Subject: Re: CCL:Java code for standard orientation transformation?

From: Jonathan Brecher <[email-masked]>
Date: Mon, 5 Apr 1999 09:18:01 -0400

>So does anybody know of (or have) some Java code for transforming molecules
>to the standard orientation?

I don't have any such code, but could I even one-up the question:
Does anybody know of a *definition* of "standard orientation"?  Sounds like
a useful thing, but I've never heard of it before.

Jonathan Brecher
CambridgeSoft Corporation
[email-masked]

---

From: Jonathan Brecher <[email-masked]>
Date: Mon, 5 Apr 1999 13:48:55 -0400

>a useful thing, but I've never heard of it before.

Thanks to the folks who have already responded.  For those interested, Jen
Sorensen provided me the fullest explanation:

Excerpted from the Gaussian Programmer's Reference (Chpt 10.6.2)

Goals:
1.  The molecule is oriented so as to simplify the 3x3 transformation
matrix.
2.  Two z-matrices differing only in the values of the internal
coordinates but which are identical as regards the integer quantities
(such as occurs on subsequent points of a geometry optimization) shall
produce the same orientation of the molecule.
3.  Two different z-matrices for the same molecule shall produce the same
coordinates, save for a possible renumbering of the atoms.
4.  The number of molecular orbital coefficients zero by symmetry should
be maximized.

General Considerations:
1.  A right-handed coordinate system will be used throughout.
2.  The molecule will be translated so that its center of charge is at the
origin.
3.  Atoms will not be reordered relative to their order upon input.
4.  The cartesian axes will be considered to increase in priority in the
order x < y < z.

***

Neat.  Unfortunately, I was hoping for something a little more
general-purpose, for example something that said that toluene should be
drawn with the methyl group at the 12:00 position rather than the 6:00
position (in 2D space).  Seems like everyone was talking about a "standard
orientation" defined in terms of 3D space, and in particular in terms of
the Gaussian application.  Also useful, but not what I was hoping for.  Oh,
well!

Jonathan Brecher