Parse Molecule

parseMolecule.coffee

parseMolecule = (formula) ->
  # console.log 'formula ' + formula
  elements = {}

  countElements = (input) ->
    # console.log 'count elements ' + input
    elts = input.match /[A-Z]([a-z])?(\d+)?/g
    for i in [0..elts.length - 1] by 1
      elt = (elts[i].match /[A-Z]([a-z])?(?=\d+)?/)[0]
      count = elts[i].match /\d+/
      count = if not count then 1 else (count.map (item) -> parseInt(item))[0]
      elements[elt] = if elements[elt] >= 0 then elements[elt] + count else count
  
  openBrackets = (input, closingBracket) ->
    # console.log 'open brackets, input ' + input
    output = ''
    multiplier = if (input.split closingBracket)[1] is '' then 1 else parseInt((input.split closingBracket)[1])
    # console.log multiplier
    elts = input.match /[A-Z]([a-z])?(\d+)?/g
    for i in [0..elts.length - 1] by 1
      elt = elts[i]
      eltName = (elt.match /^[A-Z]([a-z])?/)[0]
      atoms = if elt.match /\d+$/ then parseInt((elt.match /\d+$/)[0]) else 1
      atoms *= multiplier
      output += eltName + atoms
    # console.log 'output ' + output
    formula = formula.replace input, output
    return output
  
  if /(\[|\]|\{|\}|\(|\))/.test formula
    # console.log 'extract inner round brackets first'
    formulaDecomp = formula.match /\([^\(\)]+\)\d*/g
    if formulaDecomp
      # console.log 'extract round, formulaDecomp ' + formulaDecomp
      for i in [0..formulaDecomp.length - 1] by 1
        item = formulaDecomp[i]
        openBrackets item, ')'
    # console.log 'extract middle square brackets'
    formulaDecomp = formula.match /\[[^\[\]]+\]\d*/g
    if formulaDecomp
      # console.log 'extract square, formulaDecomp ' + formulaDecomp
      for i in [0..formulaDecomp.length - 1] by 1
        item = formulaDecomp[i]
        openBrackets item, ']'
    # console.log 'extract outer curly brackets'
    formulaDecomp = formula.match /\{[^\[\]]+\}\d*/g
    if formulaDecomp
      # console.log 'extract curly, formulaDecomp ' + formulaDecomp
      for i in [0..formulaDecomp.length - 1] by 1
        item = formulaDecomp[i]
        openBrackets item, '}'

  if not /(\[|\]|\{|\}|\(|\))/.test formula
    # console.log 'no brackets'
    countElements formula
  
  # console.log 'elements ' + elements
  return elements


# TEST
parseMolecule 'H2O' # {H: 2, O: 1})
parseMolecule 'Mg(OH)2' # {Mg: 1, O: 2, H: 2})
parseMolecule 'K4[ON(SO3)2]2' # {K: 4, O: 14, N: 2, S: 4})
parseMolecule 'As2{Be4C5[BCo3(CO2)3]2}4Cu5' # {As: 2, B: 8, Be: 16, C: 44, Cu: 5, Co: 24, O: 48}

parseMolecule.js

function parseMolecule(formula) {
  // console.log('formula:', formula);
  let elements = {};
  function countElements(input) {
    // console.log('count elements, input:', input);
    const elts = input.match(/[A-Z]([a-z])?(\d+)?/g);
    for (let i in elts) {
      const elt = elts[i].match(/[A-Z]([a-z])?(?=\d+)?/)[0];
      let count = elts[i].match(/\d+/);
      count = (!count) ? 1 : count.map(Number)[0];
      // console.log(elt, '|', count);
      if (elements.hasOwnProperty(elt)) { elements[elt] += count; }
      else { elements[elt] = count; }
    }
    // console.log('elements:', elements);
  }
  function openBrackets(input, closingBracket = ')') {
    let output = '';
    const multiplier = parseInt(input.split(closingBracket)[1]) || 1;
    const elts = input.match(/[A-Z]([a-z])?(\d+)?/g);
    // console.log('elts: ',elts);
    for (let elt of elts) {
      const eltName = elt.match(/^[A-Z]([a-z])?/)[0];
      // console.log('eltName:', eltName);
      let atoms = (elt.match(/\d+$/)) ? parseInt(elt.match(/\d+$/)[0]) : 1;
      // console.log('init atoms:', atoms);
      atoms *= multiplier;
      // console.log('resulting atoms:', atoms);
      output += eltName + atoms;
    }
    // console.log(output);
    formula = formula.replace(input, output);
    return output;
  };
  if (/(\[|\]|\{|\}|\(|\))/.test(formula)) {
    // console.log('brackets detected, extract elements from brackets:', formula);
    // extract inner round brackets first
    let formulaDecomp = formula.match(new RegExp(/\([^\(\)]+\)\d*/, 'g'));
    // console.log('formulaDecomp, round brackets:', formulaDecomp);
    if (formulaDecomp) {
      for (let item of formulaDecomp) {
        //console.log('item:', item);
        openBrackets(item, ')');
        // console.log(' >> formula:', formula);
      }
    }
    // extract middle square brackets
    formulaDecomp = formula.match(new RegExp(/\[[^\[\]]+\]\d*/, 'g'));
    // console.log('formulaDecomp, square brackets:', formulaDecomp);
    if (formulaDecomp) {
      for (let item of formulaDecomp) {
        openBrackets(item, ']');
        // console.log(' >> formula:', formula);
      }
    }
    // extract outer curly brackets
    formulaDecomp = formula.match(new RegExp(/\{[^\[\]]+\}\d*/, 'g'));
    // console.log('formulaDecomp, curly brackets:', formulaDecomp);
    if (formulaDecomp) {
      for (let item of formulaDecomp) {
        openBrackets(item, '}');
        // console.log(' >> formula:', formula);
      }
    }
  }
  if (!/(\[|\]|\{|\}|\(|\))/.test(formula)) {
    // console.log('no brackets, count elements:', formula);
    countElements(formula);
  }
  return elements;
}

// TEST
parseMolecule('H2O'); // {H: 2, O: 1})
parseMolecule('Mg(OH)2'); // {Mg: 1, O: 2, H: 2})
parseMolecule('K4[ON(SO3)2]2'); // {K: 4, O: 14, N: 2, S: 4})
parseMolecule('As2{Be4C5[BCo3(CO2)3]2}4Cu5'); // {As: 2, B: 8, Be: 16, C: 44, Cu: 5, Co: 24, O: 48}

ParseMolecule.markdown

Parse Molecule

The function parseMolecule counts the number of atoms of each element contained in the molecule, in a given chemical formula represented by a string, and returns an object.

Sample output for formula H2O: {H: 2, O: 1}

A script by V.

License.