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
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:
-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
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
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
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:
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
-
| 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
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
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 -
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),
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
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
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
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
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).
> 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
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
/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
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
/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
; 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:
>
>>
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
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
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
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
-
| 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
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,
>
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
>
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
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.
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-
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
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
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
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
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.
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:
>
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
;>>>>>> python and try to import Chem ("from rdkit import Chem") appears an
>>>>>>> error
>>>>>>> message:
>>>>>>> Traceback (most recent call last):
>>>>>>> File "", line 1,
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
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"
>
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"
>
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
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
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
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
is, one or more, mistakes)?
>>>>
>>>> Thanks!
>>>>
>>>> --
>>>> Wandré Nunes de Pinho Veloso
>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>> Doutorando em Bioinformática - Universid
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
?
-
| 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
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
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:
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,
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
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:
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
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
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.
>
... 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
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
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
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 <
+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
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
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
-
| 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
, 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
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,
>
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
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:
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:
>
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
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
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
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
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
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
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
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
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 :-)
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
...@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
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
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
-- 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
-- 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
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
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,
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
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
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
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
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,
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
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
and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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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
://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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Markus Sitzmann, Ph.D.
Chemical Biology Laboratory
Center for Cancer Research
National Cancer Institute
National Institutes of Health
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301-846-5974 (office)
301-846-6033 (fax)
sitzm
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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