Beware of using atomIndex and atom/model deletion.
When deleting atoms, atomIndex is not changed. There are just some missing.
When a model is deleted, whole sections of the model atom array are
excised, and all objects referring to atoms by atom number are recreated.
However, there is a bug. Using zap {1.1} after deleting atoms in model 2.1
results in those deleted atoms in magically reappearing but not behaving
properly.
Bob
On Mon, May 5, 2014 at 9:44 AM, Otis Rothenberger <[email protected]>wrote:
> Bob,
>
> In a sequence of model editing operations involving the following, I end
> up with some atomno/atom-index confusion. The editing steps are:
>
> 1) Model bond change.
> 2) Model duplication.
> 3) Single model delete.
>
> After this sequence, atomno seems to lose its mathematical relationship to
> atom index. This is based on the observation that using bond pick callback
> atomno to calculate atom index leads to branch selection problems. That the
> relationship between atomno and atom index is the problem is verified by
> the following:
>
> select atomno=18;prompt({selected}.atomIndex) -- where 18 represents
> any atomno being tested.
>
> Prior to the editing, the above produces the expected atomno-1. After the
> above editing, the above produces atomno+1.
>
> This is not a problem with simple single model editing. The above
> convolution of steps seems to create the issue.
>
> Is this a bug or just the consequence of convolution? Perhaps I should
> just use atomno for my subsequent operations.
>
> Otis
>
>
>
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
>
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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