are not. Any idea?
Best regards,
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry
CNRS UMR 6229
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax :33 3 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.univ-reims.fr/LSD/JmnSoft
-Marc Nuzillard
Institute of Molecular Chemistry
CNRS UMR 6229
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax :33 3 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.univ-reims.fr/LSD/JmnSoft
?
I read something about HappyDoc in RDKit_Overview.pdf.
I tried to install HappyDoc but no setup.py file for its installation.
Maybe a few lines about documentation generation could be added in
the INSTALL file of the RDKit.
Best regards,
Jean-Marc Nuzillard
Dear Greg,
Reading the web, I have found references to ALogP, XLogP, SLogP, CLopg
descriptors.
Is MolLogP one of these?
Are there significant differences between them?
Best regards,
Jean-Marc Nuzillard
hit on line 114
[22:30:46] ERROR: moving to the begining of the next molecule
Count: 0
The 264 other molecules in my isomer collection are OK.
Any idea about the origin of this problem?
Best regards,
Jean-Marc Nuzillard
mol226.sdf
Description: StarMath document
mol226.ps
Description
observation will help you.
Best regards,
Jean-Marc Nuzillard
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Better than sec? Nothing is better than sec when it comes to
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http
-Marc
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CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft
= SAVE[format.upper()] # unknown format
1685
1686 if isPath(fp):
KeyError: 'PNG'
Out[4]:
rdkit.Chem.rdchem.Mol at 0x457ba70
I installed a lot of python modules recently :-)
Any idea about the one I missed?
Many thanks in advance,
Jean-Marc
--
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and reinstalled Pillow.
The structure of benzene appeared as expected.
Many thanks !!
Jean-Marc
-greg
On Monday, June 8, 2015, Jean-Marc Nuzillard
jm.nuzill...@univ-reims.fr mailto:jm.nuzill...@univ-reims.fr wrote:
Dear Greg,
Le 08/06/2015 04:41, Greg Landrum a écrit
Dear Greg,
Le 08/06/2015 04:41, Greg Landrum a écrit :
On Sun, Jun 7, 2015 at 10:44 PM, Jean-Marc Nuzillard
jm.nuzill...@univ-reims.fr mailto:jm.nuzill...@univ-reims.fr wrote:
Hello,
I just installed RDKit on Windows7, with the intention of
using it from IPython.
I
--
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Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft
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CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
I do not have the feeling that the handling of a C=P bond should be
different of the one of a C=C bond.
Jean-Marc
Le 11/03/2016 10:12, Greg Landrum a écrit :
On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr&g
of diester triphenylphosphonium ylides with an
ylidic ester or keto and ester ylidic groups
Best regards
Marco
On 11 Mar 2016, at 10:12, Greg Landrum <greg.land...@gmail.com
<mailto:greg.land...@gmail.com>> wrote:
On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard
Too simple.
Thanks,
Jean-Marc
Le 16/03/2016 19:34, Greg Landrum a écrit :
On Wed, Mar 16, 2016 at 10:58 AM, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:
thank you for this efficient answer.
Just one question.
Ho
clk?id=278785231=/4140
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51687 REI
, Mar 16, 2016 at 8:23 AM, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear All,
Is there a way, in Python, to add an alias to an atom in a
molecule so
that is appears
in an "A" line when the molecule is
of Anaconda
might be a source a trouble.
Best regards,
Jean-Marc
Le 22/11/2016 à 17:34, Riccardo Vianello a écrit :
Hi Jean-Marc,
On Tue, Nov 22, 2016 at 11:31 AM, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:
Hi,
I am currentl
quot; problem has to do with conda but not with RDKit.
Has someone already experienced such a problem, and possibly
found a workaround?
Best regards,
Jean-Marc
PS. Sorry for the preceding empty message.
--
Jean-Marc Nuzillard
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la
Hi,
--
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax :33 3 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD/
http://eos.univ-reims.fr/LSD
Thanks !
