[Rdkit-discuss] SD tag reordering follow up

with sd_writer.SetProps() but that didn't work. Turns out mol.GetPropNames() returns a list in alphabetical order instead of order of appearance. Is there a way to preserve SD tag orders? https://sourceforge.net/p/rdkit/mailman/message/32036716/ Thanks, JW ___ JW Feng, Ph.D. Denali

Re: [Rdkit-discuss] SD tag reordering follow up

Hi Greg, Thanks for the examples. I will give it a try. JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 201 Gateway Blvd. South San Francisco, CA 94080 | (650) 270-0628 On Thu, Oct 22, 2015 at 2:06 AM, Greg Landrum <greg.land...@gmail.com> wrote: > Hi JW, > >

[Rdkit-discuss] 2012 UGM slide link broken?

Hi, I tried to download JP Ebejer's conformer generation using RDKit deck but this link appears to be broken. http://rdkit.org/UGM/2012/Ebejer_20110926_RDKit_1stUGM.pdf Would you mind moving these slides to github.org? Thanks, JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

Hi Greg and Sereina, Thanks for confirming the bug. I also vote for changing the code to use only heavy atoms. Is symmetry taken into consideration when calculating RMS during the pruning step? Best, JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd

[Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

oms are included. Pairwise RMS are <0.5 for many conformers when only heavy atoms are included. Thanks, JW _______ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650) 270-0628 21843_confs_output.sdf Description: Binar

Re: [Rdkit-discuss] tautomers in rdkit

ely familiar with QuacPac Best, JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650) 270-0628 On Tue, Apr 11, 2017 at 6:52 AM, <rdkit-discuss-request@lists.s ourceforge.net> wrote: > Send Rdkit-discuss

Re: [Rdkit-discuss] The RDKit and GSoC 2020

t, > -greg > > On Sat, Mar 7, 2020 at 2:22 AM JW Feng wrote: > >> Project suggestion: >> >> Project 1: >> Implement 2D structure depiction in Google Spreadsheets. My colleagues >> at Google think this is very doable. Being able to depict structures in &

Re: [Rdkit-discuss] The RDKit and GSoC 2020

Project suggestion: Project 1: Implement 2D structure depiction in Google Spreadsheets. My colleagues at Google think this is very doable. Being able to depict structures in Google Spreadsheets will dramatically increase collaboration between scientists. Imaging being able to provide comments

Re: [Rdkit-discuss] The RDKit and GSoC 2020

even further, or even >>> turned into a colab snippet <https://stackoverflow.com/a/53875826> for >>> easier use. >>> >>> Also, since colab doesn't play well with conda (as far as pre-installed >>> deps are concerned), we would at least need a pip-installa

[Rdkit-discuss] Google Research Job Opening - Drug Discovery Scientist

ntists to accelerate drug discovery. Please visit the job post <https://careers.google.com/jobs/results/91113763815465670-research-scientist-drug-discovery/> and apply. Best, JW Feng (LinkedIn <https://www.linkedin.com/in/jwfeng/>) ___ Rdkit-discuss

Re: [Rdkit-discuss] Availability of new command line Psi4 scripts powered by RDKit

Hi Manish, This is great. I used Psi4 extensively for torsional scans while at Denali. Do you plan to include scripts for torsional scans? Best, JW On Wed, Apr 21, 2021 at 9:11 AM Manish Sud wrote: > Hi All, > > > > I'll like to share with you the availability of the following new command >

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 121, Issue 15

The Daylight website is a very good resource for SMILES, SMARTS, and SMIRKS. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650) 270-0628 On Wed, Nov

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 123, Issue 26

Another +1 for MolVS. ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650) 270-0628 On Tue, Jan 16, 2018 at 10:04 AM, < rdkit-discuss-requ...@lists.sourceforge.net> wrote: > Send Rdkit-discuss mai

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 124, Issue 10

How about setting up a donation fund on rdkit.org to pay for summer students to document code? For companies that benefited from using RDKit, it is a worthy cause to pay it forward. ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South San Francisco

[Rdkit-discuss] Seg fault importing rdkit.Chem on Mac 10.13.2 and Python 3.6.3

using this conda command "conda install --channel https://conda.anaconda.org/rdkit rdkit" [image: Inline image 1] Python 2.7 works just fine. Thanks, JW _______ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650

Re: [Rdkit-discuss] Seg fault importing rdkit.Chem on Mac 10.13.2 and Python 3.6.3

Thanks, my colleague Katrina Lexa found that python 3.6.1 worked. Conda version is 4.4.6 conda create --name test-rdkit --channel https://conda.anaconda.org/rdkit rdkit python=3.6.1 Best, JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South

[Rdkit-discuss] want advice for good teaching data set

Hi Andrew, What about building QSAR models to predict activity for a particular ChEMBL assay? This would allow you to discuss strength and limitations of QSAR models. Best, JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA