GGA Software Services

Developer's Manual

• Editor Mode
  • Installation
  • Ketcher Object
    • ketcher.setMolecule()
    • ketcher.getSmiles()
    • ketcher.getMolfile()
    • ketcher.addFragment()
• Ketcher interaction example
• Ketcher Server

Editor Mode

Installation

The installation package contains all required sources.

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

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

• To embed Ketcher in another page, use IFrame:

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

Ketcher Object

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.

ketcher.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.

ketcher.getSmiles()

Export current structure as a SMILES string.

ketcher.getMolfile()

Export current structure as a Molfile/Rxnfile string.

ketcher.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:

Query	Action	Type	Parameters
/knocknock	Server availability check	GET	-
/open	Query for loading files from disk	POST	filedata
/save	Query for saving files to disk	POST	filedata
/layout	Query for converting SMILES to Molfile	POST	moldata
/automap	Query for reaction auto-mapping	POST	moldata, mode
/aromatize	Query for aromatization	POST	moldata
/dearomatize	Query for dearomatization	POST	moldata

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.