Class: ChemScanner::Interpreter::Molecule

Inherits:
Object
  • Object
show all
Defined in:
lib/chem_scanner/interpreter/element/molecule.rb

Overview

Molecule class

Constant Summary collapse

RGB_RED = 
"FF0000"
CHEMDRAW_RDKIT_BTYPE_MAP = 
{
  0 => 0,
  1 => 1,
  2 => 2,
  3 => 3,
  4 => 4,
  5 => 5,
  6 => 6,
  1.5 => 7,
  2.5 => 8,
  3.5 => 9,
  4.5 => 10,
  5.5 => 11,
  "ionic" => 13,
  "hydrogen" => 14,
  "dative" => 17,
}.freeze

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fragment = nil) ⇒ Molecule

Returns a new instance of Molecule.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 36

def initialize(fragment = nil)
  @polygon = fragment.polygon unless fragment.nil?
  @text = ""
  @label = ""
  @mdl = ""
  @cano_smiles = ""
  @abbreviation = ""
  @text_ids = []
  @boxed = fragment.boxed unless fragment.nil?
  @details = OpenStruct.new

  @fragment = fragment

  @atom_bookmark_map = {}
  @atom_map = {}
  @rw_mol = RDKitChem::RWMol.new
  @conf = RDKitChem::Conformer.new
  @rw_mol.add_conf(@conf)

  @bond_map = {}

  @dash_bonds = []
  @dative_bonds = []
end

Instance Attribute Details

#abbreviation ⇒ Object

Returns the value of attribute abbreviation.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 11

def abbreviation
  @abbreviation
end

#atom_map ⇒ Object (readonly)

Returns the value of attribute atom_map.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def atom_map
  @atom_map
end

#boxed ⇒ Object

Returns the value of attribute boxed.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 11

def boxed
  @boxed
end

#cano_smiles ⇒ Object (readonly)

Returns the value of attribute cano_smiles.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def cano_smiles
  @cano_smiles
end

#clone_from ⇒ Object

Returns the value of attribute clone_from.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 11

def clone_from
  @clone_from
end

#dash_bonds ⇒ Object (readonly)

Returns the value of attribute dash_bonds.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def dash_bonds
  @dash_bonds
end

#dative_bonds ⇒ Object (readonly)

Returns the value of attribute dative_bonds.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def dative_bonds
  @dative_bonds
end

#details ⇒ Object

Returns the value of attribute details.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 11

def details
  @details
end

#fragment ⇒ Object (readonly)

Returns the value of attribute fragment.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def fragment
  @fragment
end

#is_red ⇒ Object (readonly)

Returns the value of attribute is_red.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def is_red
  @is_red
end

#label ⇒ Object

Returns the value of attribute label.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 11

def label
  @label
end

#mdl ⇒ Object (readonly)

Returns the value of attribute mdl.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def mdl
  @mdl
end

#polygon ⇒ Object (readonly)

Returns the value of attribute polygon.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def polygon
  @polygon
end

#rw_mol ⇒ Object (readonly)

Returns the value of attribute rw_mol.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 14

def rw_mol
  @rw_mol
end

#text ⇒ Object

Returns the value of attribute text.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 11

def text
  @text
end

#text_ids ⇒ Object

Returns the value of attribute text_ids.



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 11

def text_ids
  @text_ids
end

Class Method Details

.new_from_smiles(id, smiles) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 458

def self.new_from_smiles(id, smiles)
  mol = new(nil)
  rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
  mol.set_rw_mol(rw_mol)

  fragment = OpenStruct.new(id: id)
  mol.set_fragment(fragment)

  mdl = rw_mol.mol_to_mol_block(true, -1, false)
  mol.set_output_formats(smiles, mdl)

  mol
end

Instance Method Details

#add(other) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 348

def add(other)
  @fragment.add(other.fragment)
  @polygon = fragment.polygon

  @text += " #{other.text}"
  @label = ""
  @label += " #{other.label}" unless other.label.empty?
  @text_ids.concat(other.text_ids)
  @boxed |= other.boxed
  odetails = other.details.marshal_dump
  @details = OpenStruct.new(@details.marshal_dump.merge(odetails))

  @atom_map.merge!(other.atom_map)

  combined = RDKitChem.combine_mols(@rw_mol, other.rw_mol)
  @rw_mol = RDKitChem::RWMol.new(combined)

  @dash_bonds.concat(other.dash_bonds)
  @dative_bonds.concat(other.dative_bonds)
end

#add_bond(bond) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 102

def add_bond(bond)
  order = bond.order
  return -1 unless CHEMDRAW_RDKIT_BTYPE_MAP.key?(order)

  begin_id = bond.begin_id
  end_id = bond.end_id
  stereo = bond.stereo

  inverse_direction = [4, 7, 10, 12].include?(stereo)
  begin_id, end_id = end_id, begin_id if inverse_direction

  batom = @atom_map[begin_id]
  eatom = @atom_map[end_id]
  bidx = batom.get_idx
  eidx = eatom.get_idx

  bonds = get_atom_bonds(begin_id) + get_atom_bonds(end_id)
  duplicate = bonds.detect do |b|
    b.has_endpoint?(begin_id) && b.has_endpoint?(end_id)
  end
  return -1 unless duplicate.nil?

