Hi Ansgar,
On Wed, Jul 24, 2019 at 9:33 AM Schuffenhauer, Ansgar
<ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>> wrote:
Very useful. Thank you. I’ll be able to deal with the SMARTS part
myself
Great.
But your answer has left me with another series of questions:
You are saying that I am still using the old MolVS code for
tautomer processing. That explains why the performance in terms of
execution speed is not yet fully at the level I am used to expect
from rdkit (no complaint meant, you just have set the bar quite
high with rdkit in general).
You say such nice things. :-)
I haven't spent enough time looking at the tautomer enumeration code
to know whether or not the poor performance you are seeing is
something inherent in the process or an implementation artifact that
can be fixed.
Are you saying, that actually with respect to tautomer
standardization there is no C++ port from Google Summer of Code?
Or is there something, which is not quite ready? Or is there a
tautomer code in the C++ and I am just not using it? In this case,
what would be the right function to use? What is your
recommendation when it comes to tautomer standardization? .
Susan (who did the MolVS port) got a first version of the tautomer
enumeration done but did not finish the scoring code that is necessary
to get a "canonical" tautomer. Since the tautomer code in general
wasn't finished, we didn't do a Python wrapper for any of it.
For the sake of clarity I am looking for a tautomer standardizer,
that does produce a uniform, canonical tautomer, I am not asking
for the pyhsical.-chemical right, that is lowest energy energy
one, as this is a task I assume no simple rule based tautomer
standardizer can perform.
At the moment the only real option is to stick with the Python-based code.
Completing the tautomer enumeration/canonicalization work is something
that is on my ToDo list, but it hasn't managed to bubble up to the
top. Having people in the community[1] requesting it helps raise the
priority.
-greg
[1] Particularly people in the community who also happen to work for
companies that have RDKit support contracts.
Is the C++ port everything that is in
rdkit.Chem.MolStandardize.rdMolStandardize?
Best regards
Ansgar
*Ansgar Schuffenhauer*
Senior Investigator I
T +41 79 608 9063
ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>__
*Novartis Pharma AG*
NIBR
*From:*Greg Landrum <greg.land...@gmail.com
<mailto:greg.land...@gmail.com>>
*Sent:* Dienstag, 23. Juli 2019 14:43
*To:* Schuffenhauer, Ansgar <ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>>
*Cc:* rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>
*Subject:* Re: rdkit.MolStandardize tautomer
Hi Ansgar,
This is still using the MolVS tautomer-handling code since we
didn't finish the canonicalization part during last year's Google
Summer of Code.[1]
That means it's not using the parameter file that you found. The
rules that are used are here:
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/MolStandardize/tautomer.py
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rdkit_rdkit_blob_master_rdkit_Chem_MolStandardize_tautomer.py&d=DwMFaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I&m=BnaAWSqyTt4tDiaikrUZmNMgOhNeWPi73bwdA9j4-T8&s=d5ldgC12XWgrCnPLSa9hZ9_B2zYRiw8riuv93BTPsz0&e=>
You can change those at runtime, but it you need to be careful to
properly re-import modules after doing so. Here's an example
showing how to do that:
https://gist.github.com/greglandrum/4ac2b4e7f8c61e25836e106467aef150
<https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com_greglandrum_4ac2b4e7f8c61e25836e106467aef150&d=DwMFaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I&m=BnaAWSqyTt4tDiaikrUZmNMgOhNeWPi73bwdA9j4-T8&s=Q-EeeeZdfD5bjCY_U7PrtfL5iHexxeP7faW30BsozuM&e=>
I'm not going to claim that the SMARTS which I constructed to
change the 1,3 (thio)ketol/enol is the right one, but it does at
least show how to make the changes and reload the standardize
module so that it takes effect.
I hope this helps,
-greg
[1] and I haven't made it a priority because I dread the "no,
that's not the right canonical tautomer" arguments that will ensue
On Tue, Jul 23, 2019 at 8:54 AM Schuffenhauer, Ansgar
<ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>> wrote:
Hi Greg
Thanks for your quick answer. What I am doing is essentially
the following:
from rdkit.Chem import MolStandardize
my_standardizer = MolStandardize.standardize.Standardizer()
standard_tautomer = my_standardizer.tautomer_parent(input_mol)
I assume that at the stage I construct my_standardizer there
would be some opportunity slip in an alternative configuration
info
By the way, I think also that one of the two cases of
vanishing stereo-chemistry reported in
https://github.com/rdkit/rdkit/issues/2363
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rdkit_rdkit_issues_2363&d=DwMFaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I&m=BnaAWSqyTt4tDiaikrUZmNMgOhNeWPi73bwdA9j4-T8&s=bALfjkh7w44Zp0A885uv77DRWnreozm-_FML9XdeW60&e=>
is caused by an overly eager keto/enol tautomerizer.
Best regards
Ansgar
*Ansgar Schuffenhauer*
Senior Investigator I
T +41 79 608 9063
ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>
*Novartis Pharma AG*
NIBR
*From:*Greg Landrum <greg.land...@gmail.com
<mailto:greg.land...@gmail.com>>
*Sent:* Montag, 22. Juli 2019 17:42
*To:* Schuffenhauer, Ansgar <ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>>
*Cc:* rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>
*Subject:* Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 141,
Issue 16
Hi Ansgar,
It is possible to specify the tautomer parameter file that is
used, but in order for me to explain how, I need to know how
you are currently using the code to enumerate tautomers (i.e.
which function you are calling).
As for the format: it's tab-delimited and the first entry is
the name. The "r/f" flag is an indicator of which direction
the transform is going that is just there to make the name unique.
In the SMARTS the first atom is the one with the mobile H and
the last atom is where it should be moved to.
-greg
On Mon, Jul 22, 2019 at 3:08 PM Schuffenhauer, Ansgar
<ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>> wrote:
Dear all
For the standardizer module (Chem.MolStandardize), what is
the best way to change some of the tautomerizer rules?
There is a data file in
share/RDKit/Data/Molstandardize/tautomerTransforms.in
which I assume to define the default.
// Name SMARTS Bonds Charges
1,3 (thio)keto/enol f [CX4!H0]-[C]=[O,S,Se,Te;X1]
1,3 (thio)keto/enol r [O,S,Se,Te;X2!H0]-[C]=[C]
1,5 (thio)keto/enol f
[CX4,NX3;!H0]-[C]=[C][CH0]=[O,S,Se,Te;X1]
1,5 (thio)keto/enol r [O,S,Se,Te;X2!H0]-[CH0]=[C]-[C]=[C,N]
...
Now my questions are
1. What is the Syntax of this file? What does the "f" and
the "r" stand for? Do the smarts have to start with the
atom carrying the mobile H?
2. How can I instruct rdkit not to use this default file,
but the one supplied by the user.
The background for this question that the smarts for
keto/enol seems to be a bit too generic, as it catches
also the alpha C-atoms of carboxylic acids and amides.
Generation of tautomers here leads to a epimerization of
stereo-centers in alpha positions of carboxylic acids and
amides. That appears odd to me, as such stereo-centers are
quite stable (in contrast to those of "real" ketones and
aldehydes).
Best regards
Ansgar
Ansgar Schuffenhauer
Senior Investigator I
T +41 79 608 9063
ansgar.schuffenha...@novartis.com
<mailto:ansgar.schuffenha...@novartis.com>
Novartis Pharma AG
NIBR
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