Re: [Rdkit-discuss] RDKit and Binder

I don't have direct experience with RDKit and binder but I would guess that the recommended way would be to use conda in binder (default is pip) and add rdkit in channels and rdkit in dependencies in environment.yml. Example:

[Rdkit-discuss] RDKit tutorials

Hi RDKit fans, It's been a while since RDKit UGM in Berlin and I only now took time to make a pool request (rdkit tutorial repo ) to submit a notebook I made during the hackaton. I would like to take this opportunity and encourage other hackaton

Re: [Rdkit-discuss] Clustering

Hi All, I have to admit I was commenting about PCA->k-means without actually trying. Out of curiosity I implemented it here: https://github.com/samoturk/cheminf-notebooks/tree/master/Python#pca-k-meanspy It can process 4M compounds in ~60 minutes on desktop i5 and it should work with 16GB or

Re: [Rdkit-discuss] RDKit on armv7h

est regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > 2017-06-03 20:02 GMT+02:00 Samo Turk <samo.t...@gmail.com>: > >> It compiled successfully, unfortunately importing rdkit crashes python >> interpreter (Segmentation fault). But I didn't have time to look m

Re: [Rdkit-discuss] RDKit on armv7h

, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > 2017-06-03 8:46 GMT+02:00 Gianluca Sforna <gia...@gmail.com>: > >> On Thu, Jun 1, 2017 at 12:03 AM, Samo Turk <samo.t...@gmail.com> wrote: >> > Thanks! It seems to work, but it's still co

Re: [Rdkit-discuss] RDKit on armv7h

doesn't exist on arm7 > > > > > Brian Kelley > > On May 31, 2017, at 5:08 PM, Samo Turk <samo.t...@gmail.com> wrote: > > Dear RDKit community, > > I have trouble compiling RDKit on Arch Linux on armv7h cpu. It has to be > something with CPU architecture since the

[Rdkit-discuss] RDKit on armv7h

Dear RDKit community, I have trouble compiling RDKit on Arch Linux on armv7h cpu. It has to be something with CPU architecture since the same build script is working on Arch Linux on x86_64. Package versions are the same on both computers: gcc 7.1.1, boost 1.64.0, python 3.6.1 and build script is

[Rdkit-discuss] Ring detection difference between mol and query

Hi RDKit enthusiasts, There is a difference in ring detection between a molecule (FromSmiles) and query (FromSmarts). Like in this example: smiles = 'c1ccc2nncn2n1' # Construct mol m = Chem.MolFromSmiles(smiles) Chem.FastFindRings(m) ri = m.GetRingInfo() # Construct query q =

[Rdkit-discuss] GetAvalonFP returns ValueError: Sanitization error: Can't kekulize mol

Hi RDKiters, I have problems with substructure matching in pandas and it's caused by AvalonTools (L178 in current version of PandasTools). I'm not sure if this is a bug or I'm doing something wrong. Here is a version of the code with just Avalon part: from rdkit.Avalon import pyAvalonTools as

Re: [Rdkit-discuss] GetAvalonFP returns ValueError: Sanitization error: Can't kekulize mol

d also be possible to do this for > a molecule contructed from SMARTS, in which case this would be a bug, but > I'm going to have to play with it a bit to be sure > > -greg > > On Fri, Mar 18, 2016 at 5:44 AM, Samo Turk <samo.t...@gmail.com> wrote: > >> >> I hav

Re: [Rdkit-discuss] identify which bonds are rotatable

Hi Dimitrios! Yes there is a way. You just have to use smarts pattern for rotatable bond (you can find it in Lipinski module https://github.com/rdkit/rdkit/blob/1bf6ef3d65f5c7b06b56862b3fb9116a3839b229/rdkit/Chem/Lipinski.py#L47 ): In [75]: mol = Chem.MolFromSmiles('CCc1cc(OC)ccc1') In [76]:

Re: [Rdkit-discuss] Export pandas DataFrame to xlsx with molecule images

width issues. Good luck! Grégori On 30. 10. 14 16:49, Samo Turk wrote: Hi rdkiters, Due to popular demand I started to work on a function to export pandas DataFrame to xlsx with molecule images embedded. Because of the xlsx specifics the code is not optimal. The most annoying

Re: [Rdkit-discuss] UGM2014: interactive SDF viewer - code on GitHub

Very nice effort! Cheers, Samo On Mon, Nov 3, 2014 at 12:11 PM, Pahl, Axel axelp...@gmx.de wrote: Hi Andrew, thanks a lot, that's a great idea. I do hope that people will like it. For those who could not attend the excellent meeting (just teasing...) I have also included the