  if order == "dative"
    bond.order = 1
    order = 1

    if batom.charge.zero? && eatom.charge.zero?
      batom.set_formal_charge(-1)
      eatom.set_formal_charge(1)
    end

    @dative_bonds.push(bond.id)
  end

  if stereo == 1
    @dash_bonds.push(bond.id)
    return -1
  end

  begin
    rd_bond = RDKitChem::Bond.new(order)
    rd_bond.set_begin_atom_idx(bidx)
    rd_bond.set_end_atom_idx(eidx)
    # bid = @rw_mol.add_bond(bidx, eidx, order)

    # Stereo handling
    sdir = { 3 => 2, 4 => 2, 6 => 1, 7 => 1 }
    if sdir.key?(stereo)
      rd_bond.set_bond_dir(sdir[stereo])
      @chiral_possible = true
    end

    rd_bond.set_owning_mol(@rw_mol)
    bid = @rw_mol.add_bond(rd_bond)

    return bid
  rescue RuntimeError
    return -1
  end
end

#charged_atom_ids ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 291

def charged_atom_ids
  @atom_map.each_with_object([]) do |(key, atom), ids|
    charge = atom.charge
    next ids if charge.zero?

    ids.push(key)
  end
end

#check_red ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 262

def check_red
  ncolors = @fragment.node_map.values.map(&:color).uniq
  bcolors = @fragment.bond_map.values.map(&:color).uniq

  if ncolors.count != 1 || bcolors.count != 1
    @is_red = false
    return
  end

  ncolor = ncolors.first
  bcolor = bcolors.first

  if ncolor != bcolor
    @is_red = false
    return
  end

  color = @fragment.parser.color_table[ncolor].upcase
  color == RGB_RED
end

#clone ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 300

def clone
  cloned = self.class.new(@fragment.clone)
  cloned.process
  cloned.update_output_formats

  cloned.clone_from = @clone_from.nil? ? id : @clone_from
  cloned.label = @label
  cloned.text_ids = @text_ids
  cloned.text = @text

  cloned
end

#get_atom(id) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 283

def get_atom(id)
  @atom_map[id]
end

#get_atom_bonds(atom_id) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 98

def get_atom_bonds(atom_id)
  @bond_map.values.select { |b| b.has_endpoint?(atom_id) }
end

#get_cano_smiles ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 313

def get_cano_smiles
  @rw_mol.mol_to_smiles(true)
end

#get_mdl ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 317

def get_mdl
  @dash_bonds.each do |bid|
    bond = @fragment.bond_map[bid]
    bid = bond.begin_id
    eid = bond.end_id
    bidx = @atom_map[bid].get_idx
    eidx = @atom_map[eid].get_idx

    @rw_mol.add_bond(bidx, eidx, 17)
  end

  mdl = @rw_mol.mol_to_mol_block(true, -1, false)

  @dash_bonds.each do |bid|
    bond = @fragment.bond_map[bid]
    bid = bond.begin_id
    eid = bond.end_id
    bidx = @atom_map[bid].get_idx
    eidx = @atom_map[eid].get_idx

    @rw_mol.remove_bond(bidx, eidx)
  end

  mdl.force_encoding(Encoding::UTF_8)
end

#group_transform(aid, group, value) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 418

def group_transform(aid, group, value)
  text = @atom_map[aid].alias_text.dup
  return unless text.include?(group)

  text.sub!(group, value)
  info = OpenStruct.new(text: text, id: aid)

  try_expand_atoms([info])
  update_output_formats
end

#id ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 61

def id
  @fragment.id
end

#inspect ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 429

def inspect
  (
    "#<Molecule: id=#{fragment.id}, " +
      "polygon: #{polygon}," +
      "text: #{text}, " +
      "label: #{label}, " +
      "mdl: #{mdl}, " +
      "cano_smiles: #{cano_smiles}, " +
      "text_ids: #{text_ids}, " +
      "boxed: #{boxed}, " +
      "details: #{details}, " +
      "dash_bonds: #{dash_bonds}, " +
      "dative_bonds: #{dative_bonds} >"
  )
end

#kekulize ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 163

def kekulize
  RDKitChem.kekulize(@rw_mol)
end

#min_distance_to_point(point) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 248

def min_distance_to_point(point)
  min = 9_999_999

  @fragment.node_map.values.reject(&:expanded).each do |node|
    next if node.x.nil? || node.y.nil?

    npoint = Geometry::Point.new(node.x, node.y)
    dist = npoint.distance_to(point)
    min = dist if dist < min
  end

  min
end

#n_atom_transform(aid, num) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 369

def n_atom_transform(aid, num)
  return false if num == 1

  bonds = @fragment.bond_map.values.select do |b|
    [b.begin_id, b.end_id].include?(aid)
  end
  return false unless bonds.count == 2

  others = bonds.reduce([]) do |arr, bond|
    arr.concat([bond.begin_id, bond.end_id] - [aid])
  end
  return false unless others.count == 2

  ref_mol = RDKitChem::RWMol.new(@rw_mol)

  target_atom = @atom_map[aid]
  target_idx = target_atom.get_idx

  others.each do |other|
    oidx = @atom_map[other].get_idx
    @rw_mol.remove_bond(target_idx, oidx)
  end

