Re: [Rdkit-discuss] Postgres query performance

At some point, in the not too distant future (I hope), there will be an updated version of the cartridge. On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha wrote: > Thanks Riccardo. > > While I can see Rdkit 2017.09.2.0 is available on conda ( >

Re: [Rdkit-discuss] Putting Recursive SMARTS in reactions

Hi Nitzan, On Wed, Dec 6, 2017 at 5:12 PM, Nitzan Tzanani wrote: > > I am trying to write a RDkit reaction, using Recursive SMARTS to better > define the atoms participating in the reaction. > > For example, in this fragmentation reaction: > > rxn =

Re: [Rdkit-discuss] Reaction Arrows

Hi Libby, There's not currently anything directly available to do this, but some pieces that might help are sort of there. You could imagine getting drawings of the reactions as SVG and then adding the arrows that indicate the mechanism to that. In order to do this, you'd likely want to be able

Re: [Rdkit-discuss] Cartridge upgrades

On Fri, Dec 1, 2017 at 7:24 PM, Tim Dudgeon wrote: > If upgrading PostgreSQL to a new version of the RDKit cartridge is any > maintenance needed? > > Either rebuild the indexes or regenerate the fingerprints and rebuild the > indexes? > It depend on the release. Usually

[Rdkit-discuss] Support for newer conda versions

Dear all, I'm starting the uploads of the conda builds of the 2017.09.2 RDKit release. These builds have been done using the "new" conda version (4.3.30) and numpy v1.12. The linux builds are available now, Windows builds will be there later this morning. I'm having some problems getting the Mac

Re: [Rdkit-discuss] Explicit hydrogens in substructure search

Hi Andrey, On Thu, Nov 30, 2017 at 1:17 AM, Andrey wrote: > Dear RDKit community, > > I'm setting up a chemical search engine based on RDKit, and I have > question about accounting explicit hydrogens. > I'm using Ketcher and Marvin JS as molecular editors to draw structure >

Re: [Rdkit-discuss] Having trouble getting RDKIT to recognize LiAsF6

On Fri, Nov 24, 2017 at 10:32 PM, Yoolhee Kim wrote: > > Thank you for your reply! > > I'm not super familiar with RDKIT... could you please elaborate on how to > fix this problem? > > Ah, sorry, it's something that needs to be fixed in the C++ code. The bug report is

Re: [Rdkit-discuss] Stop bond highlights

Hi Nick, When you import IPythonConsole it monkey patches the substructure function so that it saves info about the results when you do a substructure search on a molecule. The data member is called __sssAtoms, and if you delete that you should no longer get the coloring: Heres a bit of demo: In

Re: [Rdkit-discuss] Having trouble getting RDKIT to recognize LiAsF6

This is happening because the code doesn't recognize 7 as a valid valence state of As. This is, as you note, inconsistent with how P is handled, which doesn't make a lot of sense. Fortunately, it's a fixable problem. :-) On Tue, Nov 21, 2017 at 12:03 AM, Yoolhee Kim

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

ld disable or rewrite halogenCleanup() in > MolOps.cpp. Is this the only function which would need to be changed? > I think so. And you'd need to add the additional acceptable valence states in atomic_data.cpp -greg > Best regards, > Chris > > On 22 November 2017 at 07:59, Greg

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

At the moment the only way to do this is to disable the "cleanup" functionality in SanitizeMol(). This can be done, but it will also have the consequence that things like the hypervalent N in nitro groups (i.e. "-N(=O)=O") is not cleaned up. In [2]: m =

Re: [Rdkit-discuss] Rigid 3D alignment of molecule to fragment

Jan, Do you want to do a supervised alignment (i.e. you specify which atoms in the fragment map to which atoms in the molecule) or unsupervised alignment (where the algorithm needs to figure this out)/ It sounds like you're interested in the first; this blog post may be useful

Re: [Rdkit-discuss] Definition of basic groups in the Morgan Fingerprints

Hi Richard, On Mon, Nov 13, 2017 at 4:01 PM, Richard Marchese Robinson < r.l.marcheserobin...@leeds.ac.uk> wrote: > > > Firstly, thank you for making such a great tool available to the community > and for continuing to develop it. > > You're welcome! Thanks for the kind words. > > > I have

