Class: ChemScanner::Interpreter::Reaction

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

Overview

Reaction

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Reaction

Returns a new instance of Reaction.



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

def initialize
  @arrow = nil

  @reactant_ids = []
  @reagent_ids = []
  @product_ids = []
  @text_ids = []

  @reactants = []
  @reagents = []
  @products = []
  @reagent_smiles = []
  @reagent_abbs = []

  @description = ""
  @temperature = ""
  @yield = ""
  @time = ""
  @details = OpenStruct.new

  @steps = []
end

Instance Attribute Details

#arrow ⇒ Object

Returns the value of attribute arrow.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def arrow
  @arrow
end

#arrow_id ⇒ Object

Returns the value of attribute arrow_id.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def arrow_id
  @arrow_id
end

#clone_from ⇒ Object

Returns the value of attribute clone_from.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def clone_from
  @clone_from
end

#description ⇒ Object

Returns the value of attribute description.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def description
  @description
end

#details ⇒ Object

Returns the value of attribute details.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def details
  @details
end

#product_ids ⇒ Object

Returns the value of attribute product_ids.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def product_ids
  @product_ids
end

#products ⇒ Object

Returns the value of attribute products.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def products
  @products
end

#reactant_ids ⇒ Object

Returns the value of attribute reactant_ids.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def reactant_ids
  @reactant_ids
end

#reactants ⇒ Object

Returns the value of attribute reactants.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def reactants
  @reactants
end

#reagent_abbs ⇒ Object

Returns the value of attribute reagent_abbs.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def reagent_abbs
  @reagent_abbs
end

#reagent_ids ⇒ Object

Returns the value of attribute reagent_ids.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def reagent_ids
  @reagent_ids
end

#reagent_smiles ⇒ Object

Returns the value of attribute reagent_smiles.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def reagent_smiles
  @reagent_smiles
end

#reagents ⇒ Object

Returns the value of attribute reagents.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def reagents
  @reagents
end

#steps ⇒ Object

Returns the value of attribute steps.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def steps
  @steps
end

#temperature ⇒ Object

Returns the value of attribute temperature.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def temperature
  @temperature
end

#text_ids ⇒ Object

Returns the value of attribute text_ids.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def text_ids
  @text_ids
end

#time ⇒ Object

Returns the value of attribute time.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def time
  @time
end

#yield ⇒ Object

Returns the value of attribute yield.



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 7

def yield
  @yield
end

Instance Method Details

#all_ids ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 73

def all_ids
  @reagent_ids + molecule_ids
end

#clone ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 122

def clone
  cloned = self.class.new
  unless @arrow.nil?
    cloned.arrow_id = @arrow.get_tempid
    cloned.arrow = @arrow.clone
  end

  %w[reactant reagent product].each do |group|
    cloned_groups = cloned.send("#{group}s")
    groups = instance_variable_get("@#{group}s")

    groups.each { |m| cloned_groups.push(m.clone) }
    cloned.send("#{group}_ids=", cloned_groups.map(&:id))
  end

  cloned.reagent_smiles = @reagent_smiles.dup

  cloned.description = @description.dup
  cloned.temperature = @temperature.dup
  cloned.yield = @yield.dup
  cloned.time = @time.dup
  cloned.details = @details.dup

  cloned.clone_from = @clone_from.nil? ? arrow_id : @clone_from

  cloned
end

#debug_print ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 59

def debug_print
  "reaction #{@arrow_id}: "\
  "#{reactant_ids} > #{reagent_ids} > #{product_ids}"
end

#debug_print_smiles ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 64

def debug_print_smiles
  "reaction #{@arrow_id}: "\
  "#{reactant_ids} - #{reagent_ids} - #{product_ids}: #{reaction_smiles}"
end

#delete_id(id) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 77

def delete_id(id)
  [@reactant_ids, @reagent_ids, @product_ids].each do |group|
    group.delete(id) if group.include?(id)
  end
end

#delete_molecule_by_id(id) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 107

def delete_molecule_by_id(id)
  [@reactants, @reagents, @products].each do |group|
    group.delete_if { |mol| mol.id == id }
  end
end

#inspect ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 166

def inspect
  (
    "#<Reaction: id=#{@arrow.id}, " +
    "reactant_ids=#{@reactant_ids}, " +
    "reagent_ids=#{@reagent_ids}, " +
    "product_ids=#{@product_ids}, " +
    "text_ids=#{@text_ids}, " +
    "reactants=#{@reactants}, " +
    "reagents=#{@reagents}, " +
    "products=#{@products}, " +
    "reagent_smiles=#{@reagent_smiles}, " +
    "description=#{@description}, " +
    "temperature=#{@temperature}, " +
    "yield=#{@yield}, " +
    "time=#{@time}, " +
    "details=#{@details} >"
  )
end

#molecule_ids ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 69

def molecule_ids
  @reactant_ids + @product_ids
end

#product_molfiles ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 55

def product_molfiles
  @products.map { |r| r[:mdl] }
end

#reactant_molfiles ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 47

def reactant_molfiles
  @reactants.map { |r| r[:mdl] }
end

#reaction_smiles ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 37

def reaction_smiles
  reactant_smiles = @reactants.map(&:cano_smiles).join(".")
  product_smiles = @products.map(&:cano_smiles).join(".")

  reagent_smiles = @reagents.map(&:cano_smiles).compact
  reagent_smiles = reagent_smiles.concat(@reagent_smiles).join(".")

  "#{reactant_smiles}>#{reagent_smiles}>#{product_smiles}"
end

#reagent_molfiles ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 51

def reagent_molfiles
  @reagents.map { |r| r[:mdl] }
end

#replace_id(old_id, new_id) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 83

def replace_id(old_id, new_id)
  [@reactant_ids, @reagent_ids, @product_ids].each do |group|
    next unless group.include?(old_id)

    group.delete(old_id)
    group.push(new_id)
  end
end

#replace_molecule(old_id, new_mol) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 92

def replace_molecule(old_id, new_mol)
  oid = old_id

  [@reactants, @reagents, @products].each do |group|
    idx = group.index { |m| [m.id, m.clone_from].include?(old_id) }
    next if idx.nil?

    m = group[idx]
    oid = m.clone_from unless m.clone_from.nil?
    group[idx] = new_mol
  end

  replace_id(oid, new_mol.id)
end

#status ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 113

def status
  return "Failed" if @arrow.cross
  return "Planned" if @arrow.line_type == 1

  return "Failed" unless @products.detect(&:check_red).nil?

  "Succesful"
end

#to_hash ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/reaction.rb', line 150

def to_hash
  {
    id: arrow_id,
    reactants: @reactants.sort_by(&:cano_smiles).map(&:to_hash),
    reagents: @reagents.sort_by(&:cano_smiles).map(&:to_hash),
    products: @products.sort_by(&:cano_smiles).map(&:to_hash),
    steps: @steps.map(&:to_hash),
    reagent_smiles: reagent_smiles.sort,
    description: @description,
    temperature: @temperature,
    yield: @yield,
    time: @time,
    details: @details.to_h,
  }
end