I’m glad you were able to track that down, it’s an interesting one.

I’ll have to look, but we may be able to fix that on the C++ side.

________________________________
From: thomas....@boehringer-ingelheim.com <thomas....@boehringer-ingelheim.com>
Sent: Tuesday, October 17, 2017 2:27:39 AM
To: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] GetAlignmentTransform

Ok, mystery solved…argsort returns (at least on my Linux box) an int64, which 
GetAlignmentTransform obviously cant handle.

Best,
Th.

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
mailto:thomas....@boehringer-ingelheim.com<mailto:%7bemail%7d>


Pflichtangaben finden Sie unter: 
https://www.boehringer-ingelheim.de/unser-unternehmen/gesellschaften-in-deutschland
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Von: thomas....@boehringer-ingelheim.com 
[mailto:thomas....@boehringer-ingelheim.com]
Gesendet: Montag, 16. Oktober 2017 16:40
An: rdkit-discuss@lists.sourceforge.net
Betreff: [Rdkit-discuss] GetAlignmentTransform

Hi,
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.

Best,
Th.


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
mailto:thomas....@boehringer-ingelheim.com<mailto:%7bemail%7d>


Pflichtangaben finden Sie unter: 
https://www.boehringer-ingelheim.de/unser-unternehmen/gesellschaften-in-deutschland
Mandatory information can be found at: 
https://www.boehringer-ingelheim.de/unser-unternehmen/gesellschaften-in-deutschland

Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichem 
Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie bitte 
diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail und geben 
den Inhalt der E-Mail nicht weiter. Jegliche unbefugte Bearbeitung, Nutzung, 
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