Rajarshi Guha wrote:
Going by Christoph's suggestion of doing a best fit, you could try using
the Kabsch alignment on the two molecules (though I'm not sure what will
happen when it is asked to align 2D coordinates)
Alternatively, each time the structure is rendered, rotate the structure
so that the principal axes of inertia are aligned to some reference
frame (say the X and Y axes). This of course is only applicable is the
structures for a given molecule differ by a rotation, each time they are
generated.
Both ways are practical. The first is the method of choice for JChemPaint
cleanups, where there is an initial structures to align with.
In cases where there isn't an initial set of coordinates, there are some basic
rules of how to set molecules:
- Longest axis should be horizontal
- As many bonds as possible should be exactly horizontal or vertical.
Based on these simple rules one, can calculate a prefered canonical orientation.
Cheers,
Chris
--
Priv. Doz. Dr. Christoph Steinbeck ([EMAIL PROTECTED])
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
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