Hi Dimitri,
my (tried & tested) "spell" to install RDKit via conda is the following
(on Linux):
conda create -c conda-forge -n chem python=3.8 rdkit cairo cffi
pillow matplotlib
After activation of the environment, finalize with a
pip install cairocffi
The cairo- and ffi-related inst
Hi Charmaine,
coming from Python, for single page applications I can really recommend
Panel: https://panel.holoviz.org/
There is also a very nice OSS chemistry plugin (which I have not yet
tried myself): https://github.com/MarcSkovMadsen/panel-chemistry
Kind regards,
Axel
On 05.07.22 11:53, Cha
Hi Chris,
this might not be a great help, but it works for me on Ubuntu 22.04 with
RDKit 2021.09.5:
import rdkit
print(rdkit.__version__)
from rdkit import Chem
from rdkit.Chem.rdMolDescriptors import CalcNumAtoms
m = Chem.MolFromSmiles("c1c1C(=O)NC")
print(CalcNumAtoms(m))
Output:
2021.09.5
Dear RDKitters,
does someone have a good SMARTS definition for basic nitrogen (aliphatic
and aromatic), which they would be able to share?
My Google-fu is failing me.
Many thanks in advance.
Kind regards,
Axel
___
Rdkit-discuss mailing list
Rdkit-dis
Great!
Thanks a lot, Jan!
Kind regards, Axel
On 06.10.22 12:23, Jan Halborg Jensen wrote:
Hi Axel
Have a look at https://github.com/jensengroup/protonator
Best regards, Jan
On 6 Oct 2022, at 12.09, Axel Pahl wrote:
Dear RDKitters,
does someone have a good SMARTS definition for basic
nd pyrrole
nitrogens, but include aliphatic amines, anilines, pyridines,
hydroxylamines, imines etc
best wishes
wim
On Thu, Oct 6, 2022 at 12:12 PM Axel Pahl wrote:
Dear RDKitters,
does someone have a good SMARTS definition for basic nitrogen
(aliphatic and aromatic), which they wo
Oh, indeed.
I did not think about that, thank you.
KR Axel
On 06.10.22 13:09, Jonas Bostrom wrote:
Hey Axel,
The Daylight SMARTS example page can also be a useful source:
https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html
All the best
Jonas
*From:*Axel Pahl
Dear fellow RDKitters,
I have an SD file with 2D molecules generated by another Cheminformatics
toolkit (yes, there are others! ;-) ).
When I depict them with RDKit (with Draw.MolToImage()) they look very
condensed with too short bonds and just appear not right.
When I re-generate the coordinate
Mon, Sep 19, 2016 at 8:41 AM, Axel Pahl <mailto:axelp...@gmx.de>> wrote:
Dear fellow RDKitters,
I have an SD file with 2D molecules generated by another
Cheminformatics
toolkit (yes, there are others! ;-) ).
When I depict them with RDKit (with Draw.MolToImage()) the
Hi Paul,
very interesting, thanks a lot for sharing!
Looking forward to the presentation at the UGM!
Kind regards,
Axel
On 27.09.2016 06:13, Paul Czodrowski wrote:
Dear RDKitters,
Our target prediction method – fully based on RDKit – has become online:
OCEAN: *O*ptimized *C*ross r*EA*ctivit
Dear all,
amongst other options, I can generate an RDKit mol object by one of
these two ways:
mol1 = Chem.MolFromSmiles()
mol2 = Chem.MolFromSmarts()
Is there a possibility to detect for a given mol object whether it was
generated from Smiles or Smarts?
Many thanks in advance.
Kind regards,
the smarts molecules have this property by default and smiles don't.
> Greg can confirm, and I can double check later today.
>
>
> Brian Kelley
>
>> On Nov 7, 2016, at 7:57 AM, Paul Emsley wrote:
>>
>>> On 07/11/2016 12:37, Axel Pahl wrote:
>>>
ck later today.
Brian Kelley
> On Nov 7, 2016, at 7:57 AM, Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
>
>> On 07/11/2016 12:37, Axel Pahl wrote:
>>
>> amongst other options, I can generate an RDKit mol object by one
Dear fellow RDKitters,
has someone by any chance tried to implement in RDKit the scaffold
distance algorithm by Jürgen Bajorath et al. (and would be willing to
share some code)?
Li, R.; Stumpfe, D.; Vogt, M.; Geppert, H.; Bajorath, J.
Development of a Method to Consistently Quantify the Structu
Well, I guess this means no.
