Re: [Rdkit-discuss] Beta of the 2022.03.1 release available

Hi Greg, to give you some feedback: I switched my current research project to the beta version and didn't find any problem yet ;-) Best, Markus On Fri, Mar 18, 2022 at 1:32 PM Greg Landrum wrote: > Dear all, > > I tagged the first beta of the 2022.03 RDKit release this morning. > Assuming

Re: [Rdkit-discuss] Cheminformatics Graduate School Recommendations?

Hi Patrick, labs I would take a look at (in no particular order and well, a bit heavy on European labs): Irwin Lab, UCFS: https://profiles.ucsf.edu/john.irwin Bajorath Group, Bonn, Germany:

Re: [Rdkit-discuss] Chembience Postgres RDKit extension

-2020.09 chembience/postgres-rdkit:postgres-12.rdkit-2020.03 chembience/postgres-rdkit:postgres-11.rdkit-2019.09 Best, Markus On Mon, Mar 8, 2021 at 8:49 AM Greg Landrum wrote: > That's really cool, thanks Markus! > > On Sat, Mar 6, 2021 at 7:34 PM Markus Sitzmann > wrote: > &g

[Rdkit-discuss] Chembience Postgres RDKit extension

Hello, I have reworked the Postgres RDKit extension module of Chembience and made it a spin-off project of its own which is available at: https://github.com/chembience/docker-postgres-rdkit-compile It is now based on a fork of the Official Postgres Docker Image repository at GitHub just adding

Re: [Rdkit-discuss] RDKit/tautomers

Hi Benny, that is a pure InChI problem (not a RDKit one). Back then when the Standard InChI was defined, the 15T and the KET option for the InChI calculation weren't either available or still experimental (I don't remember :-)), so they didn't make it into the standard set of options for the

Re: [Rdkit-discuss] Install RDKit (Docker, rapids, rdkit=2020.03.2) ?/

Hi Joey, maybe the Dockerfile of my Chembience project helps: https://github.com/chembience/chembience/blob/master/context/build/rdkit/Dockerfile The chembience/python-base image it starts from actually doesn't do much except providing a very basic setup, its Dockerfile is here:

Re: [Rdkit-discuss] RD Kit PostgreSQL in a container

Hi, I am working on for this for the next Chembience release (0.3.0 which I hope will be out in January). It adds RDKit to the official Postgres container repository at https://hub.docker.com/_/postgres If you checkout https://github.com/chembience/chembience-postgresql-rdkit.git *and use branch

Re: [Rdkit-discuss] Inchi/smiles conversion issue

- | Markus Sitzmann | markus.sitzm...@gmail.com > On 18. Jun 2019, at 18:41, Alexis Parenty > wrote: > > Dear Jennifer, > Many thanks for your response. Very useful tutorial on Inchi. I did not know > about the FixedH option: > inchi = Chem.MolToInchi(mol, options='/Fixe

Re: [Rdkit-discuss] History of RDKit

Hi Paul, maybe this is helpful, too: https://cactus.nci.nih.gov/presentations/meeting-08-2011/Fri_Aft_Greg_Landrum_RDKit-PostgreSQL.pdf Markus On Tue, Apr 23, 2019 at 11:45 AM Czodrowski, Paul < paul.czodrow...@tu-dortmund.de> wrote: > Dear RDKitters, > > > > I’m using RDKit (of course!) for

Re: [Rdkit-discuss] 2019.03.1 RDKit Release

I appreciate this release and updated all Chembience components to RDKit 2019.03: https://github.com/chembience/chembience/releases/tag/0.2.10 Best, Markus On Tue, Apr 9, 2019 at 5:43 AM Greg Landrum wrote: > Dear all, > > I'm pleased to announce that the next version of the RDKit - 2019.03 -

Re: [Rdkit-discuss] Beta of the 2019.03 release available

Hi Greg, my Chembience RDKit image build with version 2019.03-b1b went fine (well, I just pull it with conda; in case someone is interested it is available with tag 0.2.10-beta-1 at Dockerhub). For the Postgres extension (which I still compile myself during the Docker build against Postgress),

Re: [Rdkit-discuss] chemfp preprint

Yes, we all love ref 57. - | Markus Sitzmann | markus.sitzm...@gmail.com > On 22. Mar 2019, at 20:39, Andrew Dalke wrote: > > Hi RDKit users, > > This week I submitted a paper about chemfp for publication. I also submitted > a pr

