I vote yes include it. Ask chatGPT ;-)
Envoyé de mon iPhone
> Le 16 mars 2023 à 09:11, Francois Berenger a écrit :
>
> Dear list,
>
> Am I right that rdkit has an UFF implementation, but the
> recommended partial charges for UFF cannot be computed by rdkit?
> Those charges are called QEq in t
Hi Yankang Jing,
From my chemical background I would recommend to not turn off the
aromatization cause tautomers are formed thanks to this equilibrium in such
system of multiple rings.
BR
guillaume
De : Yankang Jing
Date : mercredi, 15 juin 2022 à 01:05
À : rdkit-discuss@lists.sourceforge.
Hello,
You can use the “topological” distance Matrix to have the atoms at a given
distance of one atom. It’s not direct but it’s a good start:
https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.GetDistanceMatrix
Guillaume
De : cmaye...@umbc.edu
Date : jeudi, 1 avri
Hi Pat,
Hum, I’ve got same error as you.
By the way I have to change code to use this
from rdkit.Chem.rdMolDescriptors import CalcExactMolWt
to avoid another error.
Which version of rdkit do you use ?
BR
Guillaume
De : Patrick Walters
Date : lundi, 22 mars 2021 à 14:20
À : Guillaume GODIN
Hi Pat,
Do you have a small example file to proceed , or can I use esol.csv for example
?
Thanks
Guillaume
De : Patrick Walters
Date : lundi, 22 mars 2021 à 13:51
À : rdkit-discuss
Objet : [*External*] Re: [Rdkit-discuss] Using the RDKit with Dask
Apologies, there was a bug in the code I sen
Nacional de Córdoba
UNITEFA-CONICET
El mié., 11 de nov. de 2020 02:24, Guillaume GODIN via Rdkit-discuss
mailto:rdkit-discuss@lists.sourceforge.net>>
escribió:
Look at 3D descriptors in RDKit, I reproduced all of them and it’s part of the
core of RDKit.
De : Michal Krompiec
mailto:michal
Look at 3D descriptors in RDKit, I reproduced all of them and it’s part of the
core of RDKit.
De : Michal Krompiec
Date : mardi, 10 novembre 2020 à 23:32
À : RDKit Discuss , nils.wesk...@gmail.com
Objet : [*External*] Re: [Rdkit-discuss] Dragon fingerprints?
Hi Nils,
Yes, of course, I meant de
Dear all,
There is also a good example of JAX + rdkit interaction in the pull request
https://github.com/rdkit/rdkit/pull/2654
from Proteneer
BR
Guillaume
De : Greg Landrum
Date : mercredi, 4 novembre 2020 à 08:38
À : Lewis Martin
Cc : RDKit Discuss
Objet : [*External*] Re: [Rdkit-discuss]
Dear Nimal,
You are using atoms to enumerate bonds and a bond has 2 atoms so the number of
bonds are not the real ones.
