Help on using Jarp and Ward

Hi,





I am a new in using JChem and have absolutely no idea on how to go about using it.





1. I have an sdf file. Can I use sdf file for clustering instead of MS Access or other databases? SDF files work for cxcalc so I was just wondering.





2. How do I do clustering with for example, logP, using jarp and ward? I mean I am asking for what the syntax should be.





Thank you so much

Hi,





1. The JKlustor user manual is a good starting point, it provides some typical examples, among them the use of SDFiles to input structures: http://www.chemaxon.com/jchem/doc/user/Jarp.html#examples, Example #6 appears to be the most relevant for you, and in http://www.chemaxon.com/jchem/doc/user/Ward.html#examples perhaps #7 should suit your needs.





2. Check the --dimensions parameter (http://www.chemaxon.com/jchem/doc/user/Jarp.html#comments). Values need to be provided in a plane text file, one line per object, values are separated by space or tab characters (see http://www.chemaxon.com/jchem/doc/user/Jarp.html#input). Same applies for Ward.





HTH





Miklos