That leaves more fun for me... :-P
-Axel
On 23.03.2017 09:38, Axel Pahl wrote:
> Dear fellow RDKitters,
>
> has someone by any chance tried to implement in RDKit the scaffold
> distance algorithm by Jürgen Bajorath et al. (and would be willing to
>
folds:
------
Axel Pahl
<http://www.mail-archive.com/search?l=rdkit-discuss@lists.sourceforge.net&q=from:%22Axel+Pahl%22>
Fri, 22 May 2015 04:39:33 -0700
<http://www.mail-archive.com/search?l=rdkit-discuss@lists
It is "SetProp" with a capital "S".
Kind regards,
Axel
On 07.04.2017 11:30, François-Régis Chalaoux wrote:
Hi,
when I try to set a new property, existing or not, in an Mol objet I
got the following message:
I Use rdkit through myChembl.
rdBase.rdkitVersion
'2015.03.1'
Hi Paul,
I just tried the example Notebook that you provided and it runs just as
in Greg's blog post, i.e. with the interactive slider (see attached
screenshot).
This is the configuration I used (in Anaconda):
python 3.5.3
rdkit 2017.03.2
notebook 5.0.0
ip
Hi Paul,
when using pillow and Python 2 I recommend to also install pycairo
(avail. via conda install).
For Python 3 you would need cairo from conda and cairocffi from pip.
(http://rdkit.org/docs/Install.html#recommended-extras)
Kind regards,
Axel
On 05.07.2017 08:09, Paul Czodrowski wrote:
Dear fellow RDKitters,
does someone have a script that he or she could share for the
deglycosylation of chemical structures?
Many thanks in advance.
Kind regards,
Axel
--
Check out the vibrant tech community on one of
Dear RDKitters,
here is a project idea for GSoC 2018 (actually brought up by Greg during
the Hackathon of RDKitUGM2016):
Project: RDKit lite
Brief explanation:
Create a minimal version of the RDKit that only contains basic
functionality (like MolFrom/ToSmiles and substructure search
capabil
Hi Carlos,
insert this in your loop:
if not mol: continue
Kind regards,
Axel
On 23.01.2018 03:59, Carlos Faerman wrote:
Hello,
My code is very simple:
suppl4 = Chem.SDMolSupplier("/Volumes/MyPassportForMac/chembl_23.sdf")
i = 0
for mol in suppl4:
smile = Chem.MolToSmiles(mol,isome
Dear all,
my google-fu is failing is me.
Is it possible in substructure searches to have chain atoms NOT match
ring atoms?
In essence, I would like the following example query for n-propane in
cyclo-hexane to return False (currently it is returning True):
mol = Chem.MolFromSmiles("C1C1"
, Stephen Roughley wrote:
Axel,
You need to use a SMARTS query:
q = Chem.MolFromSmarts("[CR0][CR0][CR0]")
Have a look at
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
Steve
On 29 June 2018 at 08:04, Axel Pahl <mailto:axelp...@gmx.de>> wrote:
Dear all,
afe3a
Cheers,
p.
On 06/29/18 08:04, Axel Pahl wrote:
Dear all,
my google-fu is failing is me.
Is it possible in substructure searches to have chain atoms NOT match
ring atoms?
In essence, I would like the following example query for n-propane in
cyclo-hexane to return False (currently it is retu
tosco/26af473fc1f3129878ca86cb070afe3a
Cheers,
p.
On 06/29/18 08:04, Axel Pahl wrote:
Dear all,
my google-fu is failing is me.
Is it possible in substructure searches to have chain atoms NOT match ring
atoms?
In essence, I would like the following example query for n-propane in
cyclo-hexane to return False (currently
Dear fellow RDKitters,
the Max Planck institute of Molecular Physiology (department 4, Chemical
Biology, Prof. Waldmann) is looking for a Cheminformatics PostDoc to
work on two interesting projects in the highly relevant context of
chemical biology.
For details, please have a look at the job p
Hi Andrew,
on Linux, using Anaconda, RDKit and Python 3.6, I always need to
additionally install cairocffi via pip:
pip install cairocffi
Kind regards,
Axel
On 31.08.2018 15:05, Andrew Dalke wrote:
On Aug 31, 2018, at 11:58, Andrew Dalke wrote:
I am unable to see an inline structure depic
Hi,
looking very much forward to the UGM, thanks a lot for organizing it.
Are there any recommended hotels?