Re: [Rdkit-discuss] RDKIT Build Problems

Thanks Greg. I have the problem at CI, too. It was 100% failure rate the last two days. At home, occasionally. At least, it isn’t only me :-) Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 6. Mar 2019, at 17:25, Greg Landrum wr

[Rdkit-discuss] RDKIT Build Problems

Hi everybody, Currently (the last couple of days) the build of one of my Docker images stopped working: https://github.com/chembience/chembience/blob/develop/context/build/rdkit-postgres-compile/Dockerfile That occurred to me sporadically already over the last few years and usually disappeared

Re: [Rdkit-discuss] RDKit Release 2018.09.2 available

nd without this step and why it is necessary although I start building the containers basically from scratch and the newest version, I still don't know. Best, Markus On Sat, Feb 23, 2019 at 12:29 AM Dimitri Maziuk via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > On 2/22

Re: [Rdkit-discuss] RDKit Release 2018.09.2 available

Hi Greg, I just saw it is available in the conda-forge channel (with a time stamp of 2 hours + a few minutes), however, if I install it from there (in a fresh container) I receive 2018_09_1 - only when I explicitly force version 2018_09_2 I receive it (and at a very fast glance it is running).

Re: [Rdkit-discuss] Dividing inputstream over threads

> SQLalchemy creates a fairly specific ecosystem that you have to buy > into for it to make sense. When you don't have objects, only a table > of properties, OR mapper is just bloat. There is no need for objects with SQLAlchemy, SQLAlchemy's Core and its expression language is pretty excellent

Re: [Rdkit-discuss] InChI to Mol to InChi

create straight from InChI. Probably the minimization of the structure during the embedding is “turning around” the stereochemistry (probably you could have a long discussion whether this is a bug or a feature), Markus - | Markus Sitzmann | markus.sitzm

Re: [Rdkit-discuss] Chembience

/markussitzmann/status/105216581521409 Markus On Tue, Apr 24, 2018 at 10:44 AM Markus Sitzmann wrote: > Hello, > > since it includes RDKit as one of its major components I am happy to > announce the first release of my new open-source project Chembience: > > A Docke

Re: [Rdkit-discuss] Compilation Errors on RHEL7

Re: [Rdkit-discuss] Chembience

projects on top of it which I hope creates more interest. From my Chemical Identifier Resolver days I know you have to patient. Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 24. Oct 2018, at 17:56, Greg Landrum wrote: > > Glad th

Re: [Rdkit-discuss] Chembience

/1055047319660490753 https://github.com/chembience/chembience/releases https://www.chembience.com Best, Markus On Fri, Aug 31, 2018 at 11:20 PM Markus Sitzmann wrote: > Hello, > > I have put together another Chembience release (0.2.3): update of RDKit to > version 2018.03.*4, *Postgres to

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

; on the RDKit channel" question? > This is important to me (and possibly the community), so I'd like the keep > the discussion as simple and uncluttered as possible. > > Thanks, > -greg > > > On Thu, Oct 18, 2018 at 5:26 PM Markus Sitzmann > wrote: > >>

Re: [Rdkit-discuss] Chembience

PM Markus Sitzmann wrote: > Hello, > > I have just released Chembience 0.2.1: it updates RDKit to version > 2018.03.2 and switches Postgres from the 9.x series to version 10.4 > > https://github.com/chembience/chembience > > Best, > Markus > > > On Mon, May

Re: [Rdkit-discuss] enumeration of smiles question

Oh tempora o mores. Didn't we try for ages to make our SMILES canonical and now, all of sudden, the opposite is hip :-) On Mon, Aug 6, 2018 at 1:38 PM Chris Earnshaw wrote: > Hi > > The question 'what do you mean by ALL?' springs to mind. None of the > discussion includes dot-disconnected

Re: [Rdkit-discuss] MolFromInchi with Amides

don’t use InChI as your representation format (calculate InChI as an identifier field next to it). If your input resource only provides InChI or Standard InChI then your are of course out of luck. Best, Markus - | Markus Sitzmann | markus.sitzm...@gmail.com