  @rw_mol.remove_atom(target_idx)
  @atom_map.delete(aid)

  added_id = []
  (1..num).each do
    catom = target_atom.clone
    @atom_map[catom.id] = catom
    added_id.push(catom.id)
  end

  others.insert(1, *added_id)
  # for n atoms, need n+1 bonds
  (1..num + 1).each do |i|
    begin_idx = @atom_map[others[i - 1]].get_idx
    end_idx = @atom_map[others[i]].get_idx
    @rw_mol.add_bond(begin_idx, end_idx, 1)
  end

  begin
    @rw_mol.compute_2dcoords(ref_mol)
  rescue RuntimeError
  end

  update_output_formats
end

#process ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 65

def process
  @fragment.node_map.each do |nid, node|
    atom = Atom.new(node, @rw_mol)
    atom.process

    @atom_map[nid] = atom
  end

  @chiral_possible = false
  @fragment.bond_map.each do |k, bond|
    bid = add_bond(bond)
    next if bid.negative?

    @bond_map[k] = bond
  end

  @rw_mol.detect_atom_stereo_chemistry(@conf) if @chiral_possible

  @rw_mol.clear_single_bond_dir_flags
  @rw_mol.detect_bond_stereo_chemistry(@conf)

  @rw_mol.remove_hs(false, false, false)

  begin
    kekulize
    RDKitChem.sanitize_mol(@rw_mol)
  rescue RuntimeError
  end

  try_expand
  check_red
end

#set_fragment(fragment) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 449

def set_fragment(fragment)
  @fragment = fragment
end

#set_output_formats(smiles, mdl) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 453

def set_output_formats(smiles, mdl)
  @cano_smiles = smiles
  @mdl = mdl
end

#set_rw_mol(rw_mol) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 445

def set_rw_mol(rw_mol)
  @rw_mol = rw_mol
end

#to_hash ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 287

def to_hash
  { id: @fragment.id, smiles: @cano_smiles, label: @label, text: @text }
end

#try_expand ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 167

def try_expand
  list_ids_with_text = []

  @fragment.node_map.each do |nid, node|
    # Node_Type = 8: AnonymousAlternativeGroup
    next if !node.is_alias || node.type == 8 || node.alias_text.empty? \
            || node.nested_fragment.count.positive? || !node.warning

    atext = node.alias_text
    list_ids_with_text.push(OpenStruct.new(text: atext, id: nid))
  end

  return if list_ids_with_text.empty?

  try_expand_atoms(list_ids_with_text)
  update_output_formats
end

#try_expand_atoms(list_expand) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 185

def try_expand_atoms(list_expand)
  ref = RDKitChem::RWMol.new(@rw_mol)

  delete_ids = []
  list_expand.each do |info|
    next try_expand_hydrogen(info.id) if info.text == "H"

    smiles = ChemScanner.get_superatom(info.text)
    next if smiles.empty?

    expand_mol = RDKitChem::RWMol.mol_from_smiles(smiles)

    atom = @atom_map[info.id]
    delete_ids.push(info.id)
    idx = atom.get_idx

    target_bonds = get_atom_bonds(info.id)
    first_expand_idx = @rw_mol.get_num_atoms

    @rw_mol.insert_mol(expand_mol)

    target_bonds.each do |bond|
      other_id = bond.other_endpoint(info.id)
      other_idx = @atom_map[other_id].get_idx

      @rw_mol.remove_bond(other_idx, idx)
      # after combined, first atom should be the target to link with
      @rw_mol.add_bond(other_idx, first_expand_idx, bond.order)
    end

    target_bonds.each { |b| @bond_map.delete(b.id) }
  end

  delete_ids.each do |aid|
    atom = @rw_mol.get_atom_with_bookmark(aid)
    @rw_mol.remove_atom(atom)
    @atom_map.delete(aid)
  end

  # Generate added atom coords
  begin
    @rw_mol.compute_2dcoords(ref)
  rescue RuntimeError
    return
  end
end

#try_expand_hydrogen(atom_id) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 232

def try_expand_hydrogen(atom_id)
  target_bonds = get_atom_bonds(atom_id)
  return if target_bonds.count == 2

  target_bond = target_bonds.first
  other = target_bond.other_endpoint(atom_id)
  other_atom = @atom_map[other]
  atom = @atom_map[atom_id]

  @rw_mol.remove_bond(other_atom.get_idx, atom.get_idx)
  @rw_mol.remove_atom(atom.get_idx)

  @atom_map.delete(atom_id)
  @bond_map.delete(target_bond.id)
end

#update_output_formats ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/molecule.rb', line 343

def update_output_formats
  @cano_smiles = get_cano_smiles
  @mdl = get_mdl
end