Class: Rubabel::Atom

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

Instance Attribute 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 48

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 46

def ob
  @ob
end

Instance Method Details

#amide_nitrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 346

def amide_nitrogen?() @ob.is_amide_nitrogen end

#anti_clockwise? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 353

def anti_clockwise?() @ob.is_anti_clockwise end

#aromatic? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 334

def aromatic?() @ob.is_aromatic end

#aromatic_noxide? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 349

def aromatic_noxide?() @ob.is_aromatic_noxide end

#atomic_mass ⇒ Object 



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

def atomic_mass
  @ob.get_atomic_mass
end

#atomic_num ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 126

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 118

def atoms
  each_atom.map.to_a
end

#axial? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 351

def axial?() @ob.is_axial end

#bond!(arg, bond_order = 1) ⇒ Object Also known as: <<

connects the atom-like specifier to this atom through Molecule#add_atom! returns the atom that was just added for chaining. Takes any argument that Molecule#add_atom! will take.



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# File 'lib/rubabel/atom.rb', line 74

def bond!(arg, bond_order=1)
  mol.add_atom!(arg, bond_order, self)
end

#bonds ⇒ Object

returns the bonds. Consider using each_bond.



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# File 'lib/rubabel/atom.rb', line 101

def bonds
  each_bond.map.to_a
end

#carbon? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 329

def carbon?() @ob.is_carbon end

#carbonyl_carbon? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 393

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

#carbonyl_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 388

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 384

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

#carboxyl_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 342

def carboxyl_oxygen?() @ob.is_carboxyl_oxygen end

#chiral? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 350

def chiral?() @ob.is_chiral end

#chiral_volume? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 357

def chiral_volume?() @ob.has_chiral_volume end

#chirality_specified? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 356

def chirality_specified?() @ob.has_chirality_specified end

#clockwise? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 352

def clockwise?() @ob.is_clockwise end

#connect!(atom, bond_order = 1) ⇒ Object

connects a Rubabel::Atom object with a bond



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# File 'lib/rubabel/atom.rb', line 80

def connect!(atom, bond_order=1)
  @ob.get_parent.add_bond(@ob.get_idx, atom.ob.get_idx, bond_order)
end

#connected? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 339

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 401

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

#dec_implicit_valence! ⇒ Object

decrease by one the maximum number of connections expected for this atom



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# File 'lib/rubabel/atom.rb', line 320

def dec_implicit_valence!
  @ob.decrement_implicit_valence
end

#do_with_hydrogens(&block) ⇒ Object

doesn’t take into account pH (use Molecule#do_with_hydrogens)



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# File 'lib/rubabel/atom.rb', line 180

def do_with_hydrogens(&block)
  _obmol = @ob.get_parent
  had_hydrogens = _obmol.has_hydrogens_added
  _obmol.add_hydrogens(self.ob) unless had_hydrogens
  reply = block.call(had_hydrogens)
  _obmol.delete_hydrogens(self.ob) unless had_hydrogens
  reply
end

#do_without_hydrogens(&block) ⇒ Object

doesn’t take into account pH (use Molecule#do_without_hydrogens)



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# File 'lib/rubabel/atom.rb', line 170

def do_without_hydrogens(&block)
  _obmol = @ob.get_parent
  had_hydrogens = _obmol.has_hydrogens_added
  _obmol.delete_hydrogens(self.ob) if had_hydrogens
  reply = block.call(had_hydrogens)
  _obmol.add_hydrogens(self.ob) if had_hydrogens
  reply
end

#double_bond? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 376

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 106

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 84

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

#element ⇒ Object Also known as: el

elemental symbol, properly capitalized and returned as a Symbol



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# File 'lib/rubabel/atom.rb', line 66

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 247

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 130

def exact_mass
  @ob.get_exact_mass
end

#explicit_hydrogen_count ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 371

def explicit_hydrogen_count
  @ob.explicit_hydrogen_count
end

#formal_charge ⇒ Object Also known as: charge 



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# File 'lib/rubabel/atom.rb', line 134

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 139

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 96

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 358

def hbond_acceptor?() @ob.is_hbond_acceptor end

#hbond_donor? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 359

def hbond_donor?() @ob.is_hbond_donor end

#hbond_donor_h? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 360

def hbond_donor_h?() @ob.is_hbond_donor_h end

#hetero_valence ⇒ Object

not recognizing get_heavy_valence right now for some reason def heavy_valence

@ob.get_heavy_valence

end



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# File 'lib/rubabel/atom.rb', line 149

def hetero_valence
  @ob.get_hetero_valence
end

#heteroatom? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 337

def heteroatom?() @ob.is_heteroatom end

#hyb ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 153

def hyb
  @ob.get_hybridization
end

#hydrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 328

def hydrogen?() @ob.is_hydrogen end

#hydrogen_count ⇒ Object Also known as: num_h

the total number of hydrogens bonded to the atom (implicit + explicit)



