Get Molecule Information

With the instance of molecule, user can use a series of properties and methods provided by the toolkit to reveal the information of molecule, from the intuitive atom/bond count to more complicated feature such as ring set and stereo center.

Iterating over Atoms and Bonds

Once you have a molecule, it’s easy to loop over its atoms and bonds:1

// iterate all nodes(atoms)
for (var i = 0, l = mol.getNodeCount(); i < l; ++i)
{
  var node = mol.getNodeAt(i);
  console.log('node ' + i, node.getClassName(), node.getLabel());
}
// iterate all connectors(bonds)
for (var i = 0, l = mol.getConnectorCount(); i < l; ++i)
{
  var connector = mol.getConnectorAt(i);
  console.log('connector ' + i,
    connector.getClassName(), connector.getBondOrder? connector.getBondOrder(): '?');
}

The atom or bond inside a molecule can also be accessed by its id:

var atom1 = mol.getNodeById('atom1');  // returns the atom with id 'atom1'
var bond1 = mol.getConnectorById('bond1');  // returns the bond with id 'bond1'

To individual node(atom) or connector(bond), their belonged molecule (or structure fragment) can be get by method getParentFragment:

var mol = atom.getParentFragment();
var mol = bond.getParentFragment();

In the molecule, atoms and bonds connected with each other, their relations can be gained by properties linkedConnectors, linkedObjs of node and connectedObjs of connector:

var bondsAroundAtom = atom.getLinkedConnectors();
  // returns an array of connectors linked with this atom
var neighborAtoms = atom.getLinkedObjs();
  // returns neighbor atoms linked with this atom by only one bond
var objectsLinkedByOneBond = bond.getConnectedObjs();
  // returns array of objects connected by connector

Molecule Formula

Formula can be calculated from atoms in molecule:1

// get molecule in editor
var mol = getCurrMol();
// get the formula object
var formula = mol.calcFormula();
// turn formula object into text
console.log(formula.getText());

Ring Information

Kekule.js provides method to easily find all rings and SSSR(Smallest Set of Smallest Rings) of a molecule. The following codes can be used to get all rings:1

var mol = getCurrMol();
// find all rings of molecule
var rings = mol.findAllRings();

The result of method mol.findAllRings is a JavaScript array, each item of it is an object represents a ring in the molecule, all nodes(atoms) and connectors(bonds) in the ring can be access by item.nodes and item.connectors:1

var ringCountMap = [];
// iterate over those rings
for (var i = 0, l = rings.length; i < l; ++i)
{
  var ring = rings[i];
  var nodeCount = ring.nodes.length;
  ringCountMap[nodeCount] = (ringCountMap[nodeCount] || 0) + 1;
}
// report
console.log('Find ' + (rings.length || 0) + ' rings');
for (var i = 0, l = ringCountMap.length; i < l; ++i)
{
  var count = ringCountMap[i] || 0;
  if (count)
    console.log('ring with ' + i + ' atoms: ', count);
}

For example, the codes above to find all rings in phenanthrene will shows the following logs in the console panel of web browser:

Find 6 rings
ring with 6 atoms:  3
ring with 10 atoms:  2
ring with 14 atoms:  1

The SSSR rings can be found with method findSSSR:1

var mol = getCurrMol();
if (mol)
{
  // find SSSR of molecule
  var rings = mol.findSSSR();
  var ringCountMap = [];
  // iterate over those rings
  for (var i = 0, l = rings.length; i < l; ++i)
  {
    var ring = rings[i];
    var nodeCount = ring.nodes.length;
    ringCountMap[nodeCount] = (ringCountMap[nodeCount] || 0) + 1;
  }
  // report
  console.log('Find ' + (rings.length || 0) + ' SSSR rings');
  for (var i = 0, l = ringCountMap.length; i < l; ++i)
  {
    var count = ringCountMap[i] || 0;
    if (count)
      console.log('ring with ' + i + ' atoms: ', count);
  }
}

The codes above performed on phenanthrene will shows the following logs in console panel:

Find 3 SSSR rings
ring with 6 atoms:  3

As ring searching is often to be a time consuming job to complex molecules, ring information returned by findAllRings and findSSSR will be cached until the structure of molecule been changed.

Attention

Currently, multicenter bonds and bond-bond connections are ignored during ring perception.

Aromatic Detection

Currently, to save the calculation time, aromatic detection is carried on SSSR rings of molecule in Kekule.js. You can simply call method findAromaticRings:1

var mol = getCurrMol();
if (mol)
{
  // find aromatic of molecule
  var rings = mol.findAromaticRings();
  var ringCountMap = [];
  // iterate over those rings
  for (var i = 0, l = rings.length; i < l; ++i)
  {
    var ring = rings[i];
    var nodeCount = ring.nodes.length;
    ringCountMap[nodeCount] = (ringCountMap[nodeCount] || 0) + 1;
  }
  // report
  console.log('Find ' + (rings.length || 0) + ' aromatic rings');
  for (var i = 0, l = ringCountMap.length; i < l; ++i)
  {
    var count = ringCountMap[i] || 0;
    if (count)
      console.log('ring with ' + i + ' atoms: ', count);
  }
}

The codes above performed on phenanthrene will shows the following logs in console panel:

Find 3 aromatic rings
ring with 6 atoms:  3

Stereo Perception

Chiral atoms or stereo bonds can also be revealed:1

var chiralNodes = mol.perceiveChiralNodes();
var stereoBonds = mol.perceiveStereoConnectors();

Those methods returns all stereo atoms and bonds. To simplify the calculation, configuration of atom or bond is not marked with R/S or E/Z but with a parity value: 1(odd), 2(even) or 0(unknown):1

for (var i = 0, l = chiralNodes.length; i < l; ++i)
{
  var n = chiralNodes[i];
  console.log('Chiral center: ', n.getLabel(), n.getParity());
}
for (var i = 0, l = stereoBonds.length; i < l; ++i)
{
  var c = stereoBonds[i];
  console.log('Stereo bond: ', c.getParity());
}

1(1,2,3,4,5,6,7,8)

Example of this chapter can be found and run at here.