Hi RDKit community, I am currently using the Extended Reduced Graph algorithm from the RDKit package. The Smiles string I am testing with is C1C=CC2=CC=CC=C2O1. It is basically two fused aromatic rings and one of them has an Oxygen atom. When I am passing it through the ERG algorithm it is applying
Dear all,
The beta of the 2020.03 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1b1
I've done conda builds for Python 3.6 and 3.7 for Mac, and Linux and I'm
working on the Windows builds now. These all use the beta label so that
they do not i
Dear rdkit community,
I would like to assign to atoms in a molecule membership to fragments
like the one detected by |rdkit.Chem.Fragments.fr_Al_COO(). I was hence
wondering if by any chance there was a way to |||either|:
|
|a) test membership like for the GetIsAromatic() type of functio
Very close to my current work around. Converting reaction schemes from CDX
to RXN in open babel and then with rdkit to png.
The issue with this route, is that openbabel tends to throw out catalysts
that are central to what I'm trying to do. Using reaction smiles produces
the same issue.
example:
Hi Eric,
as I mentioned, I do not have access to ChemDraw, so I am afraid I can't
help more with that.
A possible workaround is to install OpenBabel in your conda environment
and use that to do a cdx->mol conversion. While it should be possible to
use the openbabel or pybel module, for some
Hi Paolo, all,
Thank you for responding. I tried this out this morning - though I could
not find chemdraw using the combrowser.
Instead I went to the registry editor grabbed the CLSID from
HKEY_CLASSES_ROOT\ChemDraw.Application.15.0\CLSID. (As far as I understand
this should be identical to the G
Hi Eric,
it looks like the GUID in rdkit/utils/chemdraw.py might be outdated.
Unfortunately I don't have access to ChemDraw, so I can't test this
myself, but you might be able to find the current ChemDraw GUID as follows.
From a Python prompt, issue the following commands:
|fromwin32com.clie
Hello all,
I'm trying to make use of the rdkit.utils.chemdraw to automate conversion
of cdx files to png's. and other formats. However, I'm getting the
following error message: ImportError: ChemDraw version (at least version 7)
not found.
I'm currently using windows 10 with anaconda 3 with rdkit
Dear RDKit'ers,
does anyone have experience with the Chemicalite SQLite extension?
https://chemicalite.readthedocs.io/en/latest/index.html
I simply tried to compile within conda with a conda cmake 3.12 and conda
rdkit
cmake chemicalite
-DRDKit_DIR=/app/conda/pkgs/rdkit-2018.09.1-py36h4a7b924_1000
Thank you so much for your help! My problem is solved :)
On Tue, Jul 31, 2018 at 3:31 PM, Jason Biggs wrote:
> According to http://www.rdkit.org/docs/api/rdkit.Chem.rdMolAlign-module.
> html#AlignMol, the function returns the RMSD, and the probe molecule is
> modified in place. Look at the co
According to
http://www.rdkit.org/docs/api/rdkit.Chem.rdMolAlign-module.html#AlignMol,
the function returns the RMSD, and the probe molecule is modified in
place. Look at the coordinates for mol2 before and after the
transformation:
mol = Chem.MolFromSmiles('CCCOC(=O)[O-]')
> Chem.rdDistGeom.Embe
Hello everyone,
I want to align chem B based on the 3D coordinates of chemical A and output
the 3D coordinates of chemical B (alignment that center of mass of chem B
is the same as chem A). I looked at the AlignMol() and Open3D align but it
returns either a RMS value or a score. Is there a way tha
Hello,
I am writing most of my code on Java but I need to use the fingerprint
function from RDkit. Is there a way to run fingerprint function on Java?
Thank you so much for your help!
--
Phuong Chau
--
Check out the vibr
Last week, Greg gave us a nice example of substructure matching using a
SMARTS query (see below). I learned a lot from this thread, not the least
of which was to use the IPythonConsole module and to enable SVG for
beautiful drawings.
This style is indeed much better than the old drawings.
I was
Hello:
Greg and Curt your comments are very much appreciated.
Thanks for getting back to me!
Best,
Markus
On Wed, Sep 21, 2016 at 8:31 PM, Greg Landrum
wrote:
> Hi Markus,
>
> Curt's instincts are dead on: the problem here is the rings.
>
> I'll show the fix and then explain what's going on. You
Hi Markus,
Curt's instincts are dead on: the problem here is the rings.
I'll show the fix and then explain what's going on. You just need to add
one line to your code:
core = "[a]12[a][a][a][a][a]1[a][a][a]2"
pattern = Chem.MolFromSmarts(core)
Chem.GetSSSR(pattern)
AllChem.Compute2DCoords(patter
Hi Markus,
I suspect the problem is that your SMARTS query is not as specific as you
might think. For example, RDKit does not understand how many rings there
are in your SMARTS query. Each [a] could be an atom arbitrarily connected
to many other rings that wouldn't be a part of the substructure
Hello all:
I am trying to perform a 2D alignment of molecules by using a pattern for
which I am using Compute2DCoords.
If I use a smarts string matching napthalene the 2D depiction is as one
would expect.
However, if I am switching to a 5,6 aromatic smarts pattern the matched
benzoxazol the 2D st
Dear Toby,
exactly what I was looking for, thanks a lot!
RDKit and its community rock!
