Class: ChemScanner::Interpreter::Scheme

Inherits:
Object
  • Object
show all
Includes:
PostProcess, PreProcess, ReactionDetection
Defined in:
lib/chem_scanner/interpreter/scheme.rb,
lib/chem_scanner/interpreter/post_process/assemble.rb

Overview

General scheme, contains all graphics (molecules, text, arrows …)

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from PostProcess

#extract_product_yield, #extract_reaction_info, #extract_temperature, #extract_time_info, #extract_yield_info, #merge_chemdraw_with_predefined, #name_to_struct, #process_reaction_info, #range_number_regex, #refine_reagents_label, #refine_text_as_molecule, #refine_text_label, #replace_label_by_molecule, #split_text, #text_regex, #time_duration_range_regex

Methods included from ReactionDetection

#assign_molecule_group, #assign_text, #assign_to_reaction, #check_position, #check_reaction_orderring, #detect_position, #detect_reaction_step, #distance_molecule_group, #molecules_intersects_with_segment, #multi_line_chain_reaction, #nearest_arrow, #nearest_molecule, #process_reactions_step, #refine_duplicate_reagents, #remove_separated_mol, #sort_arrow_map, #text_around_arrow?, #try_detect_label_position

Methods included from SchemeBase

#add_molecule_substitution_info, #add_reaction_substitution_info, #assemble_molecule_text, #auto_fit_arrow_polygons

Methods included from PreProcess

#assemble_ionic_molecule, #detect_line_fragment, #extract_fragment_graphic, #find_fragment_inside_rectangle, #fragment_to_molecules, #populate_molecule_info, #process_orbital_as_polymer, #refine_arrow, #refine_molecules, #try_check_cross, #try_extend_split, #try_extend_tail

Constructor Details

#initialize(parser) ⇒ Scheme

Returns a new instance of Scheme.



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# File 'lib/chem_scanner/interpreter/scheme.rb', line 19

def initialize(parser)
  fragment_map = parser.fragment_map.map { |k, v| [k, Fragment.new(v)] }
  @fragment_map = fragment_map.to_h
  @fragment_group_map = parser.fragment_group_map

  @geometry_map = parser.geometry_map
  @graphic_map = parser.graphic_map

  @text_map = parser.text_map
  @bracket_map = parser.bracket_map

  @mol_map = ElementMap.new
  @mol_group_map = ElementMap.new

  @arrow_map = ElementMap.new
  # Segment or headless arrow
  @segment_map = ElementMap.new

  @mol_substitutes = {}
  @reaction_substitutes = {}

  @fragment_as_line = 0

  @reactions = []
end

Instance Attribute Details

#bracket_map ⇒ Object (readonly)

Returns the value of attribute bracket_map.



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

def bracket_map
  @bracket_map
end

#fragment_as_line ⇒ Object (readonly)

Returns the value of attribute fragment_as_line.



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

def fragment_as_line
  @fragment_as_line
end

#mol_map ⇒ Object (readonly)

Returns the value of attribute mol_map.



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

def mol_map
  @mol_map
end

#n_atoms ⇒ Object (readonly)

Returns the value of attribute n_atoms.



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

def n_atoms
  @n_atoms
end

#reactions ⇒ Object (readonly)

Returns the value of attribute reactions.



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

def reactions
  @reactions
end

#text_map ⇒ Object (readonly)

Returns the value of attribute text_map.



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

def text_map
  @text_map
end

Instance Method Details

#assemble_reaction ⇒ Object 



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# File 'lib/chem_scanner/interpreter/post_process/assemble.rb', line 7

def assemble_reaction
  @reactions.each do |r|
    %w[reactant reagent product].each do |group|
      group_ids = r.send("#{group}_ids")
      groups = r.send("#{group}s")

      group_ids.each do |id|
        if @text_map.key?(id)
          r.text_ids.push(id)
          next
        end

        if @mol_map.key?(id)
          groups.push(@mol_map[id])
          next
        end

        @mol_group_map.select do |_, mgroup|
          mgroup.molecule_ids.include?(id)
        end.each do |_, mgroup|
          groups.push(mgroup.molecules.first)
        end
      end
    end

    r.arrow = @arrow_map[r.arrow_id]
    r.text_ids.concat(r.arrow.text_arr).uniq!
  end
end

#interpret ⇒ Object 



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# File 'lib/chem_scanner/interpreter/scheme.rb', line 45

def interpret
  pre_process
  reaction_detection
  post_process

  tgi = TextGroupInterpreter.new(self)
  # Detect if molecule has any n-atom, save those infos
  tgi.retrieve_n_atoms_info

  @n_atoms = tgi.n_atoms

  # Retrieve rgroups, alias-groups of molecules
  tgi.retrieve_alias_info

  # - Find R-groups ("R1", "R2", "R", ...)
  # - Find alias-groups ("X", "Y", "Ar", "M")
  # - Detect label set ("2a,b" "3-6" ...)
  # tgi.retrieve_labels_and_groups

  # - Combine corresponding addition info detected molecule/reaction text
  #   e.g., "3: m = 1, R = H"
  # - Interpret previouse retrieved data
  # - Save those infos to generate molecules/reactions later
  # interpret_labels_and_groups

  # Try generate new molecules/reactions
  #   based on R-groups, alias-groups, n-atoms ...
  tgi.generate_elements

  @mol_group_map.each do |_, mgroup|
    mgroup.molecules.each do |m|
      @mol_map[m.id] = m unless @mol_map.key?(m.id)
    end
  end
end

#molecules ⇒ Object 



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# File 'lib/chem_scanner/interpreter/scheme.rb', line 81

def molecules
  @mol_map.values
end