Re: [Rdkit-discuss] Export pandas DataFrame to xlsx with molecule images

luck! Grégori On 30. 10. 14 16:49, Samo Turk wrote: Hi rdkiters, Due to popular demand I started to work on a function to export pandas DataFrame to xlsx with molecule images embedded. Because of the xlsx specifics the code is not optimal. The most annoying thing about

Re: [Rdkit-discuss] [Rdkit-devel] 2014.09 (Q3 2014) RDKit Release

Arch Linux PKGBUILD: https://gist.github.com/samoturk/32e36597f0b4aac51ba0 openSUSE SPEC: https://gist.github.com/samoturk/d2e717abc9204d632d5c On Thu, Oct 30, 2014 at 12:53 PM, Gianluca Sforna gia...@gmail.com wrote: On Thu, Oct 30, 2014 at 7:23 AM, Greg Landrum greg.land...@gmail.com

[Rdkit-discuss] Export pandas DataFrame to xlsx with molecule images

Hi rdkiters, Due to popular demand I started to work on a function to export pandas DataFrame to xlsx with molecule images embedded. Because of the xlsx specifics the code is not optimal. The most annoying thing about this implementation is that it has to write all images to the hard drive,

Re: [Rdkit-discuss] FYI: the RDKit is incompatible with numpy v1.9

Hi, Was this resolved? It seems to work for me with numpy v1.9.0... Samo On Mon, Sep 15, 2014 at 5:23 PM, Greg Landrum greg.land...@gmail.com wrote: Dear all, Riccardo and I have accidentally discovered that the RDKit is incompatible with the most recent version of numpy (v1.9.0). We're

[Rdkit-discuss] Windows and PandasTools again

Hi All, While we are at PandasTools and Windows. If you use Anaconda on Windows and Riccardo Vianello's excellent and convenient binstar package PandasTools also returns an error because it looks for Salts.txt at the wrong place. You can fix it by opening

Re: [Rdkit-discuss] Chem.PandasTools

Hi, You can create new object that stores MMP and has default pandas and ipython representation as base64 encoded png. This usually works for me, but I'm not sure why in this case it works only for ipython representation and not for pandas.. The code: # codecell import pandas as pd import

Re: [Rdkit-discuss] Chem.PandasTools

Hi, I'm not sure if it will work but you can try: df['new'] = df['Transformation'].map(showLine_MMP) Regards, Samo On Thu, May 8, 2014 at 4:31 PM, paul.czodrow...@merckgroup.com wrote: Dear RDKitters, I started to play around with the great Chem.PandasTool contribution provided by

Re: [Rdkit-discuss] docker.io - container for fully fledged rdkit installation on linux?

Hi, I didn't want to upset anyone. :) Anyway, maybe this short article on Wired clears things up: http://www.wired.com/wiredenterprise/2013/11/docker-linux/?cid=co15093964 Regards, Samo On Wed, Nov 27, 2013 at 9:24 PM, Jean-Marc Nuzillard jm.nuzill...@univ-reims.fr wrote: Dear Igor, Le

Re: [Rdkit-discuss] docker.io - container for fully fledged rdkit installation on linux?

Hi rdkitters, New release of Docker is availablehttp://blog.docker.io/2013/11/docker-0-7-docker-now-runs-on-any-linux-distribution/and it brings one very impotant improvement - it runs on any linux distribution (as long as the kernel is 3.8 or later). I updated RDKit Dockerfile

Re: [Rdkit-discuss] MolsToGridImage() fails with Sanitization error: Can't kekulize mol

Dear Greg, Thank you! kekulize=False works as advertised! :) I found UGM2012 IPython notebooks and one is on sanitization, so no need to explain it.. Regards, Samo On Tue, Aug 20, 2013 at 5:25 AM, Greg Landrum greg.land...@gmail.comwrote: Dear Samo, On Mon, Aug 19, 2013 at 4:04 PM, Samo

[Rdkit-discuss] Unable to build RDKit_2013_06_1 and Git version on Arch Linux

Hi, I'm trying to build RDKit on Arch Linux but make fails with RDKit_2013_06_1 and Git version with the error appended to the end of this message. Interestingly it works without a problem on RDKit_2013_03_2 and RDKit_2012_12_1 (didn't try earlier versions). Packege versions I'm using: python2

Re: [Rdkit-discuss] Unable to build RDKit_2013_06_1 and Git version on Arch Linux

? Regards, Samo On Fri, Aug 16, 2013 at 3:27 PM, Mikolaj Kowalik mx...@psu.edu wrote: On Fri, 16 Aug 2013 10:57:53 +0200 Samo Turk samo.t...@gmail.com wrote: I'm trying to build RDKit on Arch Linux but make fails with RDKit_2013_06_1 and Git version with the error appended to the end