Re: [Rdkit-discuss] compiled verion of freeSASA

Right you are. Looks like I neglected to update the build scripts there. When I do the 2017.09.2 release (which is happening soon), I will fix this. Thanks for pointing out the oversight. -greg On Mon, Nov 13, 2017 at 2:46 PM, Bastian Seifert < bastian.seif...@external.merckgroup.com> wrote: >

Re: [Rdkit-discuss] freeSASA compiling

Hi Bastian, The conda builds for linux and the mac should have freeSASA support enabled. At the time we made the release there was a problem building the code on Windows, so that wasn't there yet. You can test that it's there by doing: from rdkit.Chem import rdFreeSASA If that works, take a look

Re: [Rdkit-discuss] RDKit appears to be parsing SMILES stereochemistry differently

On Thu, Nov 9, 2017 at 6:32 AM, Brian Cole wrote: > Hi Cheminformaticians, > > This is an extreme subtlety in the interpretation of SMILES atom > stereochemistry and I think a bug in RDKit. Specifically, I think the > following SMILES should be the same molecule: > > >>>

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

Jim, I'm a bit confused by what you're trying to do. Maybe we can try simplifying. What would you like to have returned for each of these SMILES: 1) ClC=CCl 2) ClC(Cl)=CCl 3) ClC(Cl)=C(Cl)Cl If the answer is the same between 1) and 2), but different for 3), then the next question will be:

Re: [Rdkit-discuss] RDKit installation in Virtual environment

Thanks for posting that and letting us know about it! On Sun, Nov 5, 2017 at 4:56 PM, Kiran Telukunta < kiran.teluku...@indiayouth.info> wrote: > This worked after setting the PYTHONPATH and installing pandas. > > so the blog is completely ready if someone wants to use. > > On 5 November 2017

Re: [Rdkit-discuss] ctest

Hi Jim, ctest is a part of the cmake system that is used to build the rdkit: https://cmake.org/ there's great documentation available there. We use ctest after every build to run the RDKit test suite. The idea is to ensure that the code is working as expected. The tests are all run automatically

Re: [Rdkit-discuss] Find difference(s) between molecules

Hi Jens, Ed provided some good pointers to the matched pair literature, which is certainly one way to approach the problem. There are RDKit implementations of MMP analysis. A somewhat more direct (though limited) approach would be to use the MCS code to find the maximum common substructure of

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

On Mon, Oct 30, 2017 at 10:14 PM, Andy Jennings wrote: > > Next question on this topic, as I can't find it from digging into various > sources. > > The solution you pointed me to works very well. I'm now expanding it to > compare the 'color' between two conformations

Re: [Rdkit-discuss] segmentation fault 11

Hi Chenyang, This looks like the breakage caused by conda v4.3.27. There's some more information here: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg07325.html Best, -greg On Sat, Oct 28, 2017 at 5:27 AM, Chenyang Shi wrote: > Hi Everyone, > > I am

Re: [Rdkit-discuss] Conformer generation

in cs: > > conf_id_I_want = c[0] > > > > > > Paul. > > > > *From:* Greg Landrum [mailto:greg.land...@gmail.com] > *Sent:* Thursday, October 26, 2017 12:41 AM > *To:* Paul Hawkins <phawk...@eyesopen.com> > *Cc:* rdkit-discuss@lists.

Re: [Rdkit-discuss] display mol in Jupyter NB: error kekulize not defined

Crap. That's a bug. I'll fix it for the 2017.09.2 release. If you don't want to wait for that (will likely be another week or so), you can edit this file: anaconda3/envs/092017/lib/python3.6/site-packages/rdkit/ Chem/Draw/IPythonConsole.py and replace "kekulize" with "kekulizeStructures" Thanks

Re: [Rdkit-discuss] Conformer generation

On Wed, Oct 25, 2017 at 6:52 PM, Sereina wrote: > Hi Paul, > > Regarding your second question: > > On 25 Oct 2017, at 18:36, Paul Hawkins wrote: > > Also, once I generate the conformers what is best way to cluster them by > RMSD so that each

