Leo He

SimpleMDE doesn't support superscript and subscript. there are two ways to show sub/superscript.

Use html tags:

H<sub>2</sub>O
E =mc<sup>2</sup>

H₂O

E =mc²

Use ~ and ^

H~2~O
E =mc^2^

H₂O

E =mc²

SimpleMDE previews are rendered by Marked using GitHub Flavored Markdown. While Marked doesn't support using ~ and ^ mark sub/superscript. so when preview it by SimpleMDE, it will show the original code:

H~2~O
E =mc^2^

But Markdig can convert ~ and ^ to sub/superscript. so can see the sub/superscript on the blog page. because on the blog page, the content was generated by Markdig.

Installation

The installation package contains all required sources.

To run Ketcher in a separate page, use ketcher/index.html:

<a href="ketcher/index.html">Ketcher</a>

To embed Ketcher in another page, use IFrame:

<iframe id="ifKetcher" src="ketcher/index.html" width="800" height="600"></iframe>

Access Ketcher

To access Ketcher from JavaScript, use the following code to obtain the object reference:

var ketcher = ketcherWindow.ketcher;
where ketcherWindow is a separate Ketcher window or

var ketcherFrame = document.getElementById('ifKetcher');
var ketcher = null;

if ('contentDocument' in ketcherFrame)
    ketcher = ketcherFrame.contentWindow.ketcher;
else // IE7
    ketcher = document.frames['ifKetcher'].window.ketcher;

where ifKetcher is a Ketcher IFrame.

setMolecule()

This method updates the current structure in the editor. Pass it a SMILES string or a Molfile/Rxnfile:

ketcher.setMolecule('c1ccccc1');

Note: SMILES import is not available in the standalone mode.

getSmiles()

Exports current structure as a SMILES string.

getMolfile()

Exports current structure as a Molfile/Rxnfile string.

addFragment()

This method switches Ketcher to the fragment insertion mode where a user can specify where to the provided fragment. Pass it a SMILES string or a Molfile/Rxnfile:

ketcher.addFragment('c1ccccc1');

Note: SMILES import is not available in the standalone mode.

Ketcher interaction example

You can look at the source a web page with embedded Ketcher here where the web page interacts with a Ketcher object using this API.

Ketcher Server

The current version of Ketcher has a sample implementation of the server side. A simple Python script ketcher.py listens to the port 8080 and has four interfaces:

Indigo binaries and Python wrappers are required to perform automatic layout, atom-to-atom mapping or SMILES import. Ketcher server script can be executed as a standalone application and also can run under WSGI.

ketcher installation document