Subject: Comparing SMILES strings

From: <[email-masked]>
Date: Fri, 12 Sep 1997 14:26:10 -0500 (CDT)

Hello --

Ray Crawford recently asked how to ascertain whether two SMILES strings
represent the same structure.  Wolf-D. Ihlenfeldt noted that the CACTVS
toolkit could perform this task but at a rate "several orders of magnitude
slower" than the obvious alternative of comparing the "unique SMILES"
equivalents of the two original SMILES strings.  However, he suspected
that the "uniqetization" (Daylight's term) algorithm was proprietary and
unpublished.

Although Daylight and Daylight personnel are very generous in sharing
their technology, papers on the SMILES notation itself and a method for
generating canonically unique SMILES strings are amongst the very few
examples of their formal publications.

The paper describing the generation of unique SMILES is:

D. Weininger, A. Weininger, and J. L. Weininger(*), SMILES. 2. Algorithm 
for Generation of Unique SMILES Notation, JCICS, 29, 97-101, 1989.

The corresponding author, Joe Weininger, was the father of Dave and Art 
who developed the algorithm and wrote the corresponding code.

Unfortunately, the paper was written before SMILES notation supported
stereochemical qualifiers.  It is not difficult to extend the published
algorithm to include stereochemistry but, as far as I know, that extension
has not been published.  Since, I believe, the NCI database does not
include stereochemical indicators, this would not be a problem for the
original questioner (who asked about comparing alternative SMILES for
structures in the NCI database).  However, for general applications,
alternative ways of indicating the same stereochemistry must be addressed
in order to assure complete and accurate comparisons.

Obviously, the Daylight Toolkit (distributed by Daylight) includes code
to facilitate the comparison of stereochemically-qualified SMILES strings.
Those interested in developing their own code should first contact Daylight
to see if they can provide advice.  Failing that, interested parties can
contact me directly (*not* via the CCL).

  -- Bob Pearlman 

Robert S. Pearlman, Ph.D
Coulter R. Sublett Regents Chair in Pharmacy and
Director, Laboratory for Molecular Graphics 
  and Theoretical Modeling
College of Pharmacy
University of Texas
Austin, Texas 78712
512-471-3383 (voice)
512-471-7474 (FAX)
[email-masked]