[Rdkit-discuss] 2016.09 (Q3 2016) RDKit Release

Dear all, I'm pleased to announce that the next version of the RDKit -- 2016.09 (a.k.a. Q3 2016) -- is released. This one is even later than usual since the RDKit UGM was quite late this year. And then we hit some problems with the python 2.7 builds on Windows . The release notes are below. The

[Rdkit-discuss] smarts vs smiles database queries and explicit hydrogens

Hi all, I am currently exploring the possibilities of the RDKit database cartridge for substructure search- I installed everything following the tutorial from http://www.rdkit.org/docs/Install.html Very nice tutorial - worked perfectly fine. Since we are exploring solutions for browser

Re: [Rdkit-discuss] smarts vs smiles database queries and explicit hydrogens

Hi Alex, The new version of the cartridge has some capabilities that, I think, address this. There's a blog post about this: http://rdkit.blogspot.com/ 2016/07/tuning-substructure-queries-ii.html but the short version is that you can do the kind of queries it seems like you want to do quite

Re: [Rdkit-discuss] Installation of RDKit on windows 7

Dear Riccardo, I uninstalled Anaconda2 and reinstalled it for me alone (and not for all users as I did initially) and the installation of rdkit completed without any trouble. I was then able to import Chem from rdkit. Thank you for suggesting that this global/personal installation of

Re: [Rdkit-discuss] Pandas

No worries.This, and Anna's question about similarity searching and clustering illustrate a great opportunity for a tutorial on fingerprints and similarity searching.  -greg On Wed, Nov 23, 2016 at 3:00 PM +0100, "Chris Swain" wrote: Thanks for this, As a chemist

Re: [Rdkit-discuss] smarts vs smiles database queries and explicit hydrogens

If I understood Greg correctly, it will be in 2016.09 which isn't in conda just of yet, they are currently working on putting it there. Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 23 Nov 2016, at 15:29, Alexander Klenner-Bajaja

Re: [Rdkit-discuss] smarts vs smiles database queries and explicit hydrogens

Alex, I'm glad that looks right. Unfortunately those changes are in the 2016.09 version of the RDKit, which was just finalized today. We haven't completed the anaconda builds for that yet. -greg On Wed, Nov 23, 2016 at 3:29 PM, Alexander Klenner-Bajaja wrote: > Dear Greg, >

Re: [Rdkit-discuss] Pandas

Is it possible to use the bulk similarity searching functionality for better performance instead of the list comprehension? Best, Peter On Wed, Nov 23, 2016 at 9:11 AM Greg Landrum wrote: No worries. This, and Anna's question about similarity searching and clustering

Re: [Rdkit-discuss] smarts vs smiles database queries and explicit hydrogens

Thank you both Greg & Markus – I`ll happily wait for it to appear in conda in the near future ☺ Alex From: Markus Sitzmann [mailto:markus.sitzm...@gmail.com] Sent: Wednesday, November 23, 2016 3:40 PM To: Alexander Klenner-Bajaja Cc: rdkit-discuss@lists.sourceforge.net Subject: Re:

Re: [Rdkit-discuss] Pandas

Peter, If you have chemfp and can make a chemfp arena, RDKit now supports these structures for reading and searching. This, by far, is the fastest way I know of similarity searching. I believe that Greg's implementation is compatible with chemfp 1.0 which is available on pypi: