Re: [Rdkit-discuss] how to install rdkit systemwide on Ubuntu 12.04

Hi Michal, I don't think it will work, at least with Python since it requires the RDKit directory in PYTHONPATH and RDKit/lib is required in LD_LIBRARY_PATH in order that Python can find the library files created when building RDKit. Regards, Christos Kannas Sent from my Galaxy Note! On Nov 8

Re: [Rdkit-discuss] Domain of applicability

, Christos -- Christos Kannas Sent from my Galaxy Note! On Mar 19, 2013 3:42 PM, paul.czodrow...@merckgroup.com wrote: Dear RDKitters, anyone worked with RDKit (data processing descriptor calculation) scikit-learn (train Random Forests) and could share some experiences with setting up/defining

[Rdkit-discuss] [RDKit-Discuss]: Aromatic Heavy Atoms

, clogSw (like clogP), within the RDKit distribution? Kind Regards, Christos -- Christos Kannas Researcher Ph.D Student e-Health Laboratory http://www.medinfo.cs.ucy.ac.cy/ kannas.chris...@ucy.ac.cy kannas.chris...@cs.ucy.ac.cy chriskan...@gmail.com Mob: (+357) 99530608

Re: [Rdkit-discuss] Best Practice: Git model for code submissions to the RDkit

___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Christos Kannas Researcher Ph.D Student e-Health Laboratory http://www.medinfo.cs.ucy.ac.cy/ kannas.chris...@ucy.ac.cy

[Rdkit-discuss] SMARTS Substructure matching

I've created this small IPython Notebook http://nbviewer.ipython.org/gist/CKannas/9089271 Can you give me the reasons why this happens? Best, Christos -- Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile

Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn]http://cy.linkedin.com/in/christoskannas

Re: [Rdkit-discuss] SMARTS/SMARTS and SMILES/SMARTS substructure matching

Hi Greg, Thanks a lot for the explanation. It makes things clearer now. Well the reason I'm doing SMARTS-SMARTS match is because I would like to match functional groups with the reactants in reactions. Regards, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob

[Rdkit-discuss] Fragmentation Bug?

points in hydrophobe region core. Is this the normal behaviour, or a bug? Also if I merge the two families of Hydrophobe features then I do not get the error. Regards, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos

Re: [Rdkit-discuss] Opposite of GetSubstructureMatches()

Hi JP, I think smol = Chem.PathToSubmol(mol, path), where path is a list of indices, will do what you want. Best, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn]http

Re: [Rdkit-discuss] Opposite of GetSubstructureMatches()

Hi JP, Well I've noticed the same thing on my tests, the only reason I can think off is that it either takes the preceding or the ending atom to the tuple of atom indices. I hope Greg or someone else can shed some light into it. Best, Christos Christos Kannas Researcher Ph.D Student Mob (UK

Re: [Rdkit-discuss] Opposite of GetSubstructureMatches()

are mapped as hydrophobic, and I also keep terminal carbons (CH3) connected to the adjacent hydrophobic group, if any. I hope these assumptions are chemically correct. Best, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View

[Rdkit-discuss] Sanitization Errors

://nbviewer.ipython.org/gist/anonymous/11248962/Sanitization_Errors.ipynb Is this an expected behaviour? Is there something I can do as a fix? Regards, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile

Re: [Rdkit-discuss] Sanitization Errors

with carbons so chloride should be disconnected. [N+]([Cl-])(C)(C)C - [N+](C)(C)C.[Cl-] Regards, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn]http

Re: [Rdkit-discuss] autodock vina pdbqt file to mol2

Hi Jan, AutoDock has a set of tools (MGLTools) that have tools to convert pdb to pdbqt and vice-versa. If I recall it can also convert pdbqt to mol2 also. See this discussion http://autodock.1369657.n2.nabble.com/ADL-pdbqt-to-mol2-td6755769.html Best, Christos Christos Kannas Researcher Ph.D

[Rdkit-discuss] Aldehyde functional group does not identify Formaldehyde as an aldehyde

that should happen? Attached is an ipython notebook showing this behaviour. Best, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn] http://cy.linkedin.com/in/christoskannas Aldehyde