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# File 'lib/rubabel/atom.rb', line 363

def hydrogen_count
  @ob.implicit_hydrogen_count + @ob.explicit_hydrogen_count
end

#id ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 52

def id
  @ob.get_id
end

#id=(val) ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 56

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 61

def idx
  @ob.get_idx
end

#implicit_hydrogen_count ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 367

def implicit_hydrogen_count
  @ob.implicit_hydrogen_count
end

#implicit_valence ⇒ Object

maximum number of connections expected for this atom



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# File 'lib/rubabel/atom.rb', line 305

def implicit_valence
  @ob.get_implicit_valence
end

#implicit_valence=(val) ⇒ Object

set the maximum number of connections expected for this atom



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# File 'lib/rubabel/atom.rb', line 310

def implicit_valence=(val)
  @ob.set_implicit_valence(val)
end

#in_ring? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 335

def in_ring?() @ob.is_in_ring end

#in_ring_size? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 336

def in_ring_size?() @ob.is_in_ring_size end

#inc_implicit_valence! ⇒ Object

increase by one the maximum number of connections expected for this atom



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# File 'lib/rubabel/atom.rb', line 315

def inc_implicit_valence!
  @ob.increment_implicit_valence
end

#inspect ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 405

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

#inspect_internals ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 409

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 161

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 41

def mol
  @ob.get_parent.andand.upcast
end

#negative_stereo? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 355

def negative_stereo?() @ob.is_negative_stereo end

#nitro_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 345

def nitro_oxygen?() @ob.is_nitro_oxygen end

#nitrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 330

def nitrogen?() @ob.is_nitrogen end

#non_polar_hydrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 348

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 338

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 341

def one_four?() @ob.is_one_four end

#one_three? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 340

def one_three?() @ob.is_one_three end

#oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 331

def oxygen?() @ob.is_oxygen end

#partial_charge ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 165

def partial_charge
  @ob.get_partial_charge
end

#phosphate_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 343

def phosphate_oxygen?() @ob.is_phosphate_oxygen end

#phosphorus? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 333

def phosphorus?() @ob.is_phosphorus end

#polar_hydrogen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 347

def polar_hydrogen?() @ob.is_polar_hydrogen end

#positive_stereo? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 354

def positive_stereo?() @ob.is_positive_stereo end

#remove_a_hydride!(add_placeholder_hydrogens = false) ⇒ Object

removes a proton with its electrons from an atom. This gives precisely the same molecule as if the molecule were input by smiles. csmiles, formula, exact_mass, valence, implicit_valence, etc.

mol = Rubabel["CC"]
mol[1].remove_a_hydride!
mol == Rubabel["C[CH2+]"]  # in all characteristics

Note, however, that with explicit hydrogens, the partial charge is not matching up, even though every other property seems to be. I’m not sure why this is.

mol == Rubabel["C[CH2+]"].add_h!
mol[1].remove_a_hydride!
mol == Rubabel["C[CH2+]"].add_h!  # identical except in partial charge!



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# File 'lib/rubabel/atom.rb', line 234

def remove_a_hydride!(add_placeholder_hydrogens=false)
  remove_a_hydrogen!(2, add_placeholder_hydrogens)
end

#remove_a_hydrogen!(with_num_electrons = 1, add_placeholder_hydrogens = false) ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 193

def remove_a_hydrogen!(with_num_electrons=1, add_placeholder_hydrogens=false)
  self.dec_implicit_valence!
  case with_num_electrons
  when 0
    self.charge -= 1
  when 1
    raise NotImplementedError, "not doing free radicals just yet"
  when 2
    self.charge += 1
  end
  if @ob.explicit_hydrogen_count > 0
    _obmol = @ob.get_parent
    each do |atom|
      if atom.hydrogen?
        _obmol.delete_atom(atom.ob, false)
        break
      end
    end
  else
    if add_placeholder_hydrogens
      @ob.get_parent.add_hydrogens(@ob)
    end
  end
  self
end

#remove_a_proton!(add_placeholder_hydrogens = false) ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 189

def remove_a_proton!(add_placeholder_hydrogens=false)
  remove_a_hydrogen!(0, add_placeholder_hydrogens)
end

#single_bond? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 380

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 286

def spin
  @ob.get_spin_multiplicity
end

#spin=(val) ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 290

def spin=(val)
  @ob.set_spin_multiplicity(val)
end

#sulfate_oxygen? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 344

def sulfate_oxygen?() @ob.is_sulfate_oxygen end

#sulfur? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/atom.rb', line 332

def sulfur?() @ob.is_sulfur end

#type ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 294

def type
  @ob.get_type
end

#valence ⇒ Object

Returns the current number of explicit connections. Don’t confuse this for implicit_valence.



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# File 'lib/rubabel/atom.rb', line 300

def valence
  @ob.get_valence
end

#vector ⇒ Object 



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# File 'lib/rubabel/atom.rb', line 324

def vector
  @ob.get_vector
end