Kekule.js Cheminformatics Toolkit

The Kekule.ChemWidget.Viewer is a core widget used to display molecules and other chemistry objects in 2D or 3D. It supports direct user interaction via mouse or touch and can be customized with a toolbar.

Key properties for customization include:

• chemObj: The chemistry object to display.
• renderType: Set to Kekule.Render.rendererType.R2D for 2D or Kekule.Render.rendererType.R3D for 3D.
• moleculeDisplayType: Controls the visual model (e.g., SKELETAL, WIRE, SPACE_FILL).
• enableToolbar: Boolean to show/hide the functional toolbar.
• backgroundColor: CSS color format (e.g., '#ffffff').
• enableDirectInteraction: Enables zooming, rotating, or moving objects via mouse/touch.

var chemViewer = new Kekule.ChemWidget.Viewer(document);
chemViewer.setDimension('500px', '400px');
chemViewer.appendToElem(document.getElementById('parent')).setChemObj(molecule);

Kekule.js supports specialized node types beyond standard atoms:

• Pseudoatom: Use Kekule.Pseudoatom and set the type via setAtomType(Kekule.PseudoatomType.ANY).
• VariableAtom: Use Kekule.VariableAtom and define allowed isotopes using setAllowedIsotopeIds(['F', 'Cl', ...]).
• SubGroup: Use Kekule.SubGroup to create a structural fragment. You can define an anchor node using appendAnchorNode(node) to connect the subgroup to the main molecule body, and set an abbreviation using setAbbr('Et').

// Example of adding different node types
var mol = new Kekule.Molecule();

// Pseudo atom
var pseudo = new Kekule.Pseudoatom().setAtomType(Kekule.PseudoatomType.ANY).setCoord2D({x: 0, y: -0.80});
mol.appendNode(pseudo);

// Variable atom
var variable = new Kekule.VariableAtom().setAllowedIsotopeIds(['F', 'Cl', 'Br']).setCoord2D({x: 1.39, y: 0.80});
mol.appendNode(variable);

// Subgroup
var sub = new Kekule.SubGroup();
sub.appendNode(new Kekule.Atom().setSymbol('C').setCoord2D({x: 1.39, y: 0.80}));
sub.appendNode(new Kekule.Atom().setSymbol('C').setCoord2D({x: 2.0, y: 0.40}));
sub.appendBond([0, 1], 1);
sub.appendAnchorNode(sub.getNodeAt(0));
sub.setAbbr('Et');
mol.appendNode(sub);

Spectra are often linked to specific molecule structures.

1. Molecule Correlation: The refMolecules property of Kekule.Spectroscopy.Spectrum stores the related molecules.
2. Peak Assignments: Peak assignments (mapping peaks to specific atoms or bonds) are stored within Kekule.Spectroscopy.DataSection. You can access this via getExtraInfoOf(value) or getExtraInfoAt(index), which returns a Kekule.Spectroscopy.SpectrumDataDetails object containing the assignment.

// Check if a spectrum is correlated to a molecule
var molecule = chemObjList.getChildAt(0);
var spectrum = chemObjList.getChildAt(1);
console.log(spectrum.getRefMolecules()[0] === molecule); // true

// Access peak assignments
var dataSection = spectrum.getDataSectionAt(0);
for (var i = 0, l = dataSection.getDataCount(); i < l; ++i) {
    var value = dataSection.getValueAt(i);
    var extraInfo = dataSection.getExtraInfoOf(value);
    
    if (extraInfo instanceof Kekule.Spectroscopy.SpectrumDataDetails) {
        var atom = extraInfo.getAssignment();
        console.log(molecule.indexOfNode(atom)); // Returns index of the assigned atom
    }
}

The repository contains references to the GNU Lesser General Public License (LGPL) version 2.1. This license is specifically designed for software libraries to allow for more flexible linking compared to the standard GPL.

Key Concepts

• Purpose: To encourage the widest possible use of a library (e.g., making it a de-facto standard) by permitting non-free programs to link with it.
• Linking: The LGPL permits more lax criteria for linking other code with the library than the ordinary GPL. It distinguishes between a "work based on the library" (derived code) and a "work that uses the library" (combined with the library to run).
• User Freedom: Even though it is "Lesser" protective, it ensures that a user of a program linked with the library has the freedom to run that program using a modified version of the library.
• Responsibilities: If you distribute copies of the library, you must provide recipients with the same rights granted to you, including access to the source code and providing complete object files so they can relink the library after making changes.

A resource is a way to embed molecule data directly into HTML elements (like <script> or <link>) or link to external files using a resource identifier.

To use a resource:

1. Embed the data in an element with a specific id and a correct MIME type (e.g., type="chemical/x-mdl-molfile").
2. Reference the resource using a url(#id) syntax.
3. Load it asynchronously using Kekule.IO.loadResourceData with a callback function (mol, success).

Example HTML embedding:

<script id="molResInsideElem" type="chemical/x-mdl-molfile">
  <!-- MOL file data here -->
</script>

Example HTML external link:

<link id="molResExternalLink" href="./data/mol2D/porphyrin.mol" type="chemical/x-mdl-molfile" />

// resource is referred by url(#id), similar to CSS URI
var resId = 'url(#molResInsideElem)';
Kekule.IO.loadResourceData(resId, function(mol, success)
{
  if (success)
  {
    console.log('Loading from ' + resId + ' Successful');
    showMolecule(mol);
  }
  else
  {
    console.log('Loading from ' + resId + ' Failed');
  }
});