[octet-devel] Stereochemistry implementation - first pass complete

[rich a. <che...@ya...>]

I have committed the first set of changes to Octet
(http://octet.sf.net) that enable the specification
and comparison of atomic stereochemical configuration.

As I've written previously, this code is based on a
specification provided by Andreas Dietz (J. Chem. Inf.
Comput. Sci. 1995, 787).

I view this code as a first step and very rough. I
don't expect the interface definitions to change much,
but the implementation is quite inefficient and
probably buggy. In particular, the spherical polar
coordinate manipulations in BasicMoleculeBuilder are
probably more complicated than necessary.

Nevertheless, I have included a unit test
(net.sourceforge.octet.junit.StereoTest) that
demonstrates that two enantiomers of isobutanol can be
identified as having opposite configurations by this
system. This unit test also demonstrates how clients
will use the updated MoleculeBuilder interface to
define atomic configuration using spherical polar
coordinates.

I am unaware of any other implementation of this
stereochemistry specification in any language, so it
will be interesting to see how it evolves. The system
is a significant departure from every other method,
but I believe the payoff is well worth the steep
learning curve.

After I have cleaned up the implementation a bit, I
plan to tackle molecular conformation next. Once that
phase is complete, it should be possible to define
practically any stereochemical arrangement using a
single flexible formalism. An abstraction layer may be
helpful to simplify the use of this system for
standard cases (ie. tetrahedral carbon). It is at that
point that the API will be frozen in preparation for
the release of Octet 1.0 (and hopefully progress on
the QSAR project).

As always, comments and feedback are welcome.  I did
my best with the documentation of this code, but one
really needs to read Dietz' paper carefully (and
repeatedly :-)) to understand how the system works.
I'm also more than willing to try to explain how I
understand it.

best,
r


		
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