Jean-Marc
Le 11/10/2016 à 10:57, Greg Landrum a écrit :
Here's the explanation of the RDKit's aromaticity model:
https://github.com/rdkit/rdkit/blob/master/Docs/Book/RDKit_Book.rst#aromaticity
-greg
On Tue, Oct 11, 2016 at 9:28 AM, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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Sure, it works!
Thanks, Greg.
Jean-Marc
Le 14/12/2016 à 17:43, Greg Landrum a écrit :
Hi Jean-Marc,
The answer is in the error message, once you know how to read it,
which isn't really trivial:
On Wed, Dec 14, 2016 at 5:35 PM, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims
Presently, I have rdkitVersion 2016.03.1 and boostVersion 1_56.
I get similar messages with GetSubstructMatch and HasSubstructMatch.
Any idea?
All the best,
Jean-Marc
--
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
5
arc,
>
> here:
>
> https://gist.github.com/ptosco/6e4468350f0fff183e4507ef24f092a1#file-pdb_atom_names-ipynb
>
>
>
> there's an example how to use the atom aliases in RDKit.
>
> Cheers,
> p.
>
>
> On 12/16/2016 10:26 PM, Jean-Marc Nuzillard wrote:
>> Hi all
ito.it>> wrote:
Dear Jean-Marc,
here:
https://gist.github.com/ptosco/6e4468350f0fff183e4507ef24f092a1#file-pdb_atom_names-ipynb
there's an example how to use the atom aliases in RDKit.
Cheers,
p.
On 12/16/2016 10:26 PM, Jean-Marc Nuzillard wrote:
> Hi all
. That commit added functions
to get/set atom specific MDL features (RLabel, atom alias, atom value).
Best
Peter
On Sat, Dec 17, 2016 at 7:47 AM Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear Peter,
I got:
AttributeEr
Andrew
> da...@dalkescientific.com
>
>
>
> ------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.li
change anything.
What did I miss?
All the best,
Jean-Marc
--
Jean-Marc Nuzillard
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.uni
Sure !
I was only looking for a way of doing the things with bonds that
would be similar to the one with the atoms.
All the best,
Jean-Marc
Le 19/12/2016 à 11:55, Paul Emsley a écrit :
> On 19/12/2016 10:42, Jean-Marc Nuzillard wrote:
>> Thank you all!
>>
>> One more poin
! http://sdm.link/slashdot
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about the rdchem module.
So, my script started with
from rdkit import Chem
from rdkit.Chem import rdchem
I got:
NameError: name 'SetAtomAlias' is not defined.
I guess the solution is trivial.
Forgive my ignorance.
All the best,
Jean-Marc
--
Jean-Marc Nuzillard
Institut de Chimie Moléculaire
-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD
the problem?
-greg
On Mon, Jun 19, 2017 at 10:59 AM, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear All,
Chem.MolToSmiles(m, isomericSmiles=True, allHsExplicit=False) with
m being nicotine downloaded from PubChem returns
][CH]1[c]1[cH][cH][cH][n][cH]1 in which chirality
has disappeared.
Would it be possible to get H count and chirality?
All the best,
Jean-Marc
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Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP
a vector of atom indices in output order.
Brian Kelley
On Jun 17, 2017, at 1:42 PM, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr>
wrote:
Dear all,
sorry for asking for something that has certainly been already answered.
Chem.MolToSmiles(m) produced a SMILES string for the the
in finding the lowest energy conformer
of the molecule and I will be happy if the configuration of the chiral
centers and
of the double bonds (if any) in the 3D structure were in agreement
with those indicated in the SMILES string.
All the best,
Jean-Marc
--
Dr. Jean-Marc Nuzillard
Institute
?
Best,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ
of the claimed methods to switch off RDKit
logging of warnings has worked for me.
I ended up just re-directing stderr when running the script like this:
python myfile.py 2> myErrorLog.txt
Dr. Steve O'Hagan,
-Original Message-
From: Jean-Marc Nuzill
essage.
