Class: ChemScanner::Interpreter::MoleculeTextGroup

Inherits:
Object
  • Object
show all
Includes:
BoldGroup
Defined in:
lib/chem_scanner/interpreter/text_group/molecule_text_group.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from BoldGroup

#extract_alphabet_number, #extract_range_number, #group_combinations, #line_bold_groups, #normalize_bold, #normalize_bold_groups, #text_bold_groups

Constructor Details

#initialize(molecule, alias_info, scheme) ⇒ MoleculeTextGroup

Returns a new instance of MoleculeTextGroup.



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 12

def initialize(molecule, alias_info, scheme)
  @molecule = molecule
  @alias_info = alias_info
  @mol_map = scheme.mol_map
  @text_map = scheme.text_map

  # List of aliases, ex: ["R1", "R2"]
  @alias_groups = []

  # final list if text-groups and label
  @text_groups = []

  retrieve_alias_groups
end

Instance Attribute Details

#alias_groups ⇒ Object

Returns the value of attribute alias_groups.



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 10

def alias_groups
  @alias_groups
end

#bold_groups ⇒ Object

Returns the value of attribute bold_groups.



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 10

def bold_groups
  @bold_groups
end

#plain_groups ⇒ Object

Returns the value of attribute plain_groups.



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 10

def plain_groups
  @plain_groups
end

#text_groups ⇒ Object

Returns the value of attribute text_groups.



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 10

def text_groups
  @text_groups
end

Instance Method Details

#build_molecule_combis ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 40

def build_molecule_combis
  # group list without associated label
  @plain_groups = {}

  # groups with associated label
  @bold_groups = []

  @molecule.text_ids.each do |tid|
    bolds, groups = text_bold_groups(tid)
    bolds.reject!(&:empty?)

    if bolds.empty?
      @plain_groups.merge!(groups) { |_, old, new| old.concat(new) }
    else
      norm_bolds = normalize_bold_groups(bolds, groups)

      @bold_groups.concat(norm_bolds)
    end
  end

  n_atom_groups = plain_groups.reject do |k, _|
    ChemScanner::Interpreter.super_atom?(k)
  end

  combis = if n_atom_groups.empty?
             group_combinations(plain_groups)
           else
             n_atom_combinations(plain_groups)
           end

  @text_groups = @bold_groups + combis.map { |g| { group: g } }
end

#generate_molecule ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 73

def generate_molecule
  malias = @alias_info[@molecule.id]

  generated_molecules = []
  @text_groups.each do |bg|
    cmol = @molecule.clone
    group_val = bg[:group]

    generated_text = []
    malias.each do |ainfo|
      agroup = ainfo[:group]
      val = group_val[agroup]
      next if val.nil?

      if ainfo[:type] == GENERATE_N_ATOM
        next if (val =~ /\d+/).nil? || val.to_i == 1

        cmol.n_atom_transform(ainfo[:aid], val.to_i)
      else
        cmol.group_transform(ainfo[:aid], agroup, val)
      end

      generated_text << "#{agroup} - #{val}"
    end

    cmol.update_output_formats
    bg[:bold].nil? || cmol.label = bg[:bold]

    cmol.text += ". Generated with: " + generated_text.join("; ") unless generated_text.empty?
    @mol_map[cmol.id] = cmol
    generated_molecules.push(cmol)
  end

  generated_molecules
end

#inspect ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 128

def inspect
  (
    "#<MoleculeTextGroup: id=#{@molecule.id}, " +
    "alias_groups: #{@alias_groups}, " +
    "plain_groups: #{@plain_groups}, " +
    "bold_groups: #{@bold_groups} >"
  )
end

#interpret ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 36

def interpret
  build_molecule_combis
end

#n_atom_combinations(group) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 109

def n_atom_combinations(group)
  pilot_key = group.keys.first
  group.each do |k, v|
    pilot_key = k if v.count > group[pilot_key].count
  end

  combis = []
  group[pilot_key].each_with_index do |_, idx|
    combi = {}
    group.each do |k, v|
      combi[k] = v[idx] unless v[idx].nil?
    end

    combis.push(combi)
  end

  combis
end

#retrieve_alias_groups ⇒ Object 



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# File 'lib/chem_scanner/interpreter/text_group/molecule_text_group.rb', line 27

def retrieve_alias_groups
  mid = @molecule.id
  if @alias_info.key?(mid)
    @alias_groups = @alias_info[mid].map { |i| i[:group] }.compact
  end

  @alias_groups.reject!(&:empty?)
end