Module: Rubabel::Molecule::Fragmentable

Included in:
Rubabel::Molecule
Defined in:
lib/rubabel/molecule/fragmentable.rb

Constant Summary collapse

RULES =

:sp3c_oxygen_asymmetric_far_sp3, :sp3c_nitrogen_asymmetric_far_sp3, RULES = Set[ :alcohol_to_aldehyde, :peroxy_to_carboxy, :co2_loss, 

:sp3c_oxygen_double_bond_far_side_sp3, :sp3c_oxygen_double_bond_far_side_sp2, :sp3c_oxygen_double_bond_water_loss, :sp3c_nitrogen_double_bond,

] ADDUCTS = [:lioh, :nh4cl, :nh4oh] CO_RULES = Set[:alcohol_to_aldehyde, :peroxy_to_carboxy, :co2_loss, 

:sp3c_oxygen_double_bond_water_loss, :sp3c_oxygen_double_bond_far_side_sp2, :sp3c_oxygen_double_bond_far_side_sp3, :sp3c_oxygen_asymmetric_far_sp3

]

Set[:cad_o, :cad_oo, :oxed_ether]
DEFAULT_OPTIONS = 
{
  rules: RULES,
  #adduct: nil,
  #ph: 7.4,
  # return only the set of unique fragments
  uniq: false, 
}

Instance Method Summary collapse

Instance Method Details

#alcohol_to_aldehyde(carbon, oxygen, carbon_nbrs) ⇒ Object 



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# File 'lib/rubabel/molecule/fragmentable.rb', line 103

def alcohol_to_aldehyde(carbon, oxygen, carbon_nbrs)
  # alcohol becomes a ketone and one R group is released
  frag_sets = carbon_nbrs.select {|atom| atom.type == 'C3' }.map do |_atom|
    frags = feint_double_bond(carbon.get_bond(oxygen)) do |_mol|
      frags = _mol.split(carbon.get_bond(_atom))
      frags.map(&:add_h!)
    end
  end
  allowable_fragment_sets!(frag_sets)
end

#allowable_fragment_sets!(fragment_sets) ⇒ Object

add_h! to self, then selects allowable fragments



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# File 'lib/rubabel/molecule/fragmentable.rb', line 40

def allowable_fragment_sets!(fragment_sets)
  self.add_h!
  fragment_sets.select do |_frags| 
    putsv "ExMAIN:"
    putsv _frags.inspect
    putsv self.allowable_fragmentation?(_frags)
    self.allowable_fragmentation?(_frags)
  end
end

#allowable_fragmentation?(frags) ⇒ Boolean

molecules and fragments should all have hydrogens added (add_h!) before calling this method

For instance, water loss with double bond formation is not allowable for NCC(O)CC => CCC=C, presumably because of the lone pair and double bond resonance.

Returns:

  • (Boolean) 


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# File 'lib/rubabel/molecule/fragmentable.rb', line 35

def allowable_fragmentation?(frags)
  self.num_atoms == frags.map(&:num_atoms).reduce(:+)
end

#carbon_oxygen_esteal(carbon, oxygen) ⇒ Object

breaks the bond and gives the electrons to the oxygen



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# File 'lib/rubabel/molecule/fragmentable.rb', line 175

def carbon_oxygen_esteal(carbon, oxygen)
  nmol = self.dup
  nmol.ob.add_hydrogens
  ncarbon = nmol.atom(carbon.id)
  noxygen = nmol.atom(oxygen.id)
  nmol.delete_bond(ncarbon, noxygen)
  ncarbon.charge += 1
  noxygen.charge -= 1
  ncarbon.remove_an_h!
  #p ncarbon.ob.implicit_hydrogen_count
  #p ncarbon
  #ncarbon.ob.decrement_implicit_valence
  #p ncarbon.ob.implicit_hydrogen_count
  #p ncarbon
  #ncarbon.ob.increment_implicit_valence

  nmol.title = nmol.to_s
  p nmol.write("tmp.svg")
  parts = nmol.split
  p z=parts.first
  p z.formula
  p z.mass
  p z.exact_mass
  
  puts "HIAY"
end

#carbonyl_oxygen_dump(carbon, oxygen, carbon_nbr) ⇒ Object

splits the molecule between the carbon and carbon_nbr, adds a double bond between the carbon and oxygen, and moves whatever was on the oxygen (e.g., an OH or a charge) to the carbon_nbr. Returns two new molecules.



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# File 'lib/rubabel/molecule/fragmentable.rb', line 151

def carbonyl_oxygen_dump(carbon, oxygen, carbon_nbr)
  appendage = oxygen.atoms.find {|a| a.el != :c }
  if oxygen.charge != 0
    ocharge = oxygen.charge
  end
  nmol = self.dup
  new_oxygen = nmol.atom(oxygen.id)
  new_carbon = nmol.atom(carbon.id)
  new_carbon_nbr = nmol.atom(carbon_nbr.id)
  new_appendage = nmol.atom(appendage.id) if appendage
  nmol.delete_bond(new_carbon.get_bond(new_carbon_nbr))
  if new_appendage
    nmol.delete_bond(new_oxygen.get_bond(new_appendage)) 
    nmol.add_bond!(new_carbon_nbr, new_appendage)
  end
  if ocharge
    new_carbon_nbr.charge += ocharge
    new_oxygen.charge -= ocharge
  end
  new_carbon.get_bond(new_oxygen).bond_order = 2
  nmol.split
end

