[Rdkit-discuss] rdkit-cartridge: Inserting new molecules

Dear community, I was wondering on how to best insert molecules into a mol field. The documentation only show how to insert from a preexisting table with a smiles column and then use "mol_to_smiles". How can a molecule be inserted directly? eg what format need to be submitted? Second point is

[Rdkit-discuss] Jupyter Notebook Structure image size

Hi all, how can I change the default structure image size in Jupyter notebook for a - single molecule? - molecules in a pandastools dataframe? default size is way too large for my taste (takes up too much screen space) Best Regards, Thomas ___

Re: [Rdkit-discuss] proper technical term for generating virtual compounds with rdkit and smarts

Hi Brian, commercial tools usually use the term "reaction-based enumeration" or "reaction-based library design". Best Regards, Thomas Von: Bennion, Brian via Rdkit-discuss Gesendet: Freitag, 25. September 2020 07:19 An: RDKit Discuss Betreff: [Rdkit-discuss]

[Rdkit-discuss] TIL: Mol objects having varying attributes depending on rdkit imports

Dear readers, just wasted an amazing amount of time and reporting this in case someone else happens to run into this problem. if you simply do: from rdkit import Chem m = Chem.MolFromSmiles('c1c1') m.Compute2DCoords() you will get an error Mol object has no attribute Compute2DCoords.

Re: [Rdkit-discuss] RDkit in Python vs. on PostgreSQL?

Hi Deepti, for the spark part I say you simply generated all the fingerprints (locally or on the cluster) and store the generated list of fingerprints as pkl file. Then when running you test you simply load the picke file into memory. With 15GB memory and 2Mio molecules this should easily work

Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

ts size I assume it works. So I suggest to add the bondLineWidth as option to above method. Best Regards, Thomas Von: Thomas Strunz Gesendet: Donnerstag, 13. Februar 2020 09:09 An: rdkit-discuss@lists.sourceforge.net Betreff: [Rdkit-discuss] RDKit Cartridge mol

[Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

Hi All, started to play around with the rdkit cartridge and I was wondering how to correctly use the mol_to_svg function. On rdkit homepage I only found this: mol_to_svg(mol,string default ‘’,int default 250, int default 200, string default ‘’) : returns an SVG with a drawing of the molecule.

Re: [Rdkit-discuss] How does rdkit cartridge work?

Hi Greg, about your comment on custom fingerprints: "I'm not sure what you mean by substructures, but you can, from Python, use custom fingerprints in the cartridge. That's explained here: http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html; For me and I suspect

Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

13:43 Bis: Thomas Strunz; Maciek Wójcikowski Cc: rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines Hi Thomas, FWIW I ran your example code below on my VM host (CentOS 7.3, Intel(R) Xeon

Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

ójcikowski Gesendet: Donnerstag, 23. Januar 2020 11:04 An: Thomas Strunz Cc: Greg Landrum ; rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines Thomas, Could you double check if your

Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

>50% more time. So there seems to be a consistent large performance impact in VMs. Of course the VM will be a bit slower but not by that much? What am I missing? Other experiences? Best Regards, Thomas Von: Greg Landrum Gesendet: Montag, 16. Dezember 2019 17:1

[Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

Hi All, I was looking at a blog post from greg: https://rdkit.blogspot.com/2019/07/a-couple-of-substructure-search-topics.html about fingerprint screenout. The part that got me confused was the timings in his blog post because run times in my case where a lot slower. Gregs numbers:

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

Hi all, In the last couple days there has been increased foucs on this on certain tech/social media sites (MKL crippling Ryzen) for example matlab is also affected. Some of you might have seen it but there seems to be a very simple workaround to get MKL to run properly on AMD Ryzen. One

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

compatible with openblas. There are probably more such issues but I guess still better than getting everything but rdkit from pypi. Best Regards, Thomas Von: Peter St. John Gesendet: Dienstag, 12. November 2019 16:25 An: Greg Landrum Cc: Thomas Strunz ; rdk

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

Von: Greg Landrum Gesendet: Dienstag, 12. November 2019 11:06 An: Thomas Strunz Cc: rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows) Sorry I missed that you were on windows. It looks like you can

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

. best regards, Thomas Von: Greg Landrum Gesendet: Dienstag, 12. November 2019 10:13 An: Thomas Strunz Cc: rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows) Hi Thomas, I'm

[Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

Dear all, would it be possible to make RDKit package not depend on mkl (probably via numpy, pandas) and that it accepts pre-installed numpy and pandas for example from pip as sufficient? The background to this is simple. Intel MKL cripples performance on any AMD bases processor (4-5 times

Re: [Rdkit-discuss] New Drawing code: Fixed sized molecules

Thomas Von: Thomas Strunz Gesendet: Mittwoch, 13. Juni 2018 14:28 An: rdkit-discuss@lists.sourceforge.net Betreff: [Rdkit-discuss] New Drawing code: Fixed sized molecules When using the "new" drawing code according to http://rdkit.blogspot.com/2015/02/new-drawing-code.html<http:/

[Rdkit-discuss] New Drawing code: Fixed sized molecules

When using the "new" drawing code according to http://rdkit.blogspot.com/2015/02/new-drawing-code.html I also want to be able to control the size of the molecule (not image) so if for example I have to depict multiple molecules smaller

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

] 3D alignment in Python: align conformers of 2 molecules To: beginn...@hotmail.de CC: rdkit-discuss@lists.sourceforge.net On Fri, Jun 27, 2014 at 7:57 AM, Thomas Strunz beginn...@hotmail.de wrote: thanks for your quick reply. This helped to improve the alignment. I'm glad to hear it! How

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

to identify the atom-atom mapping between the molecules. -greg On Thu, Jun 26, 2014 at 2:32 PM, Thomas Strunz beginn...@hotmail.de wrote: I'm trying to align all conformers of 2 molecules (and keep the best ones) using the python api by following some of the tutorials: http

[Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

I'm trying to align all conformers of 2 molecules (and keep the best ones) using the python api by following some of the tutorials: http://nbviewer.ipython.org/gist/greglandrum/4316435/Working%20in%203D.ipynb