Re: [Rdkit-discuss] Installation of RDKit 2014 on Centos 5.10 (Final)

have to install NumPy, since it is bundled to it. Best, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn] http://cy.linkedin.com/in/christoskannas On 24 July 2014 10:05, Enrico

[Rdkit-discuss] UGM Update

Hi RDKiters, How is UGM going? Is there a tweet feed to follow? Hope you are having a nice and interesting time! Best, Christos Christos Kannas Researcher Ph.D Student [image: View Christos Kannas's profile on LinkedIn] http://cy.linkedin.com/in/christoskannas

Re: [Rdkit-discuss] Can't kelulize

Sergio, You have to use GetSubstructMatches. Look at my sample here http://nbviewer.ipython.org/gist/CKannas/5a762b97c52e389d492e. Best, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile

Re: [Rdkit-discuss] Modified Mol objects with concurrent.futures

, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn] http://cy.linkedin.com/in/christoskannas On 2 February 2015 at 09:03, Reutlinger, Michael michael.reutlin...@roche.com wrote: Hi all, I

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 88, Issue 13

Hi Samuel, The problem is that x is a tuple in your case not an rdkit molecule object. Check your code to see what mols list actually has inside. I'm guessing that x is a tuple containing a molecule object plus some other info. Best. Christos Christos Kannas Researcher Ph.D Student Mob (UK

Re: [Rdkit-discuss] install rdkit cartridge

Hi Tim, I'm not sure about this, but I think that in order to use the cartridge you have to build RDKit and cartridge from source. Regards, Christos Kannas Sent from my Galaxy Note 4. On 24 Apr 2015 13:47, Tim Dudgeon tdudgeon...@gmail.com wrote: Is it possible when using the packages? I'm

Re: [Rdkit-discuss] Count carbon atoms

att) C In [4]: pm = m.GetSubstructMatches(patt) print len(pm) 8 Regards, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On 7 October

Re: [Rdkit-discuss] comparing two or more tables of molecules

Hi Steve, I think it would be better to use a similarity metric based on fingerprints. Regards, Christos Christos Kannas Researcher Ph.D Student [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On 28 November 2016 at 18:25, Stephen O'hagan

Re: [Rdkit-discuss] adding fragment to existing molecule

. [OH-].C>>COH, and use RDKit's reaction functionality to perform the reaction on your molecules. Hope this was a bit helpful. Regards, Christos Christos Kannas Chem[o]informatics Researcher & Software Developer [image: View Christos Kannas's profile on LinkedIn] <http://cy

Re: [Rdkit-discuss] How to transform SMARTS of aromatic structures so that their aromatic atoms could be any?

ct.* Best, Christos Christos Kannas Researcher Ph.D Student [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On 19 May 2017 at 12:52, Alexis Parenty <alexis.parenty.h...@gmail.com> wrote: > Hi everyone, > > > I need a function

Re: [Rdkit-discuss] Using RDKit in PyCharm and Anaconda on Windows

for a script I think is the best approach for having different Python environments activated along with additional instances of PyCharm. Regards, Christos Christos Kannas Researcher Ph.D Student [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas>

[Rdkit-discuss] RDKit PostgreSQL

Hi RDKiters, Is it possible to install RDKit PostgreSQL cartridge via Anaconda on MacOS? Or would be better to try with a Linux VM? Best, Christos Christos Kannas Chem[o]informatics Researcher & Software Developer Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image:

Re: [Rdkit-discuss] RDKit PostgreSQL

environment. If I need to connect it to an existing PostgreSQL installation I will have to build RDKit and the cartridge from source don't I? 2. Will the cartridge work in the latest RDKit 2018 version, if I build it from the source? Best, Christos Christos Kannas Chem[o]informatics

Re: [Rdkit-discuss] RDKit PostgreSQL

, Christos Christos Kannas Chem[o]informatics Researcher & Software Developer Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On Thu, 3 May 2018 at 09:47, Paolo Tosco <

Re: [Rdkit-discuss] Exhaustive Library Enumeration

;>> Chem.MolToSmiles(ps[0][0])'C1=CC=CC=C1'>>> >>> p0 = ps[0][0]>>> >>> Chem.SanitizeMol(p0)rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE>>> >>> Chem.MolToSmiles(p0)'c1c1' ​PS: ​I forgot that the results of a reaction enu