Le 21/01/2019 à 14:55, Markus Sitzmann a écrit :
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
mailto:jm.nuzill...@univ-reims.fr>> wrote:
My problem is more to know whi
-Marc
Le 21/01/2019 à 21:04, Dimitri Maziuk via Rdkit-discuss a écrit :
On 1/21/19 1:42 PM, Jean-Marc Nuzillard wrote:
sys.stderr.write("Bad: %s\n" % (mol.GetProp("_Name"),))
I know which bond has a problem but I still do not know in which molecule.
Are yo
17/12/2018 17:07, Dmitri Maziuk via Rdkit-discuss a écrit :
On Mon, 17 Dec 2018 14:23:32 +0100
JEAN-MARC NUZILLARD wrote:
...
returns DIFFERENT.
Removing the EmbedMolecule step returns EQUAL.
How could I change that?
You could try generating multiple conformers instead and checking if
one
nc2)
print(inc1 == inc2)
Molecules m1 and m2 have identical SMILES representations
but different InChI representations, which I find odd.
All the best,
Jean-Marc
Le 18/12/2018 00:40, Dimitri Maziuk via Rdkit-discuss a écrit :
On 12/17/18 4:50 PM, JEAN-MARC NUZILLARD wrote:
Is there any more det
Dear all,
I tried to transform an InChI into a Mol and back to InChi.
The following code:
inchi1 =
"InChI=1S/C20H26O4/c1-12(2)17-11-18(22)14(4)7-5-6-13(3)8-16(21)9-15-10-19(17)24-20(15)23/h6-7,10,12,17,19H,5,8-9,11H2,1-4H3/b13-6-,14-7+/t17-,19-/m1/s1"
m = Chem.MolFromInchi(inchi1)
m =
i(m)
print(inchi_initial)
print(inchi_final)
print(inchi_initial == inchi_final) # returns False
Is there something I can do to avoid this?
The difference between the initial and final InChI strings is in the
geometry of the double bonds.
All the best,
Jean-Marc
--
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Directeur de Rec
em[o]informatics Researcher & Software Developer
[1]
On Tue, 18 Dec 2018 at 17:36, JEAN-MARC NUZILLARD
wrote:
Thank you for your answer but alatis might not be adapted to my
current
problem.
Attempting to understand what was changed by the embedding step I
wrote:
inchi1 =
"InChI=
g would be a
nice challenge for the next release.
Best,
-greg
On Wed, Apr 3, 2019 at 5:54 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear all,
I have a molecule that comes from an InChI string, that is decoded
as an iminol I would like to transform i
Problem solved. Many Thanks,
Jean-Marc
Le 04/04/2019 à 06:54, Greg Landrum a écrit :
On Wed, Apr 3, 2019 at 8:26 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear Greg,
In [10] and Out[10] of your answer below (thanks!) incited me to
b
')
gives a result but with a trivalent neutral oxygen atom.
Reading more about SMIRKS theory, I tried:
'[H:4][0:1][C:2]=[N:3]>>[O:1]=[C:2][N:3][H:4]' without any success.
Could someone indicate me the correct iminol->amide reaction SMARTS?
Best regards,
Jean-Marc
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Dire
:2. The
problem is that the hydrogen count from the reactant atom gets copied
over unless specified otherwise.
Hope this helps,
Ivan
On Wed, Feb 6, 2019 at 9:37 AM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear All,
I need to convert iminol functio
...
Best regards,
--
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Institute of Molecular Chemistry, CNRS UMR 7312
Faculté des Sciences Exactes et Naturelles, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax : 33 3 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD
Dear all,
I am looking for a way to relate atom indexes of a Mol object
and the order of appearance of the atoms along the corresponding SMILES
chain, as produced by Chem.MolToSmiles().
Thanks in advance,
Jean-Marc
--
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Institute of Molecular Chemistry, CNRS UMR 7312
fter using the function
Chem.MolToSmiles.