Re: [Rdkit-discuss] Chembience

Hello, I have just released Chembience 0.2.1: it updates RDKit to version 2018.03.2 and switches Postgres from the 9.x series to version 10.4 https://github.com/chembience/chembience Best, Markus On Mon, May 14, 2018 at 1:49 AM Markus Sitzmann wrote: > Hello, > > I have released C

Re: [Rdkit-discuss] RDKit postgres cartridge building

- | Markus Sitzmann | markus.sitzm...@gmail.com > On 24. May 2018, at 18:24, Alfredo Quevedo <maquevedo@gmail.com> wrote: > > Good morning, > > I am trying to build RDKit from source, and succeed with that following the > instructions provided in the documentati

Re: [Rdkit-discuss] convert a smiles file to a xyz file

In reminiscence of old times, you can do this with the Chemical Identifier Resolver, for instance with the SMILES string for ethanol, CCO: https://cactus.nci.nih.gov/chemical/structure/CCO/file?format=xyz On Wed, May 23, 2018 at 5:24 PM Chenyang Shi wrote: > Hi Everyone, >

Re: [Rdkit-discuss] Chembience

your personal Jupyter notebook server with all RDKit 2018.03 goodness readily available). Best, Markus On Tue, Apr 24, 2018 at 10:44 AM Markus Sitzmann <markus.sitzm...@gmail.com> wrote: > Hello, > > since it includes RDKit as one of its major components I am happy to >

Re: [Rdkit-discuss] RDKit-MolVS intergration: Google Summer of Code Project

Yes, great news. Matt has really started a very nice work there. I hope it can be turned into something like a well-documented, open standard for molecule standardization. Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 26. Apr 2018, at 00

[Rdkit-discuss] Chembience

Hello, since it includes RDKit as one of its major components I am happy to announce the first release of my new open-source project Chembience: A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.

Re: [Rdkit-discuss] Some larger-scale RDKit C++ code changes

o longer being able to just walk over and ask Nadine > how to solve the problem. :-) > > On Wed, Apr 4, 2018 at 1:20 PM, Markus Sitzmann <markus.sitzm...@gmail.com > > wrote: > >> Have you tried a merge (after branching the master to something like >> master-

Re: [Rdkit-discuss] Some larger-scale RDKit C++ code changes

6 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > > On Wed, Apr 4, 2018 at 11:27 AM, Markus Sitzmann < > markus.sitzm...@gmail.com> wrote: > >> Hi Greg, >> >> > Concretely what this means in github is that the current master >> branch wil

Re: [Rdkit-discuss] Some larger-scale RDKit C++ code changes

Hi Greg, > Concretely what this means in github is that the current master branch will be renamed to legacy and the modern_cxx branch will be renamed to master. I hope you are not actually just renaming it - although I am not affected personally, that might be a call for trouble because it

Re: [Rdkit-discuss] conda build instructions for OSX?

I am not 100% sure what your motivation is to build a certain rev or the master branch, but let me guess: you want to be independent from further changes in the development branch. Well, my suggestion for this: fork the conda-rdkit repro on github and use your fork for future builds, i.e. the

Re: [Rdkit-discuss] Issue with the latest RDKit DB build

I have the problem, too, on Debian stretch - | Markus Sitzmann | markus.sitzm...@gmail.com > On 29. Dec 2017, at 20:01, Drew Gibson via Rdkit-discuss > <rdkit-discuss@lists.sourceforge.net> wrote: > > Hello, and compliments of

Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

in my personal projects. Another point is, if you look for one of the recent post from Greg here on the list, there is another problem with the latest conda version you might run into. Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 21.

Re: [Rdkit-discuss] ImportError: No module named rdkit

Well, if you have python 2.7 and 3.5 already running ,you can use (mini)conda for the RDKit installation (conda is anaconda but instead of one huge package you can install the packages you want including RDKit) On Fri, Sep 15, 2017 at 9:12 AM, Loris Bennett wrote: >

Re: [Rdkit-discuss] ImportError: No module named rdkit

BTW, python 3.6 is out since last Christmas ;-) (and made it to sub-release .2) On Fri, Sep 15, 2017 at 8:36 AM, Greg Landrum wrote: > I'll provide a more detailed answer in a bit, but since you aren't using > the system python anyway, is there any chance that you

Re: [Rdkit-discuss] Non-redundant database of molecules

;>>>>>> python and try to import Chem ("from rdkit import Chem") appears an >>>>>>> error >>>>>>> message: >>>>>>> Traceback (most recent call last): >>>>>>> File "", line 1,

Re: [Rdkit-discuss] ImportError: No module named rdkit

Not on Centos 6 - Docker requires Centos 7 for the host system. On Thu, Sep 14, 2017 at 10:01 PM, Dimitri Maziuk wrote: > On 09/14/2017 02:58 PM, Andrew Dalke wrote: > > > If only Greg got as much money for long term RDKit support as Red Hat > > gets for long term RHEL

Re: [Rdkit-discuss] bad inchi or parsing problem?