Use this instead :
for bond in molecule.GetBonds()
bond.GetBondType() == …
best regards,
Guillaume
De : nCloud
Date : mardi, 28 avril 2020 à 05:06
À : "rdkit-d
Hello,
/*
std::vector
GETAWAYNAMES={"ITH","ISH","HIC","HGM","H0u","H1u","H2u","H3u","H4u","H5u","H6u","H7u","H8u","HTu",
"HATS0u","HATS1u","HATS2u","HATS3u","HATS4u","HATS5u","HATS6u","HATS7u","HATS8u","HATSu","H0m","H1m","H2m","H3m","H4m","H5m",
"H6m","H7m","H8m","HTm","HATS0m","HATS1m","
)
18 nbr2.SetAtomMapNum(0)
UnboundLocalError: local variable 'nbr1' referenced before assignment
Thanks for helping
Guillaume
De : Taka Seri
Date : mercredi, 20 novembre 2019 à 14:02
À : Guillaume GODIN
Cc : "rdkit-discuss@lists.sourceforge.net"
Objet : [*Ex
Dear community,
I try to reproduce this code
https://iwatobipen.wordpress.com/2019/01/18/generate-possible-molecules-from-a-dataset-chemoinformatics-rdkit/
but got an error un panda / rdkit during generation:
frame = frame[["ROMol", "Smiles", "Core", "R1", "R2", "R3"]]
frame['Core']=frame['Core
Dear All,
I try this code on ‘FreeSolv_SAMPL.csv’ file:
suppl= Chem.SmilesMolSupplier(smi_input_file,delimiter=',', titleLine=True
,smilesColumn=2)
i=0
for mol in suppl:
if mol != None:
i+=1
print(Chem.MolToSmiles(mol))
print(i)
While Code MolToSmiles works fine using a Pan
septembre 2019 à 07:22
À : RDKit Discuss
Cc : Guillaume GODIN
Objet : Re: [Rdkit-discuss] Issue with Chirality
As Dan said: you should be adding Hs to the molecule before generating
conformations. That clears up the problem:
In [17]: AllChem.EmbedMolecule(Chem.MolFromSmiles('CC[C@H](C)O'
Dear All,
One question why this is not working ?
def mol3D(mol):
tot = AllChem.EmbedMolecule(mol)
try:
X = AllChem.Get3DDistanceMatrix(mol)
except:
print('err')
print(tot)
n = mol.GetNumAtoms()
X = np.zeros(n,n)
return X
mol = Chem.MolFromS
Dear Navid,
“Zero conformations” mains that EmbedMolecule function return false. There is
no 3D. You use the default EmbedMolecule parameters.
You can try to change them to get 3D coordinates (increase maxAttempts for
example). I don’t see another way to get realistic “Angle” between atoms.
Gene
Sure have a nice week end
GG
De : Greg Landrum
Date : vendredi, 3 mai 2019 à 05:48
À : Guillaume GODIN
Cc : Henrique Castro ,
"rdkit-discuss@lists.sourceforge.net"
Objet : Re: [Rdkit-discuss] Is RDKit able to generate a Bag of Bonds Matrix?
On Thu, 2 May 2019 at 16:59, Guill
Dear Henrique,
It’s good time to push to validate this pull request.
What do you thing Greg ?
BR,
Guillaume
De : Henrique Castro
Date : jeudi, 2 mai 2019 à 16:58
À : Guillaume GODIN , Greg Landrum
Cc : "rdkit-discuss@lists.sourceforge.net"
Objet : Re: [Rdkit-discuss] Is RDK
Dear both,
I made a pull request last year with BoB matrix.
BR
Guillaume
Envoyé de mon iPhone
Le 1 mai 2019 à 06:03, Greg Landrum
mailto:greg.land...@gmail.com>> a écrit :
Hi Henrique,
Though the RDKit has functionality for extracting all the information required
to create either a bag-of-
Dear All,
How to include a seed in order to change the output of MolToSmiles using
doRandom=True ?
For example in this case each time I run this script I got same result so
random.seed only works at python level not c++:
from rdkit import Chem
import random
import time
def randseed():
Conformer is related to 3D conformer of the molecule (not atoms but one of the
possible conformer of the 3D representatives if there is more than one)
De : Cao Xuan
Date : dimanche, 4 novembre 2018 à 07:15
À : "rdkit-discuss@lists.sourceforge.net"
Objet : [Rdkit-discuss] Is that possible to get
Dear Cao Xuan,
You need to have a 3D molecule for RDF computation + RDF by definition is not
local but global to a molecule.
BR,
Guillaume
De : Cao Xuan
Date : dimanche, 4 novembre 2018 à 07:15
À : "rdkit-discuss@lists.sourceforge.net"
Objet : [Rdkit-discuss] Is that possible to get feature
Ok for me too.
De : Markus Sitzmann
Date : jeudi, 18 octobre 2018 à 17:52
À : Greg Landrum
Cc : RDKit Discuss
Objet : Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit
builds?
