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 noth
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:
https://www.limes-institut-bonn.de/forschung/arbeitsgruppen/unit-4/abteilung-bajorath/abt-bajorath-startsei
-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 t
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 Stand
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:
https://github
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='
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), yo
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 a
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
>
> boost conda-forge/linux-64::boost-1.68.0-py37h8619c78_1001
>
> boost-cpp conda-forge/linux-64::boost-cpp-1.68.0-h11c811c_1000
>
> rdkit conda-forge/linux-64::rdkit-2018.09.2-py37h270f4b7_0
>
>
>
> Maybe it wa
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).
Bu
Maybe this helps (at least, it is from Greg):
https://github.com/rdkit/rdkit/issues/642
Markus
On Mon, Jan 21, 2019 at 2:25 PM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
> My problem is more to know which molecules cause problems
> than avoiding the printing of warning messages in
> 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 wit
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 versi
; 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:
>
&g
Hmm, isn't that the problem with any build/dependency automation tool and
hard to fix in a generic way? If you are really very dependent on a
specific version of a software you have to be very careful with the
environment it sits in while you do "carefree" updates only in a carefree
environment :-)
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 SMILES
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 wrote:
>
> Good morning,
>
> I am trying to build RDKit from source, and succeed with that following the
> instructions provided in the documentation. Howvere, I am trying to u
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,
>
> I am seeking helps
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
wrote:
> Hello,
>
> since it includes RDKit as one of its major components I am happy to
> announce the first release of my new
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.
https://github.com/chembience/ch
just walk over and ask Nadine
> how to solve the problem. :-)
>
> On Wed, Apr 4, 2018 at 1:20 PM, Markus Sitzmann > wrote:
>
>> Have you tried a merge (after branching the master to something like
>> master-test-merge and then merge modern_cxx) ? How horrible does it loo
18 at 11:56 AM, Greg Landrum
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 will be renamed to legacy
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 inval
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 repr
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
> wrote:
>
> Hello, and compliments of the season to you, RDKitters :)
>
> I'm
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:
> Hi Greg,
>
> Greg Landrum wr
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 could switch to
> anaconda py
t;>>>> Traceback (most recent call last):
>>>>>>> File "", line 1, in
>>>>>>> File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line
>>>>>>> 18, in
>>>>>>> fro
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 support. :)
>
> Yep. But a
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"
> "[O-][N+](c1cnc2c2n1)=[N+]([O-])c3cnc4c4n3"
>
>
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"
> "[O-][N+](c1cnc2c2n1)=[N+]([O-])c3cnc4c4n3"
>
>
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 InChI string is correct and is
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 wrote:
> Strong recommendation: use the conda version:
>
> http://www.rdkit.org/docs/Install.html
>
> On Wed, Sep 13, 2017 at 9:58 PM, Wandré wrote:
>
>> I just run sudo apt-
ar 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 GMT-03:00 Markus Sitzmann :
&g
e Tanimoto coefficient and, if this value,
>>>> when I compare two molecules, is 1, this molecules are the same.
>>>>
>>>> Where is my mistake (I think that is, one or more, mistakes)?
>>>>
>>>> Thanks!
>>>>
>>>&
; 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 Dimitri Maziuk :
>
>> On
?
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 13. Sep 2017, at 17:58, Dimitri Maziuk wrote:
>
>> On 2017-09-13 10:17, Markus Sitzmann wrote:
>> Canonical SMILES are only a very rough approximation for "unique molecule"
>> as they usually don't work well for
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 regarde
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 wrote:
>
> I've never had
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, 201
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
wrote:
> Thanks Riccardo for your reply
>
> I tried both master and development -
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:
>
>
> On Wed, Apr 12, 2
n Thu, Apr 6, 2017 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
>
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 wh
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.
> You might check
... 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 o
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
t
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 big
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-Bajaj
+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 continuing to push
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 wrote:
>
> Hi,
> I have installed Rdkit on a windows laptop with conda and I can activate the
> rdkit environment OK and if I start IDLE up, rdkit works. Ho
Hi Hitesh,
there is nothing particularly special about the RDKit installation
received/built by conda. The command you used in your email created a conda
environment. If you go to the directory where you initially *installed*
conda there is an envs directory, inside this directory there should
be
, Greg.