On Thu, Sep 14, 2017 at 8:09 PM, Jason Biggs wrote: > Okay, all three of these smiles strings resolve to the same inchi, > > "O=[N+](C1=NC2=CC=CC=C2N=C1)[N-](=O)C1=NC2=CC=CC=C2N=C1" > "C1=CC=C2C(=C1)N=CC(=N2)N(=N(=O)C3=NC4=CC=CC=C4N=C3)=O" >

Re: [Rdkit-discuss] bad inchi or parsing problem?

On Thu, Sep 14, 2017 at 8:09 PM, Jason Biggs wrote: > Okay, all three of these smiles strings resolve to the same inchi, > > "O=[N+](C1=NC2=CC=CC=C2N=C1)[N-](=O)C1=NC2=CC=CC=C2N=C1" > "C1=CC=C2C(=C1)N=CC(=N2)N(=N(=O)C3=NC4=CC=CC=C4N=C3)=O" >

Re: [Rdkit-discuss] bad inchi or parsing problem?

On Thu, Sep 14, 2017 at 7:38 PM, John Mayfield wrote: > InChI is an identifier and not a representation, you should not read > InChIs... but we are beyond hope there so... > Wonderfully said - unfortunately one day they decided to make InChIs "readable" ... > The

Re: [Rdkit-discuss] Non-redundant database of molecules (Wandr?)

If you do nothing else (on purpose), SMILES *calculated* by RDKit from any input are canonical per se (BUT that is only true if you compare it to other SMILES also calculated by RDKit, you can not compare SMILES between software packages even if they canonical in the domain of each of the software

Re: [Rdkit-discuss] Non-redundant database of molecules

PS. The conda version has InChI support On Wed, Sep 13, 2017 at 10:04 PM, Markus Sitzmann <markus.sitzm...@gmail.com > wrote: > Strong recommendation: use the conda version: > > http://www.rdkit.org/docs/Install.html > > On Wed, Sep 13, 2017 at 9:58 PM, Wandré <wandr

Re: [Rdkit-discuss] Non-redundant database of molecules

o Interdisciplinar em Simulação e > Inteligência Computacional - UNIFEI > Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ > Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG > Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG > > 2017-09-13 16:55 G

Re: [Rdkit-discuss] Non-redundant database of molecules

is, one or more, mistakes)? >>>> >>>> Thanks! >>>> >>>> -- >>>> Wandré Nunes de Pinho Veloso >>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG >>>> Doutorando em Bioinformática - Universid

Re: [Rdkit-discuss] Non-redundant database of molecules

m Simulação e > Inteligência Computacional - UNIFEI > Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ > Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG > Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG > > 2017-09-13 14:19 GMT-03:00

Re: [Rdkit-discuss] Non-redundant database of molecules

? - | Markus Sitzmann | markus.sitzm...@gmail.com > On 13. Sep 2017, at 17:58, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > >> On 2017-09-13 10:17, Markus Sitzmann wrote: >> Canonical SMILES are only a very rough approximation for "unique molecule" >> as they usua

Re: [Rdkit-discuss] Non-redundant database of molecules

Canonical SMILES are only a very rough approximation for "unique molecule" as they usually don't work well for tautomeric forms of compound. InChI or Standard InChI is much better although also not perfect. The "perfect solution" depends also on how uniqueness or redundancy of molecules is

Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.

