I have a weird problem with the GetAlignmentTransform function when using the 
atomMap argument. Depending how I create the underlying tuples and pass them 
via zip into the function call, I do get back the transformation matrix or the 
error message "cannot extract desired type from sequence".

As you can see in the attached python code snippet, I either collect the atom 
mappings (= atom ids) from  the distance matrix and argsort, by generating two 
lists and transforming them into two tuples, or by explicitly setting the 
tuples. Then I use zip to generate the mappings.
In the latter two cases, things work fine, in the first case they don't. To me, 
the tuples and the list(zip()) look identical, so I do not have an idea why 
GetAlignmentTransform throws up.

I have attached two molecule files (essentially benzene and pyridine), the 
python code test.py and the output test.out

I would be very grateful if anybody could shed some light on this and explain 
what I do wrong.


Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox

Boehringer Ingelheim Pharma GmbH & Co. KG
Medicinal Chemistry
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585

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Attachment: test.out
Description: test.out

Attachment: test.py
Description: test.py

Attachment: PHo1.mol2
Description: PHo1.mol2

Attachment: BHo.mol2
Description: BHo.mol2

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