#co2_loss(carbon, oxygen, c3_nbr) ⇒ Object 



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# File 'lib/rubabel/molecule/fragmentable.rb', line 114

def co2_loss(carbon, oxygen, c3_nbr)
  # carboxyl rules ...
  # neutral carbon dioxide loss with anion gain on attaching group
  # (if carbon)
  frags = feint_double_bond(carbon.get_bond(oxygen), oxygen, c3_nbr) do |_mol|
    frags = _mol.split(c3_nbr.get_bond(carbon))
    frags.map(&:add_h!)
  end
  allowable_fragment_sets!([frags])
end

#electrophile_snatches_electrons(carbon, electrophile) ⇒ Object

warning, this method adds_h! to the calling molecule

Raises:

  • (NotImplementedError) 


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# File 'lib/rubabel/molecule/fragmentable.rb', line 67

def electrophile_snatches_electrons(carbon, electrophile)
  self.add_h!
  frags = self.split(carbon.get_bond(electrophile))
  raise NotImplementedError
  # don't check for allowable fragments because it 
  #allowable_fragment_sets!([frag_set])
end

#feint_double_bond(bond, give_e_pair = nil, get_e_pair = nil, &block) ⇒ Object

will turn bond into a double bond, yield the changed molecule, then return the bond to the original state when the block is closed returns whatever the block returned



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# File 'lib/rubabel/molecule/fragmentable.rb', line 53

def feint_double_bond(bond, give_e_pair=nil, get_e_pair=nil, &block)
  orig = bond.bond_order
  bond.bond_order = 2
  reply = 
    if give_e_pair || get_e_pair
      feint_e_transfer(give_e_pair, get_e_pair, &block)
    else
      block.call(self)
    end
  bond.bond_order = orig
  reply
end

#feint_e_transfer(give_e_pair = nil, get_e_pair = nil, &block) ⇒ Object 



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# File 'lib/rubabel/molecule/fragmentable.rb', line 75

def feint_e_transfer(give_e_pair=nil, get_e_pair=nil, &block)
  if give_e_pair
    gc_orig = give_e_pair.charge
    give_e_pair.charge = gc_orig + 1
  end
  if get_e_pair
    rc_orig = get_e_pair.charge
    get_e_pair.charge = rc_orig - 1
  end

  reply = block.call(self)
  
  give_e_pair.charge = gc_orig if give_e_pair
  get_e_pair.charge = rc_orig if get_e_pair

  reply
end

#fragment(opts = {}) ⇒ Object

an empty array is returned if there are no fragments generated. Hydrogens are added at a pH of 7.4, unless they have already been added.

:rules => queryable by :include? set of rules
:uniq => false



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# File 'lib/rubabel/molecule/fragmentable.rb', line 208

def fragment(opts={})
  only_uniqs = true
  opts = DEFAULT_OPTIONS.merge(opts)
  opts[:rules].each do |rule| 
    raise ArgumentError, "bad rule: #{rule}" unless RULES.include?(rule)
  end

  had_hydrogens = self.h_added?
  self.correct_for_ph!(7.4) unless had_hydrogens
  self.remove_h!

  fragment_sets = []

  if opts[:rules].any? {|r| [:cad_o, :cad_oo].include?(r) }
    self.each_match("C[O;h1,O]", only_uniqs) do |carbon, oxygen|
      carbon.atoms.select {|a| a.el == :c }.each do |carbon_nbr|
        fragment_sets << carbonyl_oxygen_dump(carbon, oxygen, carbon_nbr)
      end
    end
  end
  if opts[:rules].any? {|r| [:oxed_ether].include?(r) }
    self.each_match("C[O&X2]", only_uniqs) do |carbon, oxygen|
      fragment_sets << carbon_oxygen_esteal(carbon, oxygen)
    end
  end

  unless had_hydrogens
    fragment_sets.each {|set| set.each(&:remove_h!) }
    self.remove_h!
  end
  if opts[:uniq]
    # TODO: impelent properly
    raise NotImplementedError
    #fragment_sets = fragment_sets.uniq_by(&:csmiles) 
  end

  fragment_sets
end

#near_side_double_bond_break(carbon, electrophile) ⇒ Object 



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# File 'lib/rubabel/molecule/fragmentable.rb', line 93

def near_side_double_bond_break(carbon, electrophile)
  frag_sets = carbon.atoms.select {|atom| atom.type == "C3" }.map do |near_c3|
    frags = feint_double_bond(carbon.get_bond(near_c3)) do |_mol|
      frags = _mol.split(electrophile.get_bond(carbon))
      frags.map(&:add_h!)
    end
  end
  allowable_fragment_sets!(frag_sets)
end

#peroxy_to_carboxy(carbon, oxygen, carbon_nbrs, oxygen_nbr) ⇒ Object 



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# File 'lib/rubabel/molecule/fragmentable.rb', line 125

def peroxy_to_carboxy(carbon, oxygen, carbon_nbrs, oxygen_nbr)
  if oxygen_nbr.el == :o # has a neighbor oxygen
    distal_o = oxygen_nbr
    if distal_o.bonds.size == 1  # this is a peroxy
      frag_sets = carbon_nbrs.select {|atom| atom.type == 'C3' }.map do |_atom|
        self.swap!(carbon, _atom, oxygen, distal_o)
        frags = feint_double_bond(carbon.get_bond(oxygen)) do |_mol|

          # we swapped the atoms so the bond to split off is now
          # attached to the oxygen
          frags = _mol.split(oxygen.get_bond(_atom))
          frags.map(&:add_h!)
        end
        self.swap!(carbon, distal_o, oxygen, _atom)
        frags
      end
      allowable_fragment_sets!(frag_sets)
    end
  end

end