Name: Novel Use of Protecting Components

Author: Andrei Caracoti

Version: 2.0

Created: 11/2002

Modified: 8/13/2007

Purpose: This protocol demostrates a slightly unusual use for the protection and deprotection components. Here, we're interested in removing halogens from our data set. But, to complicate matters, we're happy to allow aromatic CF3, CCl3, CBr3 and CI3 groups. First of all, so we can be sure the dataset contains the groups mentioned, we filter for these groups. Then, we protect these groups using the Protect components. We then perform a filter to get rid of any remaining halogens. Notice that as the groups are now protected, they're not considered to be halogen containing anymore. Deprotection re-exposes the groups. Finally, we flatten and remove the hydrogens from the structures. So we see, our results contain the groups we were interested in but do not contain any other halogens.

Requirements: Pipeline Pilot 6.0 or later
Chemistry collection

O/S: Windows and Linux

Limitations: none known

Keyword: protect halogens substructure filter

Contents: Novel Use of Protecting Components.xml - protocol
aromaticCHalogen.mol - substructure filter file
halogenlist.mol - substructure filter file

Installation:

1. Unzip the archive.
2. Import the protocol into the Pipeline Pilot client by dragging and dropping it in the white workspace area.
3. Move or copy the .mol files into your Pipeline Pilot user directory.
4. Run the protocol.