Please find attached a very simple example of how it can be extracted.
Cheers,
Jose Manuel
On 01.02.19 13:03, Jean-Marc Nuzillard wrote:
Dear all,
I am looking for a way to relate atom indexes of a Mol object
and the order of appearance of the a
conda in Windows 10.
for mol in suppl:
mol.GetNumAtoms()
works fine.
Best,
Jean-Marc
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Institute of Molecular Chemistry, CNRS UMR 7312
Faculté des Sciences Exactes et Naturelles, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax : 33
ond in m1 is located
at the place of one of the ring closure bonds in pattern.
My question is how to write a SMARTS chain that fits in all cases for
decalin
or any other ring system and is more related to SMARTS-writing than to
RDKit, I admit.
Best,
Jean-Marc
--
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In
(pattern))
return True and True
Best regards,
Brice
Le ven. 17 janv. 2020 à 10:55, Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> a écrit :
Dear all,
I would like to write a SMARTS chain that matches any compound
with a decalin ring system,
whatever bond multiplicity.
s the file will be automatically closed and deleted for you as soon as it goes
out of scope at the end of the context manager block.
Cheers,
p.
On 29 Mar 2020, at 13:44, Jean-Marc Nuzillard
wrote:
Dear all,
The following code:
__
from rdkit import Chem
import
Ok Paulo,
with open(tempfn, 'rb') as reader:
fsuppl = Chem.ForwardSDMolSupplier(reader)
for m2 in fsuppl:
print(m2.GetProp('_Name'))
works fine for what I want to do.
Best,
Jean-Marc
Le 29/03/2020 à 16:35, Jean-Marc Nuzillard a écrit :
Hi Paolo,
neither tempfn (a string
eader file is not closed.
Trying reader.close() results in a message saying that reader has no
close() method.
Thank you in advance for helping me to get rid of the temp file.
Take care,
Jean-Marc Nuzillard
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Institut de Chimie Moléculair
Dear all,
Lipinski's rule of 5 indicates logP <5.
Is rdkit.Chem.Crippen.MolLogP() the suitable function
to calculate this logP?
JM
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Institut de Chimie Moléculaire de Reims, CNRS UMR 7312
Faculté des Sciences Exactes et Naturelles, Bâtiment 18
BP 1039
51687 REIMS Cede
d?
Thanks in advance for your help and explanations.
Best regards,
Quoc-Tuan
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CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr
of the two oxygens is sp2
and the other one is sp3.
The carbons are OK.
Is there a better way than repr(x.GetHybridization()) to access the value
of the hybridization state?
Best,
Jean-Marc
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scripting), is
there a way
to keep the value of the valence field to 0 for electrically charged
atoms when writing sdf files?
Best,
Jean-Marc
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BP 1039
51687 R
0. 0. 0. N 0 0 0 0 0 0 0 0 0 0 0 0
M CHG 1 1 1
M END
HTH, cheers
p.
On Wed, Aug 26, 2020 at 5:00 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear all,
the atom block of the Connection Table produced by RDKit
kit.Chem.rdchem.HybridizationType.SP2
rdkit.Chem.rdchem.HybridizationType.SP2
>>>
even though an oxygen atom is really SP2 but the other one is SP3.
I use version 2020.03.1 of RDKit.
Best regards,
Jean-Marc
--
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Institute of Molecular Chemistry, CNRS UMR 7312
Faculté des Sciences Exactes et Natur
olFromSmiles("O=COC")
>>> sum((a.GetHybridization() == Chem.HybridizationType.SP3) for a in
mol.GetAtoms())
1
because the two oxygen atoms are SP2.
Best regards,
Jean-Marc
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Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
degree higher than 3
// (e.g. things like CP1(C)=CC=CN=C1C, where the P
// has norbs = 4, and a conjugated bond, but clearly should
// not be SP2)
// This is Issue276
Hope this helps,
Ivan
On Tue, May 26, 2020 at 8:10 AM Jean-Marc Nuzillard
mailto:jm.nuzill...@u
the resolution process for C12H9N after a few millions of
solutions
because it could have lasted for days, if not for weeks.
