You can alter a molecule by directly editing its source in the Edit Source dialog window.
The dialog window provides standard clipboard operations and it is also possible to send the source text to the console.
You can view and edit the source in any of the supported file formats.

You can also convert it to Java String which allows easy integration of the structure to a custom Java application code.
To change the format of the source,simply

1. Select the desired one from the View Menu.

2. Editing the source text.

3. Send the structure back to the MarvinSketch canvas by invoking File > Import As, and pressing Import on the appearing dialog window. This will close the Edit Source dialog window.