I am happy with conda forge :-). And thanks for the great work.
Markus
On Thu, Oct 18, 2018 at 5
Dear Greg,
We should simplify for sure and have a main stream release, so Making a “basic”
release already increase of the toolkit.
Also, that would be interesting to have a “special” contributors releasing
thing cause we need to be agile on that part too.
BR,
Guillaume
De : Eric Jonas
Da
. Guillaume GODIN
Principal Scientist
De : Ali Eftekhari
Envoyé : samedi 11 août 2018 07:57
À : rdkit-discuss@lists.sourceforge.net
Objet : [Rdkit-discuss] Chemical Formula to SMILES
Hello,
I am new to rdkit and for the start I want to conver the chemical formula to
ique smiles independently of RDKit ?
Thanks again,
Guillaume
De : Greg Landrum
Date : lundi, 6 août 2018 à 11:40
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-discuss] enumeration of smiles question
On Thu, Aug 2, 2018 at 8:59 AM Guillaume GODIN
mailto:guillaume.go...@firmenich
Dear All RDKiters,
I have a simple question about generating all possible smiles of a given
molecule:
RDKit provides only 4 differents smiles for my molecule “CCC1CC1“:
C1C(CC)C1
CCC1CC1
C1(CC)CC1
C(C)C1CC1
While by hand we can write those 7 smiles:
CCC1CC1
C(C)C1CC1
C(C1CC1)C
C1CC(CC)1
C1C(CC)
Thanks Greg,
Based on the links, I will try option 3, cause my number of matrixes is a
parameter of my function.
BR,
Guillaume
De : Greg Landrum
Date : mardi, 8 mai 2018 à 15:30
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-discuss] returning multiples matrixes in python
Hi
Dear All,
I’m working on a c++ reimplementation of random Coulomb matrix generator via
RDKit. I was able to generate one matrix per conformer but how to pass
multiples matrixes per conformer ? At the end I need a list of matrixes in
numpy for each conformer.
Best regards,
Guillaume
***
Dear Andrew,
I have the same performance on the future in coming EEM implementation a win of
15-20% of time!!!
Guillaume
Le 25.04.18 10:50, « Andrew Dalke » a écrit :
On Apr 25, 2018, at 01:31, David Hall wrote:
> You need to turn off RDK_INSTALL_INTREE
Thanks! I've put tha
e that error message so it's more explicit.)
I think you are looking for the SMILES "C(\C(C)C)=N/O".
Andrew
da...@dalkescientific.com
> On Apr 16, 2018, at 16:15, Guillaum
Dear All,
Anyone know why this smile is not parse correctly ?
C\(C(C)C)=N/O
Best regards,
Guillaume
***
DISCLAIMER
This email and any files transmitted with it, including replies and forwarded
copies (which may
Dear All,
Just to inform you that there is already a huge meeting in the period time as
RDKit UGM.
All direct planes from Geneva were already booked.
Only planes for Luton are still open but rest of the trip is in bus every 2
hours… So I will miss the hackathon.
Is there someone that have a c
Dear All,
?
We have two openings in Cheminformatics & Machine Learning team at Firmenich,
here in Geneva.
RDKit expertise is part of the skills.
Apply here:
https://www.linkedin.com/jobs/view/532675646/
https://www.linkedin.com/jobs/view/597873120/
Best wishes, Guillaume
Dr. Guill
Dear All,
I've try to install rdkit using conda (anaconda2) with proxy settings.
I hack a little the conda python files to have some extra prints to see what is
not working:
Unfortunately there is an issue:
MacBook-Pro:Github GVALMTGG$ conda install -c rdkit rdkit
ArgumentParser(prog='conda'
atom list, holds all
the necessary information once bond orders are included, to define the molecule
object, but do you know if there is an RDKit function that does this: something
like mol = Chem.MolFromAdjacencyMatrix(adj)?