Best,
Jean-Marc Nuzillard
Le 16/06/2020 à 11:44, Joshua Meyers a écrit :
Hey Theo,
As others have mentioned, this is indeed a non-trivial problem.
One method would
om can be a chiral center:
image.png
This possibility is why FindMolChiralCenters() flags that atom as a
possible stereocenter.
-greg
On Mon, May 17, 2021 at 12:09 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear all,
The determination of the absolute co
; m = Chem.MolFromSmiles(smi)
>>>
Chem.FindMolChiralCenters(m,force=True,includeUnassigned=True,useLegacyImplementation=False)
[(1, 'S'), (3, '?'), (5, 'S')]
but the central carbon atom of this compound, indexed "3", is not an
asymmetric one, is it?
Best regards,
Jean-Marc
--
Jean
,force=True,includeUnassigned=True,useLegacyImplementation=False)
[(1, 'R')]
m
image.png
Cheers,
p.
On Wed, May 26, 2021 at 5:20 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear all,
starting from ethanol with added Hs:
>>> m = Chem.AddHs(Che
molecules, m1 and m2, with opposite absolute configurations?
Many thanks in advance,
Jean-Marc
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Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
eyword.
So, what is para-stereochemistry?
Best regards,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
F
it indicates what the IUPAC Gold Book refers to as pseudoasymmetry.
Let’s see if others agree with my interpretation.
Cheers,
P.
On 26 May 2021, at 22:28, Jean-Marc Nuzillard
wrote:
I believed I sent a message with the same title a few minutes ago, but
apparently something went wrong.
Reading
me back to the RDKit Book.
So, what is para-stereochemistry?
Best regards,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax
9165 fax: +44
(0)1223 853667
email: m...@cresset-group.com <mailto:m...@cresset-group.com>
web: www.cresset-group.com <http://www.cresset-group.com> skype:
mark_cresset
-Original Message-
From: Jean-Marc Nuzillard mailto:jm.nuzill...@univ-reims
Dear Greg, Jason, and Maciek,
many thanks for your feedback.
The reading of the IUPAC guidelines will certainly bring useful information.
Best,
Jean-Marc
Le 10/03/2021 à 09:28, Greg Landrum a écrit :
On Wed, Mar 10, 2021 at 9:05 AM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr
hydroxyl groups in general?
They are usually neglected in chemical representations, aren't they??
Ling
Jean-Marc Nuzillard mailto:jm.nuzill...@univ-reims.fr>> 於 2021年3月9日週二
上午1:04寫道：
Sure, testosterone may be drawn as
Jean-Marc
Le 08/03/202
Sure, testosterone may be drawn as
Jean-Marc
Le 08/03/2021 à 18:26, Rocco Moretti a écrit :
On Mon, Mar 8, 2021 at 11:17 AM Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 08/03/2021 13:55, Jean-Marc Nuzillard wrote:
>
> Is it always possible to repre
The structure I posted was drawn with ChemDraw (now sold by PerkinElmer).
Best,
Jean-Marc
Le 09/03/2021 à 10:44, Paul Emsley a écrit :
On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:
Sure, testosterone may be drawn as
[snip]
OK :-)
That's a top quality rendering by the way. How did you
mac...@wojcikowski.pl>
wt., 9 mar 2021 o 10:47 Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> napisał(a):
On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:
> Sure, testosterone may be drawn as
> [snip]
OK :-)
That's a top quality rendering by the
configuration hints (bond wedges pointing to the front or to the back) without
introducing any explicit hydrogen atom?
May be my question is very naive, all my apologies in advance for that.
Best,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
hydrogen atom?
May be my question is very naive, all my apologies in advance for that.
