Re: [Rdkit-discuss] rdkit and emscripten

2015-05-11 Thread Guillaume GODIN
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

2015-05-12 Thread Guillaume GODIN
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

2015-05-14 Thread Guillaume GODIN
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

2015-05-12 Thread Guillaume GODIN
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

[Rdkit-discuss] licence type

2015-05-12 Thread Guillaume GODIN
Dear All, I would like to port RDKit to nodejs. What is the licence type I should take ? 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

Re: [Rdkit-discuss] licence type

2015-05-13 Thread Guillaume GODIN
); ^ 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

2015-05-19 Thread Guillaume GODIN
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++

2015-11-09 Thread Guillaume GODIN
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

2015-11-10 Thread Guillaume GODIN
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

2015-10-29 Thread Guillaume GODIN
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

2015-09-05 Thread Guillaume GODIN
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

2015-09-06 Thread Guillaume GODIN
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++

2015-09-10 Thread Guillaume GODIN
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

2015-09-09 Thread Guillaume GODIN
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

2015-09-09 Thread Guillaume GODIN
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

2015-09-16 Thread Guillaume GODIN
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++

2015-09-10 Thread Guillaume GODIN
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

2015-09-30 Thread Guillaume GODIN
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

2016-02-08 Thread Guillaume GODIN
=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

2016-02-03 Thread Guillaume GODIN
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

2016-02-03 Thread Guillaume GODIN
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

2016-02-02 Thread Guillaume GODIN
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

2016-04-11 Thread Guillaume GODIN
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

2016-04-14 Thread Guillaume GODIN
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

2017-01-16 Thread Guillaume GODIN
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

2017-01-17 Thread Guillaume GODIN
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

2017-01-17 Thread Guillaume GODIN
​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

2017-01-15 Thread Guillaume GODIN
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

2016-09-14 Thread Guillaume GODIN
-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

2016-09-14 Thread Guillaume GODIN
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

2016-09-14 Thread Guillaume GODIN
...@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

2016-09-13 Thread Guillaume GODIN
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

[Rdkit-discuss] Enumerate all the Atom + Neighbour environement in a SDF file

2016-09-11 Thread Guillaume GODIN
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 & Datami

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

2016-10-06 Thread Guillaume GODIN
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

2016-09-21 Thread Guillaume GODIN
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

2016-09-19 Thread Guillaume GODIN
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

2016-09-22 Thread Guillaume GODIN
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

2016-10-15 Thread Guillaume GODIN
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

2016-10-15 Thread Guillaume GODIN
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

2016-10-11 Thread Guillaume GODIN
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

2016-10-11 Thread Guillaume GODIN
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

2016-10-11 Thread Guillaume GODIN
;, 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

2016-10-11 Thread Guillaume GODIN
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

2016-10-13 Thread Guillaume GODIN
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

2016-10-13 Thread Guillaume GODIN
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

2016-10-13 Thread Guillaume GODIN
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

2016-10-13 Thread Guillaume GODIN
?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

2016-12-08 Thread Guillaume GODIN
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

2017-01-15 Thread Guillaume GODIN
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

2017-01-15 Thread Guillaume GODIN
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

2017-03-10 Thread Guillaume GODIN
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 ?

2017-09-14 Thread Guillaume GODIN
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 ?

2017-09-14 Thread Guillaume GODIN
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 ?

2017-09-14 Thread Guillaume GODIN
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 ?

2017-09-14 Thread Guillaume GODIN
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

2017-10-06 Thread Guillaume GODIN
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

2017-10-02 Thread Guillaume GODIN
.__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

2017-11-22 Thread Guillaume GODIN
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

2018-05-07 Thread Guillaume GODIN
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

2018-05-08 Thread Guillaume GODIN
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

2018-01-17 Thread Guillaume GODIN
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

2018-01-17 Thread Guillaume GODIN
+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

2018-01-18 Thread Guillaume GODIN
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

2018-02-07 Thread Guillaume GODIN
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

2018-08-02 Thread Guillaume GODIN
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

2018-08-11 Thread Guillaume GODIN
. 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

2018-08-06 Thread Guillaume GODIN
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

2018-01-18 Thread Guillaume GODIN
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

2018-04-08 Thread Guillaume GODIN
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

2018-04-16 Thread Guillaume GODIN
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

2018-04-16 Thread Guillaume GODIN
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

2018-04-25 Thread Guillaume GODIN
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

2018-03-25 Thread Guillaume GODIN
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?

2018-10-18 Thread Guillaume GODIN
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

2018-11-04 Thread Guillaume GODIN
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

2018-11-04 Thread Guillaume GODIN
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

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

2018-10-18 Thread Guillaume GODIN
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