Re: [Rdkit-discuss] Exhaustive Library Enumeration

the molecules that are not valid. See this Jupyter Notebook <https://gist.github.com/CKannas/11bb9bcaa9435dd18a0bb969501219b2> at cell 5 the 1st line in the while loop. Best, Christos Christos Kannas Chem[o]informatics Researcher & Software Developer [image: View Christos Kannas's profile o

Re: [Rdkit-discuss] Matching Generalized Compounds

, Christos Christos Kannas Chem[o]informatics Researcher & Software Developer [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On Thu, 23 Aug 2018 at 12:36, Paolo Tosco wrote: > Dear Kovas, > > It looks like GetSubstructMatch()

Re: [Rdkit-discuss] seg fault when importing Chem on OS-X 10.12

Hi Patrick, I had a similar problem with RDKit 2017.09.03 on MacOS, using rdkit channel in anaconda. Using the conda-forge channel with python 3.5.5 and ipython 6.2 works fine. I can post my env tomorrow from work. Best, Christos Christos Kannas Chem[o]informatics Researcher & Soft

Re: [Rdkit-discuss] InChI to Mol to InChi

4-7+*/t17-,19-/m1/s1 m2 -> 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 Not sure why it happens, but I've seen it multiple times... Best, Christos Christos Kannas Chem[o]infor

Re: [Rdkit-discuss] InChI to Mol to InChi

ochemistry. I guess that's why there are inconsistencies [sometimes] when the molecule has been generated from a SMILES instead from a MOL block with 2D or 3D coordinates... Christos Christos Kannas Chem[o]informatics Researcher & Software Developer [image: View Christos Kannas's profile o

Re: [Rdkit-discuss] Using RdKit in Parallel

that the data to be picklable. Best, Christos Christos Kannas Cheminformatics Researcher & Software Developer [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On Wed, 20 Feb 2019 at 11:28, Stamatia Zavitsanou < stamatia.zavitsa...@oriel.ox

Re: [Rdkit-discuss] Adding molecules to pandas dataframe

ecule"] = mols Best, Christos Christos Kannas Scientific Software Developer (Cheminformatics) On Thu, 25 Jul 2019 at 15:45, Gianluca Sforna wrote: > Hi all, > is it possible to manually add molecules to a pandas dataframe? I am > reading a bunch of mol2 files, adding some propert

[Rdkit-discuss] Different InChI: RDKit Knime Vs RDKit Python

/a/EnYoHWG Best, Christos Christos Kannas Scientific Software Developer (Cheminformatics) ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] conda install rdkit

Hi Ling, Maybe you should switch to conda-forge channel. Replace "-c rdkit" with "-c conda-forge". At least that's what I'm using personally and I have no problems so far. The latest version of rdkit there is 2020.03.6. Best, Christos Christos Kannas Scientifi

[Rdkit-discuss] HasSubstructMatch & GetSubstructMatches hang when useChirality is True

True, the process hangs. Here is a notebook showing the issue https://nbviewer.jupyter.org/gist/CKannas/d54bb5ab0fa3c964086c75f18250ddac Is there any workaround for this? Looking for a solution to stop the computation in a graceful manner. Thanks, Christos Christos Kannas Research Software Engi

Re: [Rdkit-discuss] HasSubstructMatch & GetSubstructMatches hang when useChirality is True

Thanks a lot Paolo. Christos Christos Kannas Research Software Engineer (Cheminformatics) [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On Fri, 26 Mar 2021 at 16:01, Paolo Tosco wrote: > Hi Christos, > > this is a poss

Re: [Rdkit-discuss] ModuleNotFoundError: No module named 'rdkit'

Hi Andres, Maybe Spyder runs on the base conda environment. Do you run Spyder from your activated environment? Kind regards, Christos On Wed, Apr 14, 2021, 17:52 Andrés Sánchez Ruiz < andressanchezrui...@gmail.com> wrote: > Dear Greg, > > It works! It seems I can call functions of RDKit from