Hi, here's another one, unfortunately wasn't yet able to figure out a solution:
Once I have the transformation matrix from GetAlignmentTransform, I want to use it in TransformMol. So, when I use it as is, things work. When I calculate the inverse of it with linalg.inv and feed the resulting matrix into TransformMol, nothing happens, the coordinates stay the same. No error message either... When I however, print out the inverse matrix and set it explicitly in the code (does not make sense for a real-life script, only for testing) the molecule is transformed as desired. In the attached python code I have demonstrated this by using a translation in x-direction by 0.5 A. Explicitly declaring the inverse transformation (ie. Translation by -0.5A) and applying it works, feeding the calculated inverse matrix into TransformMol results in unchanged atomic positions. And again, printing out the arrays (and checking the types!) I don't see any difference... Thanks for any help, 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, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. Von: Greg Landrum [mailto:greg.land...@gmail.com] Gesendet: Dienstag, 17. Oktober 2017 12:40 An: Fox,Dr.,Thomas (RES MedChem) BIP-DE-B; rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] GetAlignmentTransform 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<mailto:thomas....@boehringer-ingelheim.com> <thomas....@boehringer-ingelheim.com<mailto:thomas....@boehringer-ingelheim.com>> Sent: Tuesday, October 17, 2017 2:27:39 AM To: rdkit-discuss@lists.sourceforge.net<mailto: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 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, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. Von: thomas....@boehringer-ingelheim.com<mailto:thomas....@boehringer-ingelheim.com> [mailto:thomas....@boehringer-ingelheim.com] Gesendet: Montag, 16. Oktober 2017 16:40 An: rdkit-discuss@lists.sourceforge.net<mailto: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, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited.
test.py
Description: test.py
BHo.mol2
Description: BHo.mol2
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