Subject: File Formats for Molecules

From: "Phil Hultin" <[email-masked]>
Date: Fri, 20 Dec 2002 09:18:52 -0600

I have been watching the discussion of file formats that arose out of the
"interoperability" thread with great interest.  Perhaps I am missing
something here - just what information do people want to encode in a
molecular data file that has created such a debate?  It must be more than
just the identity of the atoms and their spatial coordinates, to judge by
the conversations I have seen, but perhaps for those of us who are not
involved in the "chem-informatics" world, a little summary of what the
issues are would be educational.  Could somebody summarize?

I don't know if this is relevant to the discussion, but the December 2, 2002
issue of Chemical and Engineering News contains an article about the IUPAC
Chemical Identifier project.  This is aimed at devising a completely unique
way of describing any chemical structure, that can be implemented by a
computer, and used as the heart of a chem-informatics system.  The IChI
approach is hierarchical, starting with the simple connectivity and then
adding additional layers of information as required to describe the system
precisely.  Although the article does not discuss the idea, this
hierarchical approach would permit the linking of an absolutely unique
structural identifier with layers encoding property information.
Dr. Philip G. Hultin
Associate Department Head and
Associate Professor of Chemistry
University of Manitoba
Winnipeg, MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:[email-masked]
http://www.umanitoba.ca/chemistry/