function jsmeOnLoad() {
  document.getElementById("jsme_container").style.display = "none"
  jsmeApplet = new JSApplet.JSME("jsme_container", "380px", "340px", {
    "options": "oldlook,marker,markAtomOnly,nocanonize"
  });        
  jsmeApplet.setCallBack("AfterStructureModified", show_smiles);
}
 
//jsmeApplet.setNotifyStructuralChangeJSfunction("show_smiles");
                
var patt = /\[([A-Za-z][a-z]?)H?\d*:\d+\]/g; //regexp pattern for numbered atom
function show_smiles(event) {
  smiles = event.src.smiles(); //atom that are colored are numbered
  new_smiles = smiles.replace(patt, '<em>$1</em>');
  document.getElementById("smiles_container").value = new_smiles
}

<input type="text" placeholder="Enter the Solute Molecule here" name="solute" id='smiles_container' ><br> <br>