Class: ChemScanner::Export::CML

Inherits:
Object
  • Object
show all
Defined in:
lib/chem_scanner/export/cml.rb

Constant Summary collapse

CML_ATTR = 
{
  "xmlns" => "http://www.xml-cml.org/schema",
  "xmlns:convention" => "http://www.xml-cml.org/convention",
  "convention" => "convention:molecular",
  "version" => "ChemScanner v0.0.1",
}.freeze

Instance Method Summary collapse

Constructor Details

#initialize(objects, molecule_only) ⇒ CML

Returns a new instance of CML.



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# File 'lib/chem_scanner/export/cml.rb', line 16

def initialize(objects, molecule_only)
  @objects = objects
  @molecule_only = molecule_only
  @output = ""
end

Instance Method Details

#mdl_from_smiles(smiles) ⇒ Object 



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# File 'lib/chem_scanner/export/cml.rb', line 90

def mdl_from_smiles(smiles)
  rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
  rw_mol.mol_to_mol_block(true, -1, false)
end

#molecule_cml(molecule) ⇒ Object 



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# File 'lib/chem_scanner/export/cml.rb', line 42

def molecule_cml(molecule)
  rw_mol = if molecule.class == OpenStruct
             RDKitChem::RWMol.mol_from_mol_block(molecule[:mdl])
           else
             molecule.rw_mol
           end
  molecule_cml_from_rw_mol(rw_mol)
end

#molecule_cml_from_rw_mol(rw_mol) ⇒ Object 



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# File 'lib/chem_scanner/export/cml.rb', line 51

def molecule_cml_from_rw_mol(rw_mol)
  builder = Nokogiri::XML::Builder.new do |cml|
    cml.molecule("spinMultiplicity" => "2") {

      cml.atomArray {
        (0..rw_mol.get_num_atoms - 1).each do |idx|
          rd_atom = rw_mol.get_atom_with_idx(idx)
          pos = rw_mol.get_conformer.get_atom_pos(0)

          cml.atom(
            id: idx,
            elementType: rd_atom.get_symbol,
            hydrogenCount: rd_atom.get_total_num_hs,
            x3: pos.x,
            y3: pos.y,
            z3: 0,
          )
        end
      }
      cml.bondArray {
        (0..rw_mol.get_num_bonds - 1).each do |idx|
          rd_bond = rw_mol.get_bond_with_idx(idx)

          bidx = rd_bond.get_begin_atom_idx
          eidx = rd_bond.get_end_atom_idx
          atom_refs = "#{bidx} #{eidx}"

          cml.bond(
            atomRefs2: atom_refs,
            order: rd_bond.get_bond_type_as_double,
          )
        end
      }
    }
  end

  builder.doc.root.to_s
end

#molecules_cml(cml) ⇒ Object 



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# File 'lib/chem_scanner/export/cml.rb', line 36

def molecules_cml(cml)
  @objects.each do |mol|
    cml.parent << molecule_cml(mol)
  end
end

#process ⇒ Object 



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# File 'lib/chem_scanner/export/cml.rb', line 22

def process
  return false unless @objects.class == Array

  builder = Nokogiri::XML::Builder.new do |cml|
    cml.cml(CML_ATTR) {
      @molecule_only ? molecules_cml(cml) : reactions_cml(cml)
    }
  end

  @output = builder.to_xml

  @output
end

#reaction_condition_cml(cml, reaction) ⇒ Object 



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# File 'lib/chem_scanner/export/cml.rb', line 136

def reaction_condition_cml(cml, reaction)
  no_cond = (
    reaction.temperature.empty? &&
    reaction.time.empty?
  )
  return if no_cond

  temp = nil
  temp_unit = nil
  unless reaction.temperature.empty?
    temp = reaction.temperature.scan(/\d+/).first
    check_f = (
      reaction.temperature.include?("F") ||
      reaction.temperature.include?("℉")
    )
    temp_unit = check_f ? "cml:Fahrenheit" : "cml:Celsius"
  end

  duration = nil
  unless reaction.time.empty?
    time = ChronicDuration.parse(reaction.time)
    duration = ChronicDuration.output(time, :format => :chrono)
  end

  cml.conditionList {
    unless temp.nil? || temp_unit.nil?
      cml.scalar("dictRef" => "cml:temp", "units" => temp_unit) {
        cml.parent << temp
      }
    end

    unless duration.nil?
      cml.scalar("dictRef" => "cml:timeDuration", "units" => "xsd:date") {
        cml.parent << duration
      }
    end
  }
end

#reactions_cml(cml) ⇒ Object 



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# File 'lib/chem_scanner/export/cml.rb', line 95

def reactions_cml(cml)
  cml.send("reactionList") {
    @objects.each do |r|
      reaction_attr = {
        "id" => r.arrow_id
      }
      reaction_attr["yield"] = r.yield unless r.yield.empty?
      cml.reaction(reaction_attr) {
        cml.reactantList {
          r.reactants.each do |reactant|
            cml.reactant {
              cml.parent << molecule_cml(reactant)
            }
          end
          r.reagents.each do |reagent|
            cml.reactant("role" => "reagents") {
              cml.parent << molecule_cml(reagent)
            }
          end
          r.reagent_smiles.each do |smi|
            cml.reactant("role" => "reagents") {
              mdl = mdl_from_smiles(smi)
              cml.parent << molecule_cml(OpenStruct.new(mdl: mdl))
            }
          end
        }
        cml.productList {
          r.products.each do |prod|
            cml.product {
              cml.parent << molecule_cml(prod)
            }
          end
        }

        reaction_condition_cml(cml, r)
        cml.description r.description unless r.description.empty?
      }
    end
  }
end