Dear all,
I could successfully use the code from Lukas (thanks again!) for scoring
the 2D depictions of a molecule and retrieve the "best" one.
However, I noticed that the depictions seem to be dependent on the input
format? (i.e. SDF or Smiles).
Since I remove any input conformer before I compute a depiction anyway,
I thought this could have something to do with the atom index order.
However, it does not look this is the case, as this gist shows:
https://gist.github.com/jose-manuel/bc130351c4979d2c0b165f84a8469d2a
I even get a new depiction for CoordGen when converting sdf -> smiles ->
sdf, so I get three different results that are reproducible.
Would anyone have an idea why this is happening? Am I missing something
obvious?
Cheers,
Jose Manuel
On 10.04.19 17:20, Lukas Pravda wrote:
Sorry guys for the late reply,
The code is available from here:
https://gitlab.ebi.ac.uk/pdbe/ccdutils/blob/master/pdbeccdutils/core/depictions.py
Hope you will find any use of it. The class you are after is
DepictionValidator. Presently, I have a few changes on the development
branch, which are soon to be merged to master (basically I started to
calculate angle between two bonds if they share common atom because of
this http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/CPT).
Let me know if you would have any questions, or suggestions.
Lukas
*From: *Thomas Evangelidis <teva...@gmail.com>
*Date: *Tuesday, 9 April 2019 at 15:43
*To: *Lukas Pravda <lpra...@ebi.ac.uk>
*Cc: *Jose Manuel Gally <jose.manuel.ga...@gmail.com>, RDKIT mailing
list <rdkit-discuss@lists.sourceforge.net>
*Subject: *Re: [Rdkit-discuss] Which method to prefer for computing 2D
coordinates
Hello Lukas,
I am also struggling with 2D coordinate generation quite a long time
as well as what criteria to use for choosing the most appropriate.
Therefore, I would be very interest to use your code for 2D coordinate
selection.
With best regards,
Thomas
PS: very nice notebook Jose. I also wanted to write something similar
but never really found enough time to finish it.
On Tue, 9 Apr 2019 at 16:31, Lukas Pravda <lpra...@ebi.ac.uk
<mailto:lpra...@ebi.ac.uk>> wrote:
Hi Jose,
As you have shown there is no single method which would be perfect
for everything. If you don’t care that much about speed, the
possible solution could be to compute coordinates with all three
approaches and then simply select the best conformer based on some
criteria.
The solution I use is to generate 2D coordinates using multiple
approaches and then I have a set of methods which computes number
of bond collisions and atoms being close to each other using
KD-tree. Altogether this all is expressed as penalty score, where
the lower is better.
Should you need any code, let me know.
Lukas
On 09/04/2019, 14:35, "Jose Manuel Gally"
<jose.manuel.ga...@gmail.com <mailto:jose.manuel.ga...@gmail.com>>
wrote:
Dear all,
This might sound naive, but I want to compute 2D coordinates
for a set
of molecules.
For now I am considering the 3 methods below [1].
I was wondering if there was any recommendation to use one
method over
another in some cases?
For instance, very large rings are not displayed round for
CoordGen but
sometimes this method performs worse than the default (AllChem).
Computational time is not really an issue here as I generate
those
coordinates on the fly for a very small set of compounds.
Here is a gist with a few examples:
https://gist.github.com/jose-manuel/0f2a5e8eae8bf2a72c0faad7f2f2a263
Thanks in advance, any suggestion is welcome!
Cheers,
Jose Manuel
[1] Methods:
1) rdkit.AllChem.Compute2dCoors (equivqlent to
rdkit.Chem.rdDepictor.Compute2DCoords)
2) rdkit.Avalon.pyAvalonTools.Generate2DCoords
3) rdkit.Chem.rdCoordGen.AddCoords + rescale
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--
======================================================================
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech
Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
&
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic
email: teva...@gmail.com <mailto:teva...@gmail.com>
website: https://sites.google.com/site/thomasevangelidishomepage/
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