Best regard, Jan
On 18 Jan 2018, at 11:07, Guillaume GODIN
ix?
Best regards, Jan
On 17 Jan 2018, at 17:19, Guillaume GODIN
mailto:guillaume.go...@firmenich.com>> wrote:
Dear Mario,
There is a adjacency matrix available:
from rdkit import Chem
mol = Chem.MolFromSmiles('CC(C)CC')
adj = Chem.GetAdjacencyMatrix(mol)
print adj
[[0 1 0 0 0]
[1
+1 for Symmetrizer too, A must!
De : Michal Krompiec
Date : jeudi, 18 janvier 2018 à 08:18
À : Jason Biggs
Cc : RDKit Discuss, Greg Landrum
Objet : Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
+1 vote for Symmetrizer. It would be very useful for preparing input for
computational che
Dear Mario,
There is a adjacency matrix available:
from rdkit import Chem
mol = Chem.MolFromSmiles('CC(C)CC')
adj = Chem.GetAdjacencyMatrix(mol)
print adj
[[0 1 0 0 0]
[1 0 1 1 0]
[0 1 0 0 0]
[0 1 0 0 1]
[0 0 0 1 0]]
But this is not what you want…
Can you explain your output generatio
Dear All,
I’m still focus on two topics:
3D descriptors generalisation (few codes already in Github pull request)
EEM atom charge prediction (few codes already in Github pull request)
+ work of Naef & Acree prediction:
http://www.mdpi.com/1420-3049/20/10/18279
http://www.mdpi.com/1420-3049/23/
Dear RDKitters,
I have a question, I know that Indigo has a Atom-Atom Map function to identify
reaction centers of a rxn file.
But I don’t know how to convert my reaction image (chemdraw) into a rxn file:
So question 1: is there a way to do it in RDKit ?
I did not play with chemdraw since… I p
Hello,
Can you provide a small sdf contains molecules that have this issue ?
thanks in advance,
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firm
olSupplier.__init__(SDMolSupplier, str)
did not match C++ signature:
__init__(_object*, std::__1::basic_string, std::__1::allocator > fileName, bool
sanitize=True, bool removeHs=True, bool strictParsing=True)
__init__(_object*)
Best regards,
Dr. Guillaume GODIN
Principal Scientist
Che
th the previous call to that part
atom.GetNeighbors()[-1].GetBonds()
My desire output is:
0 N 1
1 O 2
2 O 2
3 C 2
4 C 2
5 C 2
6 C 2
7 C 2
8 C 2
9 C 2
10 C 2
11 C 2
12 C 2
13 C 2
14 C 2
15 C 2
16 C 2
17 C 1
18 H 1
19 H 1
20 H 1
21 H 1
22 H 1
23 H 1
24 H 1
25 H 1
26 H 1
27 H 1
t-env/bin/python
/Users/GVALMTGG/PycharmProjects/neemp/neemp.py
0 N 1
1 O 2
2 O 2
3 C 1
4 C 1
5 C 1
6 C 1
7 C 1
8 C 1
9 C 1
10 C 1
11 C 1.5
12 C 2
13 C 1
14 C 1
15 C 2
16 C 2
17 C 1
18 H 1.5
19 H 1.5
20 H 1.5
21 H 1.5
22 H 1.5
23 H 1.5
24 H 1.5
25 H 1.5
26 H 1.5
27 H 1
28 H 1
Dr. Guillaume GODIN
Pr
t-env/bin/python
/Users/GVALMTGG/PycharmProjects/neemp/neemp.py
0 N 1
1 O 2
2 O 2
3 C 1
4 C 1
5 C 1
6 C 1
7 C 1
8 C 1
9 C 1
10 C 1
11 C 1.5
12 C 2
13 C 1
14 C 1
15 C 2
16 C 2
17 C 1
18 H 1.5
19 H 1.5
20 H 1.5
21 H 1.5
22 H 1.5
23 H 1.5
24 H 1.5
25 H 1.5
26 H 1.5
27 H 1
28 H 1
Dr. Guillaume GODIN
Pr
t-env/bin/python
/Users/GVALMTGG/PycharmProjects/neemp/neemp.py
0 N 1
1 O 2
2 O 2
3 C 1
4 C 1
5 C 1
6 C 1
7 C 1
8 C 1
9 C 1
10 C 1
11 C 1.5
12 C 2
13 C 1
14 C 1
15 C 2
16 C 2
17 C 1
18 H 1.5
19 H 1.5
20 H 1.5
21 H 1.5
22 H 1.5
23 H 1.5
24 H 1.5
25 H 1.5
26 H 1.5
27 H 1
28 H 1
Dr. Guillaume GODIN
Pr
Dear Colin,
Those values are not calculated, they come from a dictionary (the
PeriodicalTable file).
