Name: Babel Integration

Author: Eddy Vande Water

Version: 3.0

Created: 05/2005

Modified: 08/16/2007

Purpose: This set of components exposes the functionality of the command-line application Babel. Babel is a program for converting various types of data files to formats that are useful for a variety of molecular vizualization packages. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. Babel has the ability to add and delete hydrogens from any file format.

This software is provided on an "as is" basis, and without warranty of any kind, including but not limited to any implied warranty of merchantability or fitness for a particular purpose. In no event shall the authors or the University of Arizona be liable for any direct, indirect, incidental, special, or consequential damages arising from use or distribution of this software. The University of Arizona also shall not be liable for any claim against any user of this program by any third party.

http://www.eyesopen.com/products/applications/babel.html

Requirements: Pipeline Pilot 6.0 or later
Chemistry collection

O/S: Windows

Limitations: none known

Keyword: babel chemistry molecule convert read write

Contents: Babel Converter.xml - component that allows for the conversion of files from one chemical format to another.
Babel Reader.xml - component that allows for reading various chemistry file formats.
Babel Writer.xml - component that allows for writing various chemistry file formats.
Babel Example Protocol - an example protocol showing the use of all three components.
obabel.exe - Babel executable.

Installing Babel:

1. Unzip the archive.
2. Copy the BABEL folder to the Pipeline Pilot server, most likely in the Program Files folder.
3. In the Pipeline Pilot Administration Portal, create a server global called babel_exe that contains the full path to the Babel executable (for instance, C:\Program Files\BABEL\obabel.exe).

Installing the components:
1. Drag the three component files into the Explorer pane of your Pipeline Pilot client. You can drop them onto your tab or the Components tab, if you want other users to be able to use them in their protocols.

Using the protocol:
1. Open the protocol by dragging and dropping the example protocol file into the workspace of the Pipeline Pilot client.
2. Run the protocol.