Hi Thomas,
oops, sorry, I gave a quick look at your script and I misinterpreted the
meaning of the headers without actually reading the code.
TL;DR: the fix is to reshape the numpy array before passing it to
AllChem.TransformMol:
tmatinv1 = np.array(linalg.inv(tmatinv), order='C')
Boring explanation:
Having investigated this by adding some debugging printout to the C++
code, the reason of the odd behaviour is that linalg.inv changes the
order in which the data is stored in the array from row-major to
column-major, so when the C++ transConformer() function extracts the raw
data from the numpy array, extracts it in the wrong order.
inData shows how the data are extracted by the C++ code. This is the
output of your original script:
<type 'numpy.ndarray'>
<type 'numpy.float64'>
[[ 1. 0. 0. 0.5]
[ 0. 1. 0. 0. ]
[ 0. 0. 1. 0. ]
[ 0. 0. 0. 1. ]]
float64
<type 'numpy.ndarray'>
<type 'numpy.float64'>
[[ 1. 0. 0. -0.5]
[ 0. 1. 0. 0. ]
[ 0. 0. 1. 0. ]
[ 0. 0. 0. 1. ]]
float64
<type 'numpy.ndarray'>
<type 'numpy.float64'>
[[ 1. -0. -0. 0.5]
[-0. 1. -0. -0. ]
[-0. -0. 1. -0. ]
[-0. -0. -0. 1. ]]
float64
original coordinates:
BH
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
1.2080 0.6971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4443 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.3951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.3949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
1 7 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
M END
nrows = 4
dSize = 16
inData = 1,0,0,-0.5,0,1,0,0,0,0,1,0,0,0,0,1
TransformMol with explicit inverse -> coordinates change:
BH
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
0.7080 0.6971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9443 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5000 1.3951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7080 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5000 -1.3949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
1 7 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
M END
second TransformMol with calculated inverse -> coordinates dont change:
nrows = 4
dSize = 16
inData = 1,-0,-0,-0,-0,1,-0,-0,-0,-0,1,-0,0.5,-0,-0,1
BH
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
0.7080 0.6971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9443 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5000 1.3951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7080 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5000 -1.3949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
1 7 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
M END
And this is the expected output after reshaping the array to row-major
order, by changing
tmatinv1 = linalg.inv(tmatinv)
into
tmatinv1 = np.array(linalg.inv(tmatinv), order='C'):
<type 'numpy.ndarray'>
<type 'numpy.float64'>
[[ 1. 0. 0. 0.5]
[ 0. 1. 0. 0. ]
[ 0. 0. 1. 0. ]
[ 0. 0. 0. 1. ]]
float64
<type 'numpy.ndarray'>
<type 'numpy.float64'>
[[ 1. 0. 0. -0.5]
[ 0. 1. 0. 0. ]
[ 0. 0. 1. 0. ]
[ 0. 0. 0. 1. ]]
float64
<type 'numpy.ndarray'>
<type 'numpy.float64'>
[[ 1. -0. -0. 0.5]
[-0. 1. -0. -0. ]
[-0. -0. 1. -0. ]
[-0. -0. -0. 1. ]]
float64
original coordinates:
BH
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
1.2080 0.6971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4443 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.3951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.3949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
1 7 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
M END
nrows = 4
dSize = 16
inData = 1,0,0,-0.5,0,1,0,0,0,0,1,0,0,0,0,1
TransformMol with explicit inverse -> coordinates change:
BH
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
0.7080 0.6971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9443 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5000 1.3951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7080 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5000 -1.3949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
1 7 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
M END
second TransformMol with calculated inverse -> coordinates dont change:
nrows = 4
dSize = 16
inData = 1,-0,-0,0.5,-0,1,-0,-0,-0,-0,1,-0,-0,-0,-0,1
BH
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
1.2080 0.6971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4443 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.3951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.3949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2080 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
1 7 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
M END
So, the fix is to reshape the numpy array before passing it to
AllChem.TransformMol.
Cheers,
p.
On 10/17/17 16:35, thomas....@boehringer-ingelheim.com wrote:
Hi Paolo,
thanks for looking into this.
However, when you look into the code (maybe I should have made this
clearer) the second and third results should **not** be the same. So I
‘TranslateMol’ the compound twice, but only the first TranslateMol has
an effect, the second one doesn’t change the coordinates, although it
should.
But good to know that you get the same results as I do – probably
should have attached my output as well…done now. And a diff with your
test.log shows no differences…
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:*Paolo Tosco [mailto:paolo.to...@unito.it]
*Gesendet:* Dienstag, 17. Oktober 2017 17:08
*An:* Fox,Dr.,Thomas (RES MedChem) BIP-DE-B
*Betreff:* Re: [Rdkit-discuss] GetAlignmentTransform
Dear Thomas,
I have just run your Python script and I get the same output in both
cases (see attachment). I am not using Anaconda Python though; I
wonder if this makes the difference.
Cheers,
p.
On 10/17/17 13:48, thomas....@boehringer-ingelheim.com
<mailto:thomas....@boehringer-ingelheim.com> wrote:
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
<mailto: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
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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
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and do not disclose its contents to any person. Any unauthorized
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prohibited.
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