Recently I have been working on SMILES/SMARTS searching in Jmol. We now have
full support for these powerful mechanisms of searching. For example, as
long as you have SOME valid SMILES code for a molecule, Jmol can check that
the model is or is not identical to that SMILES code, including aromaticity
(defined as "flat sp2-hybridized ring") an stereochemistry.
I just added a bit of code that I think could be even more interesting. A
new command in Jmol 12.0 is "compare". Up to now you had to know the 1-to-1
atom-atom mapping from one molecule to the other to use this. There are
certainly times when you do -- for example aligning known models, multiple
models from an NMR file, models in an animation, etc.
But there are times when molecules are from two totally different sources --
say, a 2D-to-3D JME translation and a known MOL file. In that case we can't
assume that the atom numbering is the same in both structures.
COMPARE/SMILES to the rescue!
Now you can do this:
load files "file1" "file2"
compare {2.1} {1.1} "[OH]cc[O]C" rotate translate
This will find an ortho-hydroxyether on an aromatic ring in both models and
move model 2.1 to align with model 1.1 in a way that will best align those
five atoms. The neat thing is that Jmol will find the atom-atom correlation
for you, because it will search both structures for the SMARTS pattern. This
provides the needed 1:1 mapping of atoms. Jmol will then calculate the
absolute best alignment based on that. Since there might be more than one
occurrance of [OH]cc[O]c in model 2.1, Jmol will search for ALL such
occurances and pick the one with the smallest standard deviation.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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