Re: [Rdkit-discuss] two rdkit versions, always one is used

Hopefully you are using conda environments and not virtual envs, but whenever this happens to me it’s because I forgot to install Jupyter in the new environment, so when I invoke Jupyter from the command line it uses the one in the default conda environment. Test for this: check that you have

Re: [Rdkit-discuss] depiction of molecules with PandasTools AddMoleculeColumnToFrame

Hi Ines, This problem should go away if you update to the most recent version of the RDKit. -greg On Tue, Oct 24, 2017 at 4:19 PM, Ines Smit wrote: > Hello RDKitters/pandaskitters, > > I'm trying to use the 'AddMoleculeColumnToFrame' in the Jupyter notebook > but the

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

Assuming I'm understanding correctly what you're asking for, the RDKit actually has code for doing exactly this. That's the good news. The bad news is that there's pretty much no documentation for it. Since it's kind of interesting code (at least I think so) and it came up in an earlier

Re: [Rdkit-discuss] SetBondDir not Affecting Chiral Centers

, 2017 at 2:41 PM, Chris Murphy < >> chris.mur...@schrodinger.com> wrote: >> >>> Greg, >>> >>> That did the trick, thanks so much for the help! >>> >>> On Wed, Oct 18, 2017 at 2:13 AM, Greg Landrum <greg.land...@gmail.com> >>

Re: [Rdkit-discuss] RDKit Font weight

Hi Mark, I'm afraid that a lot of the fine control that it looks like you want is not going to be possible. But I will do what I can. Your questions are all connected to the old, pure Python, drawing code. We're not doing anything further with this and I'm encouraging people to switch over to

Re: [Rdkit-discuss] Question about pKa prediction using RDKit

I'm slow because of travel... sorry. I did an implementation of the decision tree using the RDKit not too long after the original paper came out, when I was stlil at Novartis. It's long enough ago now that I don't remember the full details. Here's what I do remember: - correctly translating the

Re: [Rdkit-discuss] SetBondDir not Affecting Chiral Centers

On Tue, Oct 17, 2017 at 8:16 PM, Chris Murphy wrote: > > I am trying to implement a function that cleans up chiral centers by > moving the wedged/dashed stereo bond out of a ring and onto a function > group or hydrogen if possible. > As a general thing: the

Re: [Rdkit-discuss] what if all explicit hydrogens were actual atoms

Sorry this one slipped off my radar. Hopefully a late reply is still helpful. On Thu, Oct 12, 2017 at 10:10 PM, Jason Biggs wrote: > > I'm creating a public-facing data structure that uses the rdkit as the > back end. I don't want to expose three different levels of

Re: [Rdkit-discuss] GetAlignmentTransform

I’m glad you were able to track that down, it’s an interesting one. I’ll have to look, but we may be able to fix that on the C++ side. From: thomas@boehringer-ingelheim.com Sent: Tuesday, October 17, 2017 2:27:39 AM To:

Re: [Rdkit-discuss] Default behavior of certain calls

That's really cool. Thanks for pointing it out Paolo. On Thu, Oct 12, 2017 at 7:27 PM, Paolo Tosco wrote: > Dear Andy, > > you may accomplish that within the scope of a Python script using > functools.partial: > > In [1]: from rdkit import Chem > > In [2]: import functools

[Rdkit-discuss] 2017.09.1 RDKit release

I'm pleased to announce that the next version of the RDKit -- 2017.09 -- is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1 Binaries have been uploaded to anaconda.org

Re: [Rdkit-discuss] UFF atom type errors

Yeah, those atom types that you are seeing are the names of the UFF atom types that the RDKit assigns. If an atom has a hybridization/charge-state that's not recognized, you'll get those parameterization errors. If you're aware of a better way to handle this (or a way to sensibly guess

Re: [Rdkit-discuss] Implicit Hydrogens On Aromatic Hetereoatoms

Hi Chris, There's an additional step performed during sanitization that recognizes that the implicit H needs to be on the N. The steps of a normal full molecular sanitization operation are documented here: http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization The adjustHs() function

