Read Me

WebBabel is a web application that uses python and OpenBabel to convert files
from one format to another, or browse for files containing molecular structures.
It runs under Windows, Mac or Linux on your desktop, workstation or laptop.
It uses the Jmol (or Marvin) viewer to show the structures being converted.
The user interface is a web page in your browser.

WebBabel requires OpenBabel, python and the OpenBabel python bindings.
More information about these is available at http://openbabel.org, http://python.org
and http://openbabel.org/wiki/Install_Python_bindings.
These must be installed on the computer (desktop, workstation, laptop)
where WebBabel will be run.  To use the add3D option to attempt to create
3D coordinates, OpenBabel 2.2 (or later) must be used.
To display structures read (or converted) from the input file,
WebBabel can use either the Jmol or Marvin applet.
Jmol is included here and may be used without further ado.
For WebBabel to display any structures, Your browser must be capable of running java applets.

To install WebBabel, unzip the WebBabel.zip file into any folder on your
desktop/laptop computer.

To launch this application:
 Windows:
   double-click on WebBabel.py
 Linux (in a shell):
   cd to this folder
   python WebBabel.py
 Mac (in a terminal window):
   cd to this folder
   python WebBabel.py

A new page should open in your default browser.  Select an application to use.
Currently, there are two applications: convert and browse.
The browse application in not yet ready.

You can stop WebBabel at any time by closing the window in which it is running.
This is NOT the webpage, but rather the terminal window from which it was started.
Under Linux and Mac, ^C is sufficient to stop WebBabel.

To use the convert application, select a file, or paste a "file" into the text area.
Select the appropriate file format and click the Read button.  This will read the file
and convert it to sdf format.  If a viewer is available, the structure(s) will be shown.

If you click the Convert button, the file (or pasted text) will be converted
to the chosen output format.  If a viewer is available, the structure(s) will
be shown, but only if that file format can be read by the viewer.

If you click the Save button, the file (or pasted text) will be converted
to the chosen output format.   A popup will appear asking to select where the
converted file should be saved.  On Mac, the popup does not appear, but instead
the file goes to the download folder.

Notes:

If you wish to use Marvin, you must download it from
http://chemaxon.com and follow any licensing and usage agreements.
The downloaded folder must be renamed simply 'marvin'
and placed in the folder containing WebBabel.
You should then rename the jmol folder, say to jmol-hide to prevent
it from being used as the viewer.
If neither folder jmol nor marvin is present, WebBabel will not use a viewer.
It will still function as a file conversion utility.

This web application runs locally, rather than having the webserver located on
another machine.  The WebBabel.py functions as a webserver on port 8080.  It should
not be possible for others to connect to you and use WebBabel since only
connections from the localhost are allowed.

Under Internet Explorer, the Jmol.js script distributed with jmol-11.4.6 does
not work properly.  A corrected Jmol.js is provided with WebBabel.  If you download
another version of jmol, you may need to updated the Jmol.js in that distribution.

WebBabel has not been exhaustively tested with all versions of all browsers on
all platforms.  Nor have all versions of Java been tested.  WebBabel was developed
under Windows using Java Plug-in 1.6.0_10-rc
Using JRE version 1.6.0_10-rc Java HotSpot(TM) Client VM.

Some browsers and java do not seem to play well together all the time.  If you
run into problems under linux or osx or safari, try 'python WebBabel.py -a'
to start the server without automatically opening a browser.
Then open the browser yourself and enter 'http://localhost:8080' as a URL.