Kind regards,
Axel
On 15.03.19 15:29, Greg Landrum wrote:
Dear all,
This year's RDKit User Group Meeting will take place from 25-27
September in Hamburg, Germany and is being hosted by
Hi,
is there an option to set the spacing of the dashes in a downward wedge
bond using Draw.MolToImage()?
In the depiction I am currently getting (attached), the dashes are very
close to each other, I would like to increase the spacing.
Changing the values in the tuple `Draw.DrawingOptions.dash`
dashes may
become uneven (which is probably why spacing was hardcoded):
Cheers,
p.
On 03/26/19 11:20, Axel Pahl wrote:
Hi,
is there an option to set the spacing of the dashes in a downward
wedge bond using Draw.MolToImage()?
In the depiction I am currently getting (attached), the dashes are
very clo
observed in the molecule).
I hope this helps.
Best,
Sereina
On 22 Aug 2019, at 11:38, Axel Pahl mailto:axelp...@gmx.de>> wrote:
Dear fellow RDKitters,
I am experimenting with the classification example from the Cookbook
[1] using a RandomForestClassifier and Similarity Maps for visualizat
Hi,
I know that the RDKit makes no guarantees abount being able to
round-trip (Smiles -> Mol -> Smiles -> Mol) every molecule, but I would
like to know if there are any recommendations on how to handle such cases.
In my current case the problem seems to lie in different aromatic models
for a lar
be read by
`MolFromSmiles`
COC1:C:C:C2:C:C:1OC1:C:C:C(:C:C:1)/C=C\\C1:C:C(:C(OC):C:C:1CCN(C)C)OC1:C(:C(CCN(C)C):C(OC):C(OC):C:1OC)/C=C\\2
Best,
Hongbin
*发件人: *Axel Pahl <mailto:axelp...@gmx.de>
*发送时间: *2019年9月3日16:45
*收件人: *RDKit Discuss <mailto:rdkit-discuss@lists.sourceforge.net>
*主题
Hi Chris,
i too, looked for this functionality in Plotly, but I was not able to
find it.
This is the reason I switched to bokeh / holoviews.
https://github.com/apahl/mol_frame/blob/68801e16af3cfb60f846c40f471d190cbe34748b/mol_frame/mol_frame.py#L949
and
https://github.com/apahl/mol_frame/blob/68
Hi Ganesh,
are you aware that the SA Score IS implemented in RDKit:
https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score
Kind regards,
Axel
On 30.03.20 16:55, Ganesh Shahane wrote:
Dear RDKitters,
I am trying a to find a way to implement the SA score as a sum of
fragments contributi
f the whole
molecule.
--
Best,
Ganesh
On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl mailto:axelp...@gmx.de>> wrote:
Hi Ganesh,
are you aware that the SA Score IS implemented in RDKit:
https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score
Kind regards,
Axel
On 30.0
Dear all,
is anyone aware of efforts for creating "bridging" C wrappers for the RDKit?
This would make it easier to bind the toolkit to other programming
languages, in addition to Python and Java.
Could the existing SWIG interface be perused for this?
Kind regards,
Axel
/swig/tree/gsoc2012-c/).
Kind regards,
Axel
On 26.04.20 21:44, Riccardo Vianello wrote:
Hi Axel,
On Sun, Apr 26, 2020 at 6:21 PM Axel Pahl mailto:axelp...@gmx.de>> wrote:
is anyone aware of efforts for creating "bridging" C wrappers for
the RDKit?
This would make i
l number of useful functions instead of
supporting the full API:
https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib
-greg
On Sun, Apr 26, 2020 at 9:47 PM Riccardo Vianello
mailto:riccardo.viane...@gmail.com>> wrote:
Hi Axel,
On Sun, Apr 26, 2020 at 6:21 PM Axel Pahl mai
On 27.04.20 10:18, Stephan Michels wrote:
Am 27.04.2020 um 09:58 schrieb Axel Pahl mailto:axelp...@gmx.de>>:
yes, I agree that manual wrapping would be a ton of work (and hard to
maintain).
My question was not necessarily with a concrete language in mind, but
since you are asking (;
Dear Micha,
have you considered using the commandline tool molconvert that is part of MarvinSketch, which can do just that (and many other things):
molconvert mol mol.mrv -o mol.mol
It should be under bin/ in the Marvin installation
for batch processing you can e.g. use a small shel
Dear Tim,
please take a look at this README in your installation:
/Code/PgSQL/rdkit/README
It essentially boils down to this:
cd $RDBASE/Code/PgSQL/rdkit
$ make
$ sudo make install
$ make installcheck
(only the second step has to be performed as root)
Kind regards,
Axel
On 04/24/2015 01:33 PM,
The instructions below appliy to the RDKit installation from source and
are probably not applicable to the Debian package, sorry for generating
confusion.