Re: [Rdkit-discuss] Conformer generation using ETKDG

Hi Jordan, On Thu, Oct 5, 2017 at 6:48 AM, Jordan McCone wrote: > > I have a .smi file which has a number of smiles strings in it. I would > like to generate a single 3D conformer using ETKDG for every smiles string > in the list, > If you google around, you will find a

Re: [Rdkit-discuss] Atom mapping

Hi Jan, I'm not aware of an implementation of atom mapping for reactions based on the RDKit. -greg On Wed, Oct 4, 2017 at 9:03 AM, Jan Halborg Jensen wrote: > I just came across this paper http://pubs.acs.org/doi/ > abs/10.1021/acs.jctc.7b00764 which presents an variant

Re: [Rdkit-discuss] nitrogen valence issues

Hi Brian, When you pasted that into the email the formatting of the mol block did end up screwed up, which makes this hard to reproduce. Could you please attach the mol block to the message as a file? -greg On Thu, Oct 5, 2017 at 2:21 AM, Bennion, Brian wrote: > Hello, > >

Re: [Rdkit-discuss] Warning for conda users

and the python 2.7 version it installs (2.7.13). -greg On Mon, Oct 2, 2017 at 3:38 PM, Greg Landrum <greg.land...@gmail.com> wrote: > Dear all, > > I've noticed a problem with anaconda python on the Mac. This may also be a > problem on linux, but I haven't tested that yet. >

Re: [Rdkit-discuss] Fresh install of RDKit not functioning

Hi Jordan, Sorry this is frustrating. This is, unfortunately, connected to the problem I posted about here: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg07315.html At the time I thought that only the Mac (and possibly linux) was affected, but thanks to your warning I've

Re: [Rdkit-discuss] "Markush SMARTS" ?

Hi Alexis, I'm trying to make sure I understand the use case: you want to search for aromatic rings that have one F and one Cl or aromatic rings that have exactly two substitutions? If you just wanted to determine whether or not there is a match, you could use this recursive SMARTS for the first

Re: [Rdkit-discuss] How to number the outputs of a reaction?

Hi Jennifer, On Mon, Oct 2, 2017 at 12:59 AM, Jennifer Wei wrote: > > I have one more question: I am a bit stuck as to how to rebuild my rdkit. > Ideally I would like to create a separate conda environment with the > modified rdkit. I have mostly followed the

Re: [Rdkit-discuss] Building RDKit from source

Thanks for sharing that Kovas. I'm sure this will be helpful for people who don't want to/can't use anaconda. Best, -greg On Mon, Oct 2, 2017 at 7:34 PM, Kovas Palunas wrote: > Hi all, > > > I thought I'd share a script I wrote to build RDKit and Boost together >

[Rdkit-discuss] Warning for conda users

Dear all, I've noticed a problem with anaconda python on the Mac. This may also be a problem on linux, but I haven't tested that yet. Due to some changes in the way the anaconda team is doing python builds, the most recent conda python builds seem to no longer work with the RDKit. The symptom is

[Rdkit-discuss] Beta of the 2017.09 release available

Dear all, This morning I tagged the beta of the 2017.09 RDKit release in github: https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1b1 I will try to get some conda builds up over the next day or so. These will use the beta label so that they do not install by default; you'll need to

Re: [Rdkit-discuss] Masking groups as atoms in RDKit

this could be done by just defining the CoA atom > type (for example) just as the carbon or oxygen atom types are defined > (setting atomic weight, valences, etc.). > > Does this make sense? > > - Kovas > -- > *From:* Greg Landrum <greg.land...@gmai

Re: [Rdkit-discuss] Masking groups as atoms in RDKit

periodic table module in RDKit. Is it > possible to add these atoms there? > > - Kovas > > > From: Greg Landrum > Sent: Wednesday, September 27, 10:13 PM > Subject: Re: [Rdkit-discuss] Masking groups as atoms in RDKit > To: Kovas Palunas > Cc: rdkit-discuss@lists.sourceforge.n

Re: [Rdkit-discuss] Masking groups as atoms in RDKit

Where would you want to use this? Is it for depiction (i.e. drawing molecules) or something else? -greg On Tue, Sep 26, 2017 at 10:12 PM, Kovas Palunas wrote: > Hi all, > > > Has anyone tried implementing or using a group to atom masking strategy in > RDKit? By this