Best regards,?
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79
Thanks Brian,
PBF = 0 <=> 2D & PBF >0 <=> 3D.
I forget that point.
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich
Great! I also notice confusing usage of moment of Inertia in those descriptors.
For exemple in WHIM case, we need to know if the molecule is linear, planar or
3D in order to compute the descriptors.
I did not find a easy way to determine this yet.
BR,
Dr. Guillaume GODIN
Principal
said that for 2D molecules the 3nd axis PMi is
zero.
BR
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POS
have a planar molecule, the matrix is no more 3D but 2D! so it's
normal to consider that the 3nd PM is zero.
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 53
Here, Dragon results for the 3 molecules: I've included both Whim and 3D
descriptors but I don't have access to PMi!
I found the second document in agreement with Peter answer...
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORAT
n you
provide me the 3 (3d xyz matrix) of your example please ?
I also have Dragon 6
best regards,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmen
H2CH2:1 & COO:1 & CH2CH2CH2CH2:2
Di-2-Ethylhexyl Ether, C(CC)COCC(CC) => CH2:2 & CH:2 & Bu:2 & Et:2 & O:1
?any idea ?
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
Candidate
Centre for Molecular Informatics
University of Cambridge
http://www.ch.cam.ac.uk/group/bender/person/rl403
On 15 Oct 2016, at 07:41, Guillaume GODIN
mailto:guillaume.go...@firmenich.com>> wrote:
Thanks Greg & Marco,
so after reading a little around the Dictionary + 3D descriptors
t regards,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
?Dear All,
I'm looking for the definition & values of the atomic "I-State" used in Dragon
for RDF, MORSE descriptors.
Do you have a source for those physical descriptors ?
best regards,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
Hi Greg,
So I fix the compilation issues for python but I have a segmentation fault
error and I cannot find the error in RDF part...
Could you take a look please ?
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LIN
?Ho yes, sorry I didn't see that!
thanks
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-
Dear Greg,
Thanks for the tip, but same error after adding the if statement.
All the cpp & cpp test works fine, but I have not clue why python wrap failed.
BR,
Guillaume
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
^
2 errors generated.
My code is there :
https://github.com/thegodone/rdkit/commit/11ee527c132ce34346be843b7fd98453298e40a3
Do you know how to fix this please, I need to check the computation and improve
the speed ?
Best regards,
Dr. Guillaume GODIN
Principa
I'll fix rdkit.Chem.Descriptors too.
On Tue, Oct 11, 2016 at 8:37 PM, Guillaume GODIN
mailto:guillaume.go...@firmenich.com>> wrote:
Maybe I made a wrong request:
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit import rdBase
print rdBase.rdkitVersion
print rd
, 'fr_Ar_N', 'fr_Ar_NH',
'fr_Ar_OH', 'fr_COO', 'fr_COO2', 'fr_C_O', 'fr_C_O_noCOO', 'fr_C_S',
'fr_HOCCN', 'fr_Imine', 'fr_NH0', 'fr_NH1', 'fr_NH2', 'fr_N_O'
he python files were not updated correctly, I will check.
thanks, best regards,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUN
Dear all,
I'm trying to use 3D descriptors in Python after compiling without issue, there
is no new descriptors available in Python, is it normal?