Mhh, your choices of test molecules sounds like going from poster child to archenemy of conformation generation algorithms :-) - | Markus Sitzmann | markus.sitzm...@gmail.com > On 7. Sep 2017, at 18:59, Jason Biggs <jasondbi...@gmail.com> wrote:

Re: [Rdkit-discuss] Using RDKit in PyCharm and Anaconda on Windows

I definitely have it working on Linux, too, but it might have been that I also only tried it with PyCharm 2017.1.3 first. Before that, I did what Greg suggested, starting pycharm from the activated environment. Unfortunately I have no experience with Windows in this regard, too. On Thu, Jun 1,

Re: [Rdkit-discuss] Trouble with conda build in Docker

Hi Riccardo, just to tell you: my problem went away (I didn't touched it since my last email) for whatever reason (did you do something?) Markus On Thu, Apr 6, 2017 at 12:51 PM, Markus Sitzmann <markus.sitzm...@gmail.com> wrote: > Thanks Riccardo for your reply > > I tr

Re: [Rdkit-discuss] Install rdkit with anaconda3

I think if you install conda freshly now it automatically uses python 3.6. If you don't have the requirement for 3.6 you have to do this conda install python=3.5 Then you should be able do install rdkit as described. On Wed, Apr 12, 2017 at 12:29 PM, Greg Landrum wrote:

Re: [Rdkit-discuss] Trouble with conda build in Docker

017 at 12:03 AM, Markus Sitzmann < > markus.sitzm...@gmail.com> wrote: > >> Hi (Riccardo). >> >> I have trouble with the conda build in Docker (I just updated to the most >> recent version which triggered the new build) - below is the error trace. I >> took the

[Rdkit-discuss] Trouble with conda build in Docker

Hi (Riccardo). I have trouble with the conda build in Docker (I just updated to the most recent version which triggered the new build) - below is the error trace. I took the original Docker file and just edited out all non-Python35 builds - so it does only the Python35 builds and ends somewhere

Re: [Rdkit-discuss] connecting to postgres in rdkit environment

Maybe this one here helps, too, although it is basically the same what TJ said: https://devops.profitbricks.com/tutorials/install-postgresql-on-centos-7/ Markus On Sat, Feb 25, 2017 at 11:29 PM, TJ O'Donnell wrote: > The server itself must be told to allow remote connections. >

[Rdkit-discuss] If someone has build problems using conda currently ...

... I just suffered this: https://github.com/conda/conda/issues/4309 Going back to a previous conda version (4.2.12) helps. Other than that: Happy New Year (a late one :-) -- Check out the vibrant tech community on one

Re: [Rdkit-discuss] Extracting SMILES from text

Hi Alexis, you may find also so some "novel" compounds by this approach :-). Whether your tuple solution improves performance strongly depends on the content of your text documents and how often they repeat the same words again - but my guess would be it will help. Probably the best way is even

Re: [Rdkit-discuss] comparing two or more tables of molecules

Well, since George mentioned a talk by me, I wish we would have implemented our tool back then using an open-source tool like RDKit (which wasn't very well know back then), and also would have been so smart to use SMARTS for the transformation rules (partially they are implemented as SMARTS but

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] reading multiple conformers from file

+1 for a json format ... hmm, how about a general json-based molecular structure format ... let us call it "cson" (that is an homage to Google gson and Chemical Markup Language CML :-) Markus On Mon, Oct 31, 2016 at 11:18 AM, Brian Cole wrote: > I would 2nd the suggestion of

Re: [Rdkit-discuss] The RDKit and modern C++

I get the feeling, RH/Centos 6 becomes the next XP kind of story - to many legacies that make the update impossible or very hard. Also docker, a great technology that could mitigate this problem, is very painful under RH/Centos 6. --- Markus Sitzmann > On 29 Sep 2016, at 07:31, G

Re: [Rdkit-discuss] Conda installation of RDKit on W8

Hi Gonzalo, after you activated my-rdkit-env, try to install rdkit by conda install -c https://conda.anaconda.org/rdkit rdkit Alternatively, if you go a step back, you can also start with conda create -c https://conda.anaconda.org/rdkit -n give-your-environment-whatever-name-you-want rdkit

Re: [Rdkit-discuss] cannot import matplotlib in my-rdkit-env

- | Markus Sitzmann | markus.sitzm...@gmail.com > On 21.08.2016, at 16:24, chris dalton <chrisdal...@gmail.com> wrote: > > Hi, > I have installed Rdkit on a windows laptop with conda and I can activate the > rdkit environment OK and if I

