Re: [Rdkit-discuss] rdkit and emscripten

you have any advise to determine where I can find this ? best regards, Dr. Guillaume GODIN Project Manager Innovation CORPORATE RD DIVISION DIRECTLINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8

Re: [Rdkit-discuss] rdkit and emscripten

Dear Marco, I find a solution! I prepare a github to explain it best regards, Dr. Guillaume GODIN Project Manager Innovation CORPORATE RD 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

Re: [Rdkit-discuss] rdkit and emscripten

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 RD DIVISION DIRECT

Re: [Rdkit-discuss] rdkit and emscripten

any suggestions to solve that ? best regards Dr. Guillaume GODIN Project Manager Innovation CORPORATE RD 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 De : Giuseppe

Re: [Rdkit-discuss] licence type

); ^ code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h:47:11: error: use of undeclared identifier 'mmffMolProperties' if (mmffMolProperties.isValid()) { best regards, Dr. Guillaume GODIN Project Manager Innovation CORPORATE RD DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE

[Rdkit-discuss] MMFF tunning

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 RD

[Rdkit-discuss] How to have access to python descriptors in C++

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

Re: [Rdkit-discuss] Map atomindex between mol2D and canonical smile

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

[Rdkit-discuss] enumation of conjugated pi system in a molecule

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

[Rdkit-discuss] list of fingerprint that can be added to RDKit

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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich S

Re: [Rdkit-discuss] NP-score and SA-score datas

perfect! thanks David! BR, Dr. Guillaume GODIN Project Manager Innovation CORPORATE R 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 De : David Hall [li

Re: [Rdkit-discuss] SVG atom coordinate in C++

Forget i found it getDrawCoords best regards Dr. Guillaume GODIN Project Manager Innovation CORPORATE R 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 De : Guillaume

Re: [Rdkit-discuss] list of fingerprint that can be added to RDKit

ridge, 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 Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA RUE

Re: [Rdkit-discuss] list of fingerprint that can be added to RDKit

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 In

[Rdkit-discuss] example of RDKitjs using SimilarityMap for TPSA atoms contribution

on the molecule + map). best regards, Dr. Guillaume GODIN Project Manager Innovation CORPORATE R 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

[Rdkit-discuss] SVG atom coordinate in C++

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 Manager

Re: [Rdkit-discuss] Difference between ECFP and MorganFingerprint

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:

Re: [Rdkit-discuss] stereochemistry of S with degree 3

=false best regards, Dr. Guillaume GODIN Project Manager Innovation CORPORATE R 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 TEL +41(0)22 780 2211 | Fax. +41(0)22 780 3334 | www.firmenich.com

[Rdkit-discuss] reproduce this method to obtain graph using RDkit

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 Project Manager Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE

Re: [Rdkit-discuss] reproduce this method to obtain graph using RDkit

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

Re: [Rdkit-discuss] MATLAB vs. RDKit/Python

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

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

to current javascript codes. best regards, Dr. Guillaume GODIN Project Manager Innovation CORPORATE R 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 De : Greg Landrum

Re: [Rdkit-discuss] RDKit 2016.03 Installation

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

Re: [Rdkit-discuss] PMI API

trary said that for 2D molecules the 3nd axis PMi is zero. BR Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 |

Re: [Rdkit-discuss] PMI API

Thanks Brian, PBF = 0 <=> 2D & PBF >0 <=> 3D. I forget that point. BR, Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA

Re: [Rdkit-discuss] PMI API

​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

Re: [Rdkit-discuss] PMI API

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 CORPORATE R DIVISION DI

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

-100 more then expected). When it will be done I will share the code with you guys. BR, Guillaume De : Greg Landrum <greg.land...@gmail.com> Envoyé : mercredi 14 septembre 2016 12:16 À : Guillaume GODIN Cc : RDKit Discuss Objet : Re: [Rdkit-discuss] A

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

ubplots() plt.ioff() n,bins,patches = ax.hist(K,bins=100) ax.set_xlabel('Dihedral Angle') ax.set_ylabel('Counts'); plt.show() ? Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

...@gmail.com> Envoyé : 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 <guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> wrote: Your solu

[Rdkit-discuss] Angstroms Hydrogen bonding

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 This email and any files

Re: [Rdkit-discuss] Implementation details bitvectors from morgan/circular fingerprints

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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +

Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

rings + fused aromatic rings and also set guanidium salt as aromatic. Would it be possible to do that ? Best regards, Guillaume De : Greg Landrum <greg.land...@gmail.com> Envoyé : mardi 20 septembre 2016 16:41 À : Guillaume GODIN Cc : RDKit Discuss

[Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

process and restore it after and How to restore it (SetIsAromatic of atoms as true and change bondtype )? best regards, Guillaume GODIN ** DISCLAIMER This email and any files transmitted with it, including replies

Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

eep= 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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE

Re: [Rdkit-discuss] where to find I-State of atoms

t regards, Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R 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

Re: [Rdkit-discuss] where to find I-State of atoms

rd Lewis PhD 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 <guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> wrote: Thanks Greg & Marco, so after reading a

[Rdkit-discuss] Descriptor3d not exposed in python

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

Re: [Rdkit-discuss] Descriptor3d not exposed in python

check. thanks, best regards, Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R 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 __