Cheers,
Markus
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 07.07.2016, at 08:20, Greg Landrum wrote:
>
> Dear all,
>
> I was at the Sheffield Cheminformatics conference earlier this week (along
> with several people from th
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
> wrote:
>
> Hi Markus,
>
> I think the problem should
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: rdkit-postgresql-
probably the solution to your
problem.
Markus
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 21.06.2016, at 21:24, Michał Nowotka wrote:
>
> Hi Stéphane,
>
> Just to let you know about two things:
>
> 1. ChEMBL web
otherwise it would defeat the purpose of Docker :-) ).
Okay, I will stay patient and keep you posted.
Best,
Markus
On Tue, May 3, 2016 at 9:02 AM, Riccardo Vianello
wrote:
> Hi Markus,
>
> On Tue, May 3, 2016 at 1:41 AM, Markus Sitzmann
> wrote:
>>
>> thanks
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 my
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
Hmm, well - probably not, you mention the always present exception in
chemistry, Peter (Sulfoxides have a similar situation, stereochemistry
from lone pairs). But generally I still think it is more dangerous to
keep or even perceive (from 3D) stereochemistry on three-coordinated N
- you will do mor
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 wrote:
> This isn't a simple one, so it may tak
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 wrote:
>
> Maybe when you have a toolkit as blazingly fast as RDKit it cap
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 AM
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 26.05.2015, at 18:08, Michał Nowotka wrote:
>
> Sorry, for the hassle, this has now been fixed. After running 'ctest
> -R pythonTestDirChem -V' I've noticed that Pillow/PIL is missing.
>
>> On
wrong.
On Sun, May 3, 2015 at 7:04 PM, Dimitri Maziuk wrote:
> On 2015-05-03 03:56, Markus Sitzmann wrote:
>> 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
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,
Sorry, looks like my baby is getting old ... :-)
Markus
On Wed, Feb 25, 2015 at 7:26 AM, Greg Landrum wrote:
> To close the loop here: after an email exchange with Marc Nicklaus and Wolf
> Ihlenfeldt, it looks like the problem is that the NCI website is using an
> older version of the CACTVS too
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 wrote:
>
> The InChIs have me confused.
>
> I'm going to simplify the below by just showing the input
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 I
015-02-19 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 th
hu, Feb 19, 2015 at 2:06 PM, Dimitri Maziuk wrote:
> On 2015-02-19 05:58, Greg Landrum wrote:
>>
>> On Thu, Feb 19, 2015 at 10:11 AM, Markus Sitzmann
>> mailto:markus.sitzm...@gmail.com>> wrote:
>>
>> Well, at least you said something important: "conversio
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 :-)
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
InChI=1S/C24H27N3O3/c28-22(25-15-14-17-6-2-1-3-7-17)19-12-10-18(11-13-19)16-27-23(29)20-8-4-5-9-21(20)26-24(27)30/h1-9,18-19H,10-16
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.
Hi Matt,
maybe squeeze these two lines
zims = [x for x in Chem.ForwardSDMolSupplier(gzip.open('a.sdf.gz')) if
x is not None]
zims_fps=[AllChem.GetMorganFingerprintAsBitVect(x,2) for x in zims]
into one:
zims_fps=[AllChem.GetMorganFingerprintAsBitVect(x,2) for x in
Chem.ForwardSDMolSupplier(gzi
-- Forwarded message --
From: Markus Sitzmann
Date: Thu, May 8, 2014 at 3:27 PM
Subject: Re: [Rdkit-discuss] Tautomeric InChIs
To: Edward Pyzer-Knapp
Hi Edward,
since your InChI is a Standard InChI ("1S/"): tautomeric forms are
purposely *not* preserved by Stan
-- Forwarded message --
From: Markus Sitzmann
Date: Thu, May 8, 2014 at 3:14 PM
Subject: Re: [Rdkit-discuss] RDKit cartridge similarity search speeds(?)
To: James Davidson
Hi James,
I would guess, in your second query, "morganbv_fp('c1nnccc1'::mol, 2)"
has
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
wrote:
> On 2014-03-19 05:54, Greg Landrum wrote:
>
>
> On Tue, Mar 18, 2014 at 4:59 PM, Jan Holst Jensen
It is basically a VM that can be scripted from the host system. The VM
client can be preconfigured with anything your software depends on
(including databases etc and can be based on arbitrary Linux
distributions independent of the Linux distribution of the host).
On Wed, Nov 27, 2013 at 4:20 PM,
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