Re: [Rdkit-discuss] Some feedback from the Sheffield Cheminformatics Conference

, Greg. Cheers, Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 07.07.2016, at 08:20, Greg Landrum <greg.land...@gmail.com> wrote: > > Dear all, > > I was at the Sheffield Cheminformatics conference earlier this week (along

Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

Hi Riccardo, Yes, it builds again - thanks a lot for your efforts. Best, Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 30.06.2016, at 20:55, Riccardo Vianello <riccardo.viane...@gmail.com> > wrote: > > Hi Markus, >

Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

Hi Riccardo, Thanks for your efforts and sorry that I didn't reply earlier. I am not sure about all the side conditions in order this error to occur but I am glad you can reproduce it. Markus - | Markus Sitzmann | markus.sitzm...@gmail.com

Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

Hi, unfortunately I have another problem - rdkit-postgres isn't building for me since the change to Release_2016_03_2. Is that a known problem? Below is the end of the build log. I only let build the py35-part (+ncurses) of the Dockerscript. Thanks & Best, Markus BUILD START:

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

is probably the solution to your problem. Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 21.06.2016, at 21:24, Michał Nowotka <mmm...@gmail.com> wrote: > > Hi Stéphane, > > Just to let you know about two things: >

[Rdkit-discuss] Conda and Rdkit 2016-03 Pains

Hi Greg and everybody involved, thanks for your great software - unfortunately, I have some building pains. I recently decided to go from RDKit 2015-03 to 2015-09 (yes I was late) , everything still on python 2.7. As part of this migration I decided to give Conda a try and it worked nicely in

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

Hi James, I know that my opinion might sound extreme but I had this discussion many times (mostly regarding tautomerism which is, however, similar in some way). The problem is, you can look at a chemical structure in many different ways - two scenarios are: 1. What can I perceive from a chemical

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

Hehe, that is why I keep my computers always really cold when I run RDKit ... - | Markus Sitzmann | markus.sitzm...@gmail.com On 20.08.2015, at 04:33, Peter Shenkin shen...@gmail.com wrote: Maybe when you have a toolkit as blazingly fast as RDKit

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

I agree with remove - the chance that you destroy actual information by this is low - or in other words, the chance that steroinformation on three-coordinate N is spurious I would expect as high. Markus On Thu, Aug 20, 2015 at 4:30 PM, Greg Landrum greg.land...@gmail.com wrote: This isn't a

Re: [Rdkit-discuss] Two SMILES that (I think) should canonicalize to the same thing, but don't

We could consider some quantum-mechanical calculations ... well, I always hated this discussion when I heard for my web service with millions of structures, I should consider quantum-mechanical calculations as part of the structure normalization/canonicalization ;-) On Wed, Jun 17, 2015 at 8:22

Re: [Rdkit-discuss] SDF properties in case of error

No, cutting out a chunk of lines from a file might be simple, but can become an expensive operation if you want to deal with thousands of files and million of records. That is one of the reasons why I (unfortunately) couldn't consider rdkit any further for one of my projects a few years ago. So, I

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

You can report it to Marc Nicklaus ... who will probably sent it to me ... I will take a look. Whether I can fix any misbehavior is another question. On Tue, Feb 24, 2015 at 8:27 AM, Greg Landrum greg.land...@gmail.com wrote: The InChIs have me confused. I'm going to simplify the below by

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

Well, the http://cactus.nci.nih.gov/chemical/structure/ site is my baby which I had to leave behind 1 1/2 years ago (I am not with NIH anymore). Igor who replied in this thread was also involved in some parts of it. Traffic on this cactus service is between 5 to 10 million requests per month - so

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

Well, at least you said something important: conversion of InChI to molecules is something that's not in general guaranteed to work perfectly - and this is by design like this because InChI is an identifier, not a molecule representation. Unfortunately, many people seemed to forget about this :-)

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

at 2:06 PM, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 2015-02-19 05:58, Greg Landrum wrote: On Thu, Feb 19, 2015 at 10:11 AM, Markus Sitzmann markus.sitzm...@gmail.com mailto:markus.sitzm...@gmail.com wrote: Well, at least you said something important: conversion of InChI

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

...@bmrb.wisc.edu wrote: On 2015-02-19 07:27, Markus Sitzmann wrote: No, a chemical structure must calculate a unique InChI, but a InChI might cover more then one chemical structure Heh. I could swear last time I read the description it specifically mentioned databases. In the database context 'unique