Re: [Rdkit-discuss] Drawing options for the new drawing code to change background color

I normally try to do this, yes. On Mon, Sep 25, 2017 at 3:27 PM, Michał Nowotka <mmm...@gmail.com> wrote: > Perfect, are betas available via conda? > > On Mon, Sep 25, 2017 at 2:25 PM, Greg Landrum <greg.land...@gmail.com> > wrote: > > Correct. This, like a few

Re: [Rdkit-discuss] Drawing options for the new drawing code to change background color

sn't have this > function, right? > > Just tried it and got 'MolDrawOptions' object has no attribute > 'setBackgroundColour' :( > > On Sun, Sep 24, 2017 at 10:07 AM, Michał Nowotka <mmm...@gmail.com> wrote: > > Great, thanks a lot again :) > > > > On Sun, Sep 24, 20

Re: [Rdkit-discuss] Drawing options for the new drawing code to change background color

w2DCairo(300,300) In [22]: opts = d2d.drawOptions() In [23]: opts.clearBackground=False In [24]: d2d.DrawMolecule(dm) In [25]: d2d.FinishDrawing() Best, -greg On Sun, Sep 24, 2017 at 5:25 AM, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Michal, > > This is now one of the

Re: [Rdkit-discuss] Drawing options for the new drawing code to change background color

Hi Michal, This is now one of the draw options; In [3]: d2d = rdMolDraw2D.MolDraw2DSVG(300,300) In [4]: opts = d2d.drawOptions() In [6]: opts.setBackgroundColour((1,1,0)) You can set the default highlightColour the same way. There's not currently a "make it transparent" option, but that

Re: [Rdkit-discuss] SMARTS for heteroaromatic rings?

My approach to this would depend on what you're trying to accomplish in the end. If you just want all the aromatic atoms you can just use "[a]". Unless you do some extra work when you read in the molecules, any aromatic atom will be in a ring. If you want to be really sure, you can do "[a;r]" If

Re: [Rdkit-discuss] How to highligh a structure but avoid intersecting edges at the same time?

At the moment there's not a solution to that problem that I'm aware of. The constraints imposed by the alignment to the pattern end up confusing the rest of the coordinate generation code. -greg On Fri, Sep 15, 2017 at 4:08 PM, Michał Nowotka wrote: > Hi, > > Thanks for all

Re: [Rdkit-discuss] ImportError: No module named rdkit

On Fri, Sep 15, 2017 at 1:37 PM, Loris Bennett wrote: > > When I did > > make test > > some of the tests failed: > > 61% tests passed, 46 tests failed out of 117 > > but most of the failures seemed to have been caused by > > ImportError: No module named rdkit >

Re: [Rdkit-discuss] Using the new drawing code

ed by DrawMolecule? Sure, here's an example GIST with the code: https://gist.github.com/greglandrum/431483ac1f9edb03b09c8577031c10e0 -greg On Thu, Sep 14, 2017 at 4:36 PM, Greg Landrum <greg.land...@gmail.com> > wrote: > > Hi Michal, > > > > There are a couple of thing

Re: [Rdkit-discuss] ImportError: No module named rdkit

One thing that may help is this (somewhat older, but I believe still accurate) post from Riccardo: https://sourceforge.net/p/rdkit/mailman/message/30074971/ It's been a while since I looked at this (since I mainly use conda these days), but I just did a quick experiment with: mkdir build

Re: [Rdkit-discuss] ImportError: No module named rdkit

administration) a ton easier. -greg On Fri, Sep 15, 2017 at 8:19 AM, Loris Bennett <loris.benn...@fu-berlin.de> wrote: > Hi Greg, > > Greg Landrum <greg.land...@gmail.com> writes: > > > Hi Loris, > > > > On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett < >

Re: [Rdkit-discuss] ImportError: No module named rdkit

On Thu, Sep 14, 2017 at 9:58 PM, Andrew Dalke wrote: > On Sep 14, 2017, at 19:26, Dimitri Maziuk wrote: > > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > > linux distros that will be officially with us until June 30,