Re: [Rdkit-discuss] Descriptor3d not exposed in python

;, line 16, in print Descriptors.CalcRadiusOfGyration(m) AttributeError: 'module' object has no attribute 'CalcRadiusOfGyration'​ Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41

Re: [Rdkit-discuss] Descriptor3d not exposed in python

function I'll fix rdkit.Chem.Descriptors too. On Tue, Oct 11, 2016 at 8:37 PM, Guillaume GODIN <guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> wrote: Maybe I made a wrong request: from rdkit import Chem from rdkit.Chem import Descriptors from

Re: [Rdkit-discuss] adding MORSE & RDF to 3D descriptors

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 DIVISION DIRECT LINE +4

[Rdkit-discuss] adding MORSE & RDF to 3D descriptors

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 Principal Scientist Chemoinformatic & Datami

Re: [Rdkit-discuss] adding MORSE & RDF to 3D descriptors

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 DIVISION DIRECT

Re: [Rdkit-discuss] adding MORSE & RDF to 3D descriptors

?Ho yes, sorry I didn't see that! thanks Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R 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 GENE

[Rdkit-discuss] https://en.wikipedia.org/wiki/Hansen_solubility_parameter

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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE

Re: [Rdkit-discuss] PMI API

would like to test it in Matlab. can 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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41

Re: [Rdkit-discuss] PMI API

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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039

Re: [Rdkit-discuss] Van der Waals radius

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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536

[Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

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 Principal Sc

[Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

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 Principal Sc

Re: [Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

vious 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 28 H 1?

[Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

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 Principal Sc

Re: [Rdkit-discuss] UFF atom type errors

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 DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenic

Re: [Rdkit-discuss] Beta of the 2017.09 release available

.__init__(SDMolSupplier, str) did not match C++ signature: __init__(_object*, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > fileName, bool sanitize=True, bool removeHs=True, bool strictParsing=True) __init__(_object*) Best regards, Dr. Guilla

[Rdkit-discuss] Convert an reaction schema drawing into an rxn file

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

[Rdkit-discuss] returning multiples matrixes in python

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

Re: [Rdkit-discuss] returning multiples matrixes in python

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 <greg.land...@gmail.com> Date : mardi, 8 mai 2018 à 15:30 À : Guillaume GODIN <guillaume.go...@firmenich.com> Cc : RDKit Discuss &l

Re: [Rdkit-discuss] edge matrix

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

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

+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

Re: [Rdkit-discuss] edge matrix

ix? Best regards, Jan On 17 Jan 2018, at 17:19, Guillaume GODIN <guillaume.go...@firmenich.com<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) p

[Rdkit-discuss] Installation of rdkit using conda (proxy) failed

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

[Rdkit-discuss] enumeration of smiles question

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

Re: [Rdkit-discuss] Chemical Formula to SMILES

. 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

Re: [Rdkit-discuss] enumeration of smiles question

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

Re: [Rdkit-discuss] edge matrix

with the 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

[Rdkit-discuss] RDKit 7th UGM 2018 @ Cambridge

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

Re: [Rdkit-discuss] issue during parsing a smile

should improve 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:

[Rdkit-discuss] issue during parsing a smile

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

Re: [Rdkit-discuss] 2018.03.1 RDKit release

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

[Rdkit-discuss] Chemoinformatics Position at Firmenich GENEVA

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

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

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

Re: [Rdkit-discuss] Is that possible to get features/descriptors for single atoms in a molecule

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

Re: [Rdkit-discuss] Is that possible to get features/descriptors for single atoms in a molecule

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

[Rdkit-discuss] How to add random seed in Smiles generation

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():

Re: [Rdkit-discuss] Is RDKit able to generate a Bag of Bonds Matrix?

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

Re: [Rdkit-discuss] Is RDKit able to generate a Bag of Bonds Matrix?

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

Re: [Rdkit-discuss] Is RDKit able to generate a Bag of Bonds Matrix?

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

Re: [Rdkit-discuss] GetAngleDeg alternative for the case of no conformation

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.

[Rdkit-discuss] Issue with SmilesMolSupplier using FreeSolv data

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

Re: [Rdkit-discuss] Issue with Chirality

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')) Out[17

[Rdkit-discuss] Try to reproduce a code working in January

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"]]

Re: [Rdkit-discuss] [*External*] Re: Try to reproduce a code working in January

) 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 : [*External*] R

[Rdkit-discuss] Issue with Chirality

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 =

Re: [Rdkit-discuss] [*External*] GETAWAY descriptors

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",

Re: [Rdkit-discuss] [*External*] Uniqueness of bonds

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 :

Re: [Rdkit-discuss] [*External*] Re: Dragon fingerprints?

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

Re: [Rdkit-discuss] [*External*] Re: Dragon fingerprints?

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

Re: [Rdkit-discuss] [*External*] Re: GPU Implementation of shape-based 3D overlap on rdkit?

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:

Re: [Rdkit-discuss] [*External*] finding atoms at multiple bond distances from target

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

Re: [Rdkit-discuss] [*External*] Re: Using the RDKit with Dask

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

Re: [Rdkit-discuss] [*External*] Re: Using the RDKit with Dask

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

Re: [Rdkit-discuss] [*External*] Question on tautomer standardization on RDKit

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 :

Re: [Rdkit-discuss] [*External*] UFF rdkit implementation: QEq partial charges are missing?

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