Best regards,
Guillaume
Envoyé de mon iPhone
**
DISCLAIMER
This email and an
and use
the hash to determine bits that should be set"
The hashing is a simple function like modulo, etc,...
Best regards,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE
atomkeep, bondkeep= keep6aro(mol)
Chem.rdmolops.Kekulize(mol,clearAromaticFlags=True)
mol=Aromatics6ring2(mol,atomkeep,bondkeep)
return mol
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)2
all 6 rings +
fused aromatic rings and also set guanidium salt as aromatic.
Would it be possible to do that ?
Best regards,
Guillaume
De : Greg Landrum
Envoyé : mardi 20 septembre 2016 16:41
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-di
process and
restore it after and How to restore it (SetIsAromatic of atoms as true and
change bondtype )?
best regards,
Guillaume GODIN
**
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This email and any files transmitted with it, including replies and
é : mercredi 14 septembre 2016 14:14
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-discuss] Angstroms Hydrogen bonding
On Wed, Sep 14, 2016 at 4:16 AM, Guillaume GODIN
mailto:guillaume.go...@firmenich.com>> wrote:
Your solution is perfect!
glad it worked
I am cur
x27;,possibleHs='[#1]',distThresh=2.5):
conf = m.GetConformer(confId)
partners =[x[0] for x in
m.GetSubstructMatches(Chem.MolFromSmarts(possiblePartners))]
linkers =[x[1] for x in
m.GetSubstructMatches(Chem.MolFromSmarts(possiblePartners))]
hs= [x[0] f
uch
more occurences (ie. a factor of 50-100 more then expected).
When it will be done I will share the code with you guys.
BR,
Guillaume
De : Greg Landrum
Envoyé : mercredi 14 septembre 2016 12:16
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-dis
Dear RDKiters,
I have two question:
1 Does 3D coordinates of a conformer is in Angstroms ?
2 How to enumerate all HBonding to determine the bond length ?
Best regards,
Guillaume
**
DISCLAIMER
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Dear RDKiters,
I would like to enumerate all Atom + 1st Neighbours environement include in a
SDF file.
The goal is to retreive smarts in order to build fingerprint.?
Does anyone know if it's possible with RDKit ?
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & D
Dear Matt,
On my Mac 10.11 this config works fine:
Boost 1.6
Cmake 3.5
Swig 3.0.8
BR
Guillaume
Envoyé de mon iPhone
> Le 15 avr. 2016 à 01:40, Matthew Lardy a écrit :
>
> Hi all,
>
> Does someone know which version of boost, cmake, and swig seems to work best
> for the current release?
pare to current javascript codes.
best regards,
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
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De : Greg Land
AhVHSBQKHTYDB7wQ6AEIHjAA#v=onepage&q=stereochemistry%20sulfinamide%20%5BS%40%40%5D&f=false
best regards,
Dr. Guillaume GODIN
Project Manager
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Fantastic, I was thinking based on the article that was only the neural net
part of the code.
Thanks a lot Maciek
From: Maciek Wójcikowski [mailto:mac...@wojcikowski.pl]
Sent: mercredi 3 février 2016 14:41
To: Giuseppe Marco Randazzo
Cc: Guillaume GODIN; RDKit Discuss
Subject: Re: [Rdkit
ngle,
double, triple, or aromatic, whether the bond was conjugated, and whether the
bond was part of a ring."
My question: I don't see how to obtain the graph from the smile.
Best regards,
Dr. Guillaume GODIN
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Dear Mario,
No there is no direct bridge in Matlab for cheminformatics,
But you can call python in matlab to call rdkit.
Another way would be to creating mex between c level of rdkit & matlab
best regards,
Guillaume
From: Mario Lovrić [mailto:mario.lovri...@gmail.com]
Sent: mardi 2 février 2
Dear John & Greg,
This is it!