Re: [Rdkit-discuss] ImportError: No module named rdkit

On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > On 09/14/2017 10:43 AM, Greg Landrum wrote: > > > Just to do some expectation management: python 2.6 is pretty ancient and > > there's no guarantee that all of the RDKit code will work

Re: [Rdkit-discuss] counting stereocenters

Hi Daniel, this is some oddity that happens with molecules constructed from InChIs. CalcNumAtomStereoCenters() returns sensible results if you call it on the molecules constructed from SMILES: In [24]: mol_list2 = [Chem.MolFromSmiles(Chem.MolToSmiles(mol,True)) for mol in mol_list] In [25]:

Re: [Rdkit-discuss] ImportError: No module named rdkit

Hi Loris, On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett wrote: > > I am trying to install RDKit on a university cluster running Linux from > source. The build seem to go OK and 'make install' copied the > directories > > lib > rdkit > > to the NFS share where

Re: [Rdkit-discuss] Using the new drawing code

Hi Michal, There are a couple of things in here. On Fri, Aug 25, 2017 at 11:42 AM, Michał Nowotka wrote: > Hi, > > I finally decided to try the new C++ drawing code and I found some > issues with it. I'll try to descibe my problems. > > First, lets start with a code that

Re: [Rdkit-discuss] Fixed scale drawing

Hi Maciek, You can do this by calling setScale() method on MolDraw2D(). There's not a decent python example around yet (would be something for the cookbook I suppose), but the C++ code isn't too complex and demonstrates how it works:

Re: [Rdkit-discuss] HasSubstructMatch doesn't work as expected

quot;, but you likely want to do params.adjustDegree=False. it's worth being careful with makeBondsGeneric... there you could match single against triple, which is unlikely to be you want. > Thank you, Greg! > > On Thu, Sep 14, 2017 at 5:58 AM, Greg Landrum <greg.land...@gmail.com>

Re: [Rdkit-discuss] HasSubstructMatch doesn't work as expected

This isn't a really straightforward one. One solution (and I think the best one) is to change the aromaticity model used to match whatever is generating the hits (in your case it's the Symyx cartridge). The RDKit has functionality to do this already when you call the SetAromaticity() function:

Re: [Rdkit-discuss] News on 3D molecule visualization in RDKit (project: RDKit - 3Dmol.js integration)

gt; > Thank you very much for your time. Have a great day! > > sincerely, > - malitha > > On Wed, Sep 6, 2017 at 2:44 PM, Greg Landrum <greg.land...@gmail.com> > wrote: > >> The plan here is that this code will eventually be merged onto master so >> that it bec

Re: [Rdkit-discuss] Using Chem.WrapLogs()

Yeah, please go ahead and fie a bug for the windows problems. No guarantees that we can fix it, but it's worth at least capturing the problem. -greg On Fri, Sep 8, 2017 at 4:50 PM, Noel O'Boyle wrote: > Thanks Maciek, > > Both of those solutions works on Linux, which is

Re: [Rdkit-discuss] how to output multiple Kekule structures

gnized. > > Hence, I am getting different answers for the same input molecule just > because > it was drawn in different Kekule structures. > > Regards, > Jim Metz > > > > > > -Original Message- > From: Greg Landrum <greg.land...@gmail.com&

Re: [Rdkit-discuss] how to output multiple Kekule structures

Hi Jim, The code currently has no way to enumerate Kekule structures. I don't recall this coming up in the past and, to be honest, it doesn't seem all that generally useful. Perhaps there's an alternate way to solve the problem; what are you trying to do? -greg On Mon, Sep 11, 2017 at 5:04

Re: [Rdkit-discuss] Debian Stretch Python3 Does Not Find RDKit

apologies for the slow reply; I'm still getting caught up from my vacation. If you start the system python from the command line, can that find the rdkit? You can test this as follows: python -c 'from rdkit import Chem' if that works, you know that the installation worked and that the problem is

Re: [Rdkit-discuss] GetConformerRMS() vs GetBestRMS()

Hi Anikó, Both functions do an alignment. The big difference here is coming because GetBestRMS() looks at all 2D-identical alignments of the molecules to each other while GetConformerRMS() only does the alignment once: using the atom numbers. Practically speaking what does that mean for your