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

I agree with John, the InChI for mol1 and mol2 should be http://cactus.nci.nih.gov/chemical/structure/O=C(NCCc1c1)[C@H]1CC[C@H](Cn2c(O)nc3c3c2=O)CC1/stdinchi

Re: [Rdkit-discuss] New RDKit drawing code

Hi Greg and all the others involved, That looks really nice! And don't give any code to Noel anymore, it all ends up in JavaScript :-) (who would have thought 10 years ago that would make any sense). Best, Markus - | Markus Sitzmann | markus.sitzm

[Rdkit-discuss] Fwd: Tautomeric InChIs

-- Forwarded message -- From: Markus Sitzmann markus.sitzm...@gmail.com Date: Thu, May 8, 2014 at 3:27 PM Subject: Re: [Rdkit-discuss] Tautomeric InChIs To: Edward Pyzer-Knapp e.o.pyzerkn...@gmail.com Hi Edward, since your InChI is a Standard InChI (1S/): tautomeric forms

[Rdkit-discuss] Fwd: RDKit cartridge similarity search speeds(?)

-- Forwarded message -- From: Markus Sitzmann markus.sitzm...@gmail.com Date: Thu, May 8, 2014 at 3:14 PM Subject: Re: [Rdkit-discuss] RDKit cartridge similarity search speeds(?) To: James Davidson j.david...@vernalis.com Hi James, I would guess, in your second query

Re: [Rdkit-discuss] implementation of tautomer enumeration/canonicalization

Hello, I was about to ask the same (I am one of the authors of the mentioned paper) - I had seen this post (gosh, a year ago) but had no time back then to answer (job search and a move from the US to Europe). I was digging into this last week a bit, however, I can not say much yet - very initial

Re: [Rdkit-discuss] Three tests failing on CentOS 5.3 - important ?

I think the syntax except Exception as e: did't exist before python 2.6 ... are you running this on an older version? :-) Cheers, Markus On Wed, Mar 19, 2014 at 7:54 AM, Jan Holst Jensen j...@biochemfusion.com wrote: On 2014-03-19 05:54, Greg Landrum wrote: On Tue, Mar 18, 2014 at 4:59 PM,

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

And without disabling SELinux :) http://stopdisablingselinux.com/ I never said that is a good idea :-) -- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Although, since the NSA was involved into the development of SELinux maybe it doesn't matter so much anymore :-) On Wed, 11 Sep 2013 18:42:20 -0400, Markus Sitzmann sitzm...@helix.nih.gov wrote: And without disabling SELinux :) http://stopdisablingselinux.com/ I never said

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Are you trying to use it with python/mod_wsgi? Your description so far is a bit vague :-)MarkusOn Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka mmm...@gmail.com wrote:Thanks for advices. Unfortunately I can't do anything system-wide as I don't have administrator privileges on the server. Than

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

How far is your setup working so far? Can you already run python scriptsvia mod_wsgi without importing rdkit?On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka mmm...@gmail.com wrote:Yes: python, mod_wsgi, vitualenv, RHELOn Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann sitzm...@helix.nih.gov

Re: [Rdkit-discuss] name generator

Hi Sergio,there may be random entries in the Resolver database behindhttp://cactus.nci.nih.gov/chemical/structure but definitelynothing systematic.MarkusOn Wed, 28 Aug 2013 07:54:26 -0400, Sergio Martinez Cuesta sermar...@gmail.com wrote:Thanks Greg,I agree, it certainly works for molecules,

Re: [Rdkit-discuss] name generator

Yes, in this direction (structure to name) the Resolver is only a database lookup, in the other direction (name to structure), it first uses OPSIN (Daniel Lowe's library)which can resolve correct IUPAC names generically, if OPSIN "fails" it does a database lookup, too.MarkusNot sure what software

Re: [Rdkit-discuss] looking for suggestions: github vs bitbucket vs google code

I started with CVS, switch to svn, tried to learn git which made my head explode. However, for some odd reasons I didn't gave up on git, and one day it make click. Since then I switched everything to git and never looked back. I agree, when you come from CVS and svn, git changes your way of

Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu

and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann

Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu

CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov wrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO

Re: [Rdkit-discuss] retrosynthesis

://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm

Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu

Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 9:31 PM, Markus Sitzmann sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov wrote: Hi Abhik, I am

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