
end

#sulfate_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 261

def sulfate_oxygen?() @ob.is_sulfate_oxygen end

#sulfur? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 249

def sulfur?() @ob.is_sulfur end

#type ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 233

def type
  @ob.get_type
end

#valence ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 237

def valence
  @ob.get_valence
end

#vector ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 241

def vector
  @ob.get_vector
end