Best,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03
py_0 conda-forge
-greg
On Tue, Feb 23, 2021 at 5:22 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear all,
I tried to reproduce the workflow in the recent blog post by Greg
https://greglandrum.github.io/rdkit-blog/conformers/exploration/2021
gt; 73 view = py3Dmol.view(width=size[0], height=size[1])
74 view.removeAllModels()
75 try:
AttributeError: module 'py3Dmol' has no attribute 'view'
I am using a freshly installed rdkit 2020.09.4 from conda under windows.
Is there something I can do to see the 3D structure?
Best,
Jea
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--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS
to obtain what I wanted with the same code
but for other molecules and templates.
I use rdkit version 2021.03.2 .
Can you reproduce that?
Is there a better way to do it?
Best,
Jean-Marc Nuzillard
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS
Thanks, Greg!
Jean-Marc
Le 14/06/2022 à 07:50, Greg Landrum a écrit :
Hi Jean-Marc,
The question about atom data was answered elsewhere by Nils, but on
atom ordering:
On Mon, Jun 13, 2022 at 2:50 PM Jean-Marc Nuzillard
wrote:
About mol = Chem.MolFromSmiles(smi), I would like
details about these extensions?
Best,
Jean-Marc Nuzillard
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
ORCID : -0002-5120-2556
Tel : +33 (0)3 26 91 82
splay/docs/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md
that offer various additional options. To some extent, CXSMILES are
supported by RDKit:
https://www.rdkit.org/docs/RDKit_Book.html#cxsmiles-cxsmarts-extensions
Hope ths helps,
Nils
Am 13.06.2022 um 14:30 schrieb Jean-Marc
though this feature can be very helpful,
is it possible to let wedges along C-C bonds
carry out the geometry information without
introducing H atoms at the ring junction?
Best,
Jean-Marc Nuzillard
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS
()
with open(“ h_atoms_at_ring_jn.svg”, “w”) as hnd:
hnd.write(svg_image)
Cheers,
p.
On 8 Jun 2023, at 10:22, Jean-Marc Nuzillard
wrote:
I guessed that for some reason the drawing did not show up in Paolo's
reply
to my question but I did not try to investigate further to find an
explanation
nice! The picture in the thread above didn't come through for me.
I re-ran that code and got the following output, included as both an
inline PNG and an attached SVG so hopefully it shows up for folks in
at least one:
h_atoms_at_ring_jn.png
On Mon, Jun 5, 2023 at 3:15 AM Jean-Marc Nuzillard
addChiralHs=False,
wedgeBonds=False)
Chem.ReapplyMolBlockWedging(mol_draw)
drawer.DrawMolecule(mol_draw)
drawer.FinishDrawing()
SVG(drawer.GetDrawingText())
Cheers,
p.
On Thursday, June 1, 2023, Jean-Marc Nuzillard
wrote:
Dear all,
starting from this mol block:
trans-decalin
16 17 1 0
16 18 1 0
3 19 1 1
11 6 1 0
M END
_
The wedge bond (3-19) is apparently here but is not drawn as such.
Is there a remedy for that?
Best regards,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de
d='', highlightAtoms=[])
d2d.FinishDrawing()
bio = BytesIO(d2d.GetDrawingText())
draw_code = Image.open(bio)
draw_code.save(filenameOut)
Cheers.
p.
On 27 Jul 2023, at 07:31, Jean-Marc Nuzillard
wrote:
Hi David,
thank you for your suggestion.
Setting wedgeBonds=True does not change anything,
prob
se)
d2d.DrawMolecule(mol_draw, legend='', highlightAtoms=[])
d2d.FinishDrawing()
bio = BytesIO(d2d.GetDrawingText())
draw_code = Image.open(bio)
draw_code.save(filenameOut)
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
can’t try anything, but I
wonder if it’s anything to do with the ‘wedgeBonds=False’ option you
gave when preparing the drawing.
Dave
On Wed, 26 Jul 2023 at 20:45, Jean-Marc Nuzillard
wrote:
Dear all,
I use the following code to produce PNG drawings. I use RDKit
version
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