OpenBabel11041515532D
16 18 0 0 1 0 0 0 0 0999 V2000
0.1.17000. C 0 0 0 0 0 0 0 0 0 0 0 0
0.36000.63000. C 0 0 0 0 0 0 0 0 0 0 0 0
1.08000.45000. C 0 0 3 0 0 0 0
Dear All,
When we use the python RDKit version generated descriptors include some
chemical functions counting fingerprints.
How can I expose those general descriptors (chemical functions) in c++ ?
thanks in advance,
Best regards,
Guillaume GODIN
,
best regards,?
Guillaume GODIN
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Dear All,
I looking for a c++ method to enumate all conjugated pi system of a molecule.
The final goal is to list all neighbors of each conjugated pi systems.
I found the SetConjugation and GetisConjugated bonds method in rdkit api.
Is there any over functions I could use ?
related to thi
Dear Greg,
When you say as closely as I could, do you mean that all the paramaters are the
sames in ECFP and Morgan but the only divergence between them is on the way
RDKit/Pipeline handle aromaticity + hashing ?
Thanks
Guillaume
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: mercre
n the molecule + map).
best regards,
Dr. Guillaume GODIN
Project Manager
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Forget i found it getDrawCoords
best regards
Dr. Guillaume GODIN
Project Manager
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CORPORATE R&D DIVISION
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De : Guill
Dear all,
How to get the absolute atom coordinate in RDDepict::compute2DCoords (c++) ?
This function drawer.getAtomCoords return the x,y position based on an origin
(first atom), but we don't have the link between this and the image origin.
best regards,
Dr. Guillaume GODIN
Project Ma
rity number.
WPATH WPOL
no
XLogP
Constitutional Descriptor
Prediction of logP based on the atom-type method called XLogP.
XLogP
no
ZagrebIndex
Topological Descriptor
The sum of the squared atom degrees of all heavy atoms.
Zagreb
no
Dr. Guillaume GODIN
Project Manager
"numBridge, numSpiro, numMacrocycles" and loop in javascript).
I will make some tests on performances on that scores computation in RDKitjs vs
python.
BR,
Dr. Guillaume GODIN
Project Manager
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perfect! thanks David!
BR,
Dr. Guillaume GODIN
Project Manager
Innovation
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De : David Hall
,
Dr. Guillaume GODIN
Project Manager
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De : Nicholas Firth [nicholas.fi...@icr.ac.uk]
En
Dear all,
I need the original unpickle data for javascript to implement those two
descriptor in RDKitjs.
Can you provide publicnp.model.gz fpscores.pkl.gz uncompressed files please ?
thanks in advance
Best regards,
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
DI
nter.html>,
SignatureFingerprinter<http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/fingerprint/SignatureFingerprinter.html>
best regards,
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
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Firmeni
x)
?
Best regards,
Thank you.
Guillaume
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
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Dear All,
Here's my log report on RDKitjs ... that finally works:
For all I used the 2015_03_1 code not the head.
https://github.com/cheminfo/RDKitjs
> rdkit@0.0.9 test /Users/mbp/Github/RDKitjs
> npm run build-test && mocha test/unit --require should --reporter
> mocha-better-spec-repor
Dear All,
Can you explain me why MMFF optimization do not return the same result if you
run it multiple times ?
Is there a way to tune it to be able to converge ?
My moleucle example was : C=C1CC[C@@H]2C[C@H]1C2(C)C
best regards,
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&a
Dear Giuseppe,
I make progress on this topic, if you want to participate?
https://github.com/thegodone/RDKitjs
There are already some functions exposed like MMFF, addHs, fromSmiles,
fromSmarts,
Best regards,
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
DI
MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
^
code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:29:13: note: forward declaration
of 'RDKit::MMFF::MMFFMolProperties'
class MMFFMolProperties;
^
Dr. Guillaume GODIN
Project Manager
Inno
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