Re: [Rdkit-discuss] News on 3D molecule visualization in RDKit (project: RDKit - 3Dmol.js integration)

gration) > > > > Dear all, > > > > I am about to share news on 3D molecule visualization in RDKit. > > > > This summer I have worked as Google Summer Of Codes (GSoC) participant > under supervision of Paul Czodrowski and Greg Landrum. The codes were > revi

Re: [Rdkit-discuss] recent packages for Ubuntu

Michael Banck, who did the work to make the RDKit part of debichem, would be the person I'd think is best qualified to comment on this. Aside from this github issue (https://github.com/rdkit/rdkit/issues/911) I haven't seen much here. -greg On Wed, Sep 6, 2017 at 2:59 AM, Francois BERENGER <

Re: [Rdkit-discuss] remove H using ReactionFromSmarts (i.e. creating radicals)

Hi Jan, This is a small bug in the code that applies the query properties to the new molecule. In your case you can see that things are technically ok by doing: newmol[0][0].GetAtomWithIdx(0).SetNoImplicit(True) before calling Chem.MolToSmiles() Here's the bug report:

Re: [Rdkit-discuss] Custom fingerprint in PostgreSQL: null character error; convert numpy array into bit vector

I know from the subsequent post that you've moved on from this, but it's probably worth responding here anyway: On Fri, Sep 1, 2017 at 9:36 AM, Konrad Koehler wrote: > > > *First problem*: Null characters. When I run the example script (using > the Sheridan bit vector

[Rdkit-discuss] FYI: I will be on vacation until the first week of September

Dear all, I'm going to be on vacation from this weekend until the first week of September. I won't be checking email, so there will be plenty of chances for the community to answer mailling list questions without me interfering. ;-) Best, -greg

Re: [Rdkit-discuss] Substructure search in database

Hi Hiroyuki, On Fri, Aug 18, 2017 at 12:19 AM, 山崎広之 wrote: > > I use PostgreSQL with RDKit database cartridge. > > And, I want to know if I can use my structure fingerprint instead of > default fingerprint (Pattern fingerprints?) for substructure search. > That should

Re: [Rdkit-discuss] can't kekulize molecule

shu-u.ac.jp> wrote: > On 08/16/2017 06:14 PM, Greg Landrum wrote: > >> >> On Wed, Aug 16, 2017 at 3:55 AM, Francois BERENGER < >> beren...@bioreg.kyushu-u.ac.jp <mailto:beren...@bioreg.kyushu-u.ac.jp>> >> wrote: >> >> On 08/16/2017 03:36

Re: [Rdkit-discuss] can't kekulize molecule

On Wed, Aug 16, 2017 at 7:14 PM, David Liu wrote: > > > Thanks a lot for your reply! It makes sense to me. I wonder if there is a > plan for rdkit to generate the mol2 file directly from the rdkit molecule > object? > There is a pull request active for a python-based mol2

Re: [Rdkit-discuss] can't kekulize molecule

On Wed, Aug 16, 2017 at 3:55 AM, Francois BERENGER < beren...@bioreg.kyushu-u.ac.jp> wrote: > On 08/16/2017 03:36 PM, Greg Landrum wrote: > >> >> The RDKit Mol2 parser is really only validated for the atom types >> generated by corina. I'm not surprised that t

Re: [Rdkit-discuss] can't kekulize molecule

Hi Shuai, The RDKit Mol2 parser is really only validated for the atom types generated by corina. I'm not surprised that the ouput from open babel would not be understood. This is documented: http://rdkit.org/docs/api/rdkit.Chem.rdmolfiles-module.html#MolFromMol2File An aside: If you have an SDF

Re: [Rdkit-discuss] reading multiple conformers from file

PM, Thomas Evangelidis <teva...@gmail.com> wrote: > Hello, > > I was just wondering, has there been any progress on the multi-conformer > sdf file reader since last year? > > best > Thomas > > > On 27 October 2016 at 05:20, Greg Landrum <greg.land...@gmail.c