Gesendet: Mittwoch, 28. Mai 2014 um 15:45 Uhr
Von: "Toby Wright"
An: chemis...@gmx.de
Cc: "RDKit Discuss"
Betreff: Re: [Rdkit-discuss] (no subject)
Looking around I
Looking around I see references to a method called
Chem.AssignAtomChiralcodes that I couldn't get working so the following
method might not be ideal, but it seems to work:
mol = Chem.MolFromSmiles('FC(Cl)Br')
chiralCentres = Chem.FindMolChiralCenters(mol, includeUnassigned=True)
if chiralCentres:
Hi RDKitters,
I am preparing a set of compounds for a virtual screening.
While the majority are achiral compounds, there are also some racemic structures in the dataset.
For the virtual screen, I would like to enumerate the enantiomers from these racemates, e.g. from
"CC1N1" -> ["C[C@H]
Axel,
On Tue, Oct 22, 2013 at 10:15 AM, wrote:
> Dear Greg,
>
> thanks for your answer.
> This morning I have freshly compiled the whole package (rdkit + cartridge)
> and now it works!
>
Excellent news.
> I can not say what has caused the error in the first place, please excuse
> me for bothe
"RDKit Discuss"
Betreff: Re: [Rdkit-discuss] (no subject)
Hi Axel,
On Mon, Oct 21, 2013 at 4:58 PM, wrote:
I am a medicinal chemist and am using RDKit and the Postgresql cartridge with
much success in a small startup project as the backbone for the chemical /
biological databas
Hi Axel,
On Mon, Oct 21, 2013 at 4:58 PM, wrote:
>
> I am a medicinal chemist and am using RDKit and the Postgresql cartridge
> with much success in a small startup project as the backbone for the
> chemical / biological database and for cheminformatics (Lipinski and such,
> substructure and sim
sendet: Montag, 21. Oktober 2013 um 17:07 Uhr
Von: "Adrian Schreyer"
An: chemis...@gmx.de
Cc: "RDKit Discuss"
Betreff: Re: [Rdkit-discuss] (no subject)
Hi,
Did you install the PostgreSQL development (header) files? Should be a package
called postgresql-server-dev or similar.
Ad
Hi,
Did you install the PostgreSQL development (header) files? Should be a
package called postgresql-server-dev or similar.
Adrian
On Mon, Oct 21, 2013 at 3:58 PM, wrote:
>
> Hi,
> I am a medicinal chemist and am using RDKit and the Postgresql cartridge
> with much success in a small startup
Hi,
I am a medicinal chemist and am using RDKit and the Postgresql cartridge with much success in a small startup project as the backbone for the chemical / biological database and for cheminformatics (Lipinski and such, substructure and similarity searches, ...).
I have just upgraded from RDK
Hi,
There was a recent thread on the topic here:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02766.html
-greg
On Wednesday, December 26, 2012, Huw Jones wrote:
> Hi there,
>
> Just a quick question. I read that in February there was no support for an
> RDKit PosrgreSQL c
Hi there,
Just a quick question. I read that in February there was no support for an
RDKit PosrgreSQL cartridge under Windows. I was just wondering if this was
still the case?
Many thanks
Huw Jones
--
LogMeIn Rescue: Any
On Sat, Jul 28, 2012 at 12:10 PM, Gianluca Sforna wrote:
> On Sat, Jul 28, 2012 at 7:51 AM, Huw Jones wrote:
>> My question is am I using the wrong PIL or an outdated PIL (I did update the
>> PIL installed on my MacOS however that did not resolve the issue) or
>> something. The hack I used to fix
On Sat, Jul 28, 2012 at 7:51 AM, Huw Jones wrote:
> My question is am I using the wrong PIL or an outdated PIL (I did update the
> PIL installed on my MacOS however that did not resolve the issue) or
> something. The hack I used to fix the issue with no structures being
> generated was not ideal a
Hi there,
I have recently installed RDKit on my Mac using the excellent guide at:
http://edc.github.com/homebrew-rdkit/
I had one issue though. When initially trying to create depictions using:
from rdkit import Chem
from rdkit.Chem import Draw
mol = Chem.MolFromSmiles('c1ccncc1CC(=O)O')
Draw.
Hello
I'd like to know if it was possible to search in RDKIT which would isolate any
cycles.
I thought the search for chemical moiety "C1" or "C1" and save the file with
these molecules.
The more complicated now.
Is it possible to find fragments containing only the cycle and the cycle?
Basically
Hello,
I would like to know if there is someone who uses utility Cinfony with RDKit.
I use version 0.9 of Cinfony and an old version of RDKit (May 2008).
There is no problem when using both programs. But I cannot arrive to install
version Q2009P25, RDKit module is not found when I loaded.
Although
Hi Markus,
I just updated the build instructions on the wiki and checked a new
Jamroot into svn:
http://rdkit.svn.sourceforge.net/viewvc/*checkout*/rdkit/trunk/Code/Jamroot?revision=508
Please replace the $RDBASE/Code/Jamroot you have with this one, set
the environment variables as described on t
Hi Markus,
Sorry this is still all a bit difficult as I try to work out the
problems in the build system and my instructions about how to use it.
On Jan 31, 2008 6:51 PM, Markus Kossner wrote:
>
> Hi there,
> I'm quite new to compiled Programming languages and
> as can be read here my problems o
Hi there,
I'm quite new to compiled Programming languages and
as can be read here my problems occured previously.
However I dind't manage to install the Kit properly.
I modyfied the boost::random source, copied the log files as described
and was also able to do the two "bjam" commands as descri
37 matches
Mail list logo