Kind regards,
Axel
On 04/24/2015 02:24 PM, Axel Pahl wrote:
> Dear Tim,
>
> please take a look at this README in your installation
Dear RDKitters,
has someone used the RDKit to generate scaffold trees from molecules as
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58
I know that this is possible with ScaffoldHunter and that there is
> Surrey | SM2 5NG
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter
> @ICRnews
>
>
> From: George Papadatos [gpapada...@gmail.com]
> Sent: 22 May 2015 16:27
> To: Axel Pahl
> Cc: RDKit Discuss
>
Dear fellow RDKitters,
the RDKit community is always so helpful that I wanted share back two
functions that I use in the IPython Notebook from which I thought that
they could be of use to others, as well.
- show_table:
Display a list of molecules in a table with molecule properties as columns
Dear fellow RDKitters,
I use ReplaceCore and GetMolFrags to create a 2D SAR table:
tmp = Chem.ReplaceCore(mol, core_mol, labelByIndex=True)
frag_mols = list(Chem.GetMolFrags(tmp, asMols=True))
Is it also possible to do the reverse? Create a new molecule from the
core and two fragments?
I woul
Dear all,
thanks a lot for your very kind feedback on the tools!
Axel
On 03.07.2015 07:21, Greg Landrum wrote:
Hi Axel,
I agree with the others; this is extremely cool. Thanks for sharing it!
-greg
On Thursday, July 2, 2015, Axel Pahl <mailto:axelp...@gmx.de>> wrote:
De
Firth | PhD Student | Cancer Therapeutics
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
> Surrey | SM2 5NG
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter
> @ICRnews
>
>
> From:
peutics
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
> Surrey | SM2 5NG
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter
> @ICRnews
>
>
> From: George Papadatos [gpapada...@gma
|
> Surrey | SM2 5NG
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter
> @ICRnews
>
>
> From: Axel Pahl [axelp...@gmx.de]
> Sent: 02 September 2015 10:21
> To: Nicholas Firth
> Cc: George Papadatos;
Hi Jörg,
if you install the "classical" way, you could also put an "rdkit.conf"
into "/etc/ld.so.conf.d/" containing the following:
/your/path/to/RDKit/lib
and run "sudo ldconfig" after "make install" and before "ctest" to
update the library paths. Also, in the past I had problems with the
Hi Soren,
maybe this function which enumerates racemates with one stereocenter
into the corresponding enantiomers might help:
def enum_racemates(sdf_list_or_file, find_only=True, mol_id="molid"):
"""returns: result_sdf::list, racemic_molids::list
find_only==True: return new sdf as lis
Hi Jing,
you could try playing with the Drawing Options, e.g.:
Draw.DrawingOptions.atomLabelFontFace = "DejaVu Sans"
Draw.DrawingOptions.atomLabelFontSize = 18
Kind regards,
Axel
On 25.09.2015 21:30, Jing Lu wrote:
Dear RDKit users,
I use Draw.MolsToFile for plotting 2D molecules. However, th
Dear all,
I just tried to build the current Release_2016_03_2 with conda on Ubuntu
16.04 and ran into an error.
I used a fresh clone of conda-rdkit and changed the git tag in
rdkit/meta.yaml from Release_2016_03_1 to Release_2016_03_2.
Then:
$ conda build boost
This ran without problems. Then:
at 6:06 PM, Axel Pahl <mailto:axelp...@gmx.de>> wrote:
I just tried to build the current Release_2016_03_2 with conda on
Ubuntu
16.04 and ran into an error.
the recipe you started from includes a patch that is no longer
necessary (and does no longer apply correctly) in th
Hi Riccardo,
thanks, I found the problem. As suspected it was related to conda and
had nothing to do with RDKit
(https://github.com/conda/conda/issues/2212#issuecomment-228277548).
Many thanks for your help.
Kind regards,
Axel
On 27.06.2016 22:44, Riccardo Vianello wrote:
Hi Axel,
tha
Hi Greg,
that is great news, honest congratulations and thanks for sharing.
And just wait for the big event coming up end of october! Then 100% of
the talks will cover the RDKit!
Kind regards,
Axel
On 07.07.2016 09:20, Greg Landrum wrote:
Dear all,
I was at the Sheffield Cheminformatics con
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