Re: [Rdkit-discuss] Extracting data of a standard structural formula

Hi Peleg, On Sat, Aug 12, 2017 at 4:08 PM, Peleg Bar-Sapir wrote: > > I'm trying to get the 2D coordinates and info of all the atoms and bonds, > including hydrogens (i.e. atom type, bond type, etc.) of a molecule in a > standard structural formula. To clarify: I'm not

Re: [Rdkit-discuss] double bond stereochemistry question

Hi Tyler, That's a perfectly reasonable request and it is something that you should be able to do with the RDKit reaction handling code, but unfortunately it is not currently possible. This type of problem tends to not have a quick fix, but I will take a look and see. -greg On Sat, Aug 12,

Re: [Rdkit-discuss] Assigning formal charges

Hi Juuso, A quick solution that seems like it would covert most cases would be to construct a molecule from you input without doing sanitization, calculate the atomic valences in non-strict mode, and then to identify all neutral N atoms with a valence of 4 and add a positive charge to them

Re: [Rdkit-discuss] RD-Kit with numpy 1.13.1 on macOS(10.12.6) and Python 2.7

Hi Sai, This recently came up somewhere else too. We may be able to change the requirements for the conda package so that it supports more recent versions of numpy too. I will take a look over the next day or so and reply again on this thread with an answer -greg

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

The other answers on this thread have been right on point with the exception of neglecting to explicitly encourage you to call Chem.SanitizeMol() on your joined molecule before you do anything else with it. In your case you'd call: Chem.SanitizeMol(back) This will lead to the error that Nik

Re: [Rdkit-discuss] problem with AssignAtomChiralTagsFromStructure

I don't think I understand the question. The Conformer object is normally attached to/associated with a mol object. -greg On Sun, Aug 6, 2017 at 11:41 AM, Per Jr. Greisen wrote: > Thanks - worked perfectly if I was to do this conformers is there an easy > way to transform

Re: [Rdkit-discuss] using rdkit to read in chembl23 1.7 million compounds

Hi Brian, It's not that surprising. The RDKit is stricter about allowing unreasonable chemistry that the tool the ChEMBL group uses to produce SMILES or mol blocks. There are always some molecules that the RDKit just won't process. If you are concerned and see any in that group of failures that

Re: [Rdkit-discuss] canonical SMILES of a fragment

Hi Pavel, It is, unfortunately, not that easy. The canonicalization algorithm does not use atomic aromaticity when determining atom ordering, so as far as it is concerned there is no difference between atoms 0 and 2 in either of your examples. What does get used is the number of hydrogens, so you

Re: [Rdkit-discuss] How to assign stereochemistry from CIP code?

Hi Jason, There's no direct way to do this. The easiest way that I can think of to approximate it would be to set the ChiralTag on the possibly chiral atoms to CHI_TETRAHEDRAL_CW, call assignStereoChemistry(), and then loop over the possibly chiral atoms again to see if they have the absolute

Re: [Rdkit-discuss] Is it possible to compute pi and sigma partial charges with rdkit?

Hi Francois, The only partial charge implementations currently available in the RDKit are the Gasteiger-Marsilli charges and the charges associated with MMFF. Neither offers a way to decompose the charged into sigma/pi contributions. Best, -greg On Wed, Jul 26, 2017 at 6:58 AM, Francois

Re: [Rdkit-discuss] position restraints on all atoms

Hi Katrina, welcome to the RDKit community! On Mon, Jul 24, 2017 at 10:45 PM, Katrina Lexa wrote: > > I'm relatively new to RDKit, so I apologize for what may be a silly > question. I'd like to generate a set of local minimum conformations around > my input conformation, using

Re: [Rdkit-discuss] Need help with B SVG

Hi Andreas, That's a really good question, but I'm afraid that there's not good answer for it: the new drawing code does not currently have an option to support either black and white rendering or using custom colors for the elements. I just created the github item for B rendering here:

Re: [Rdkit-discuss] Is python 2.6(.6) still supported?

Hi JP, Python 2.6 is no longer supported (it's not supported by the python community either). My recommendation for using the RDKit on Centos6 (really on any system) would be to use anaconda python. -greg On Wed, Jul 19, 2017 at 10:00 PM, JP wrote: > > Dear all, > > A

Re: [Rdkit-discuss] 3d descriptors generation

To further elaborