Hi, I have gotten pharmacophore representation and matching working - the code is currently outside of the CDK, but if people agree I'll move it into it's own package (pharmacophore) in the CDK hierarchy.
From the user point of view there are two components: 1. Creating a pharmacophore query - ideally this would be done graphically, but the current classes allow programmatic access to creating a query. A query consists of pharmacophore groups (a.k.a pharmacophore atoms) and distances between pharmacophore groups (a.k.a pharmacophore bonds). A pharmacophore group is defined by a SMARTS pattern and a label. The pharmacophore bonds are defined by 2 pharmacophore groups and either an exact distance or distance range. Note that queries general to an extent - you can use pharmacophore triads, quads etc. However right now only Euclidean distances between pharmacophore groups are considered - no torsions etc. 2. Matching a query against a given 3D structure - this is performed in a manner analogous to the SMARTSQueryTool. Supply a 3D structure and a pharmacophore query and get back the matching groups. Note that the return value is a set of matching pharmacophore groups. But since each group contains the matching atoms from the actual target molecule, you can identify/color etc the matching atoms easily. Internally it uses the UniversalIsomorphismTester to perform the 3D isomorphism matching. Currently, it's designed so that you have to loop over every molecule in a set of conformers. The next step is to perform matching on a set of conformers more efficiently. The main thing that needs to be checked is the correctness of the SMARTS parser (errors are still occuring due to incorrect implicit hydrogens) ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Q: Why did the mathematician name his dog "Cauchy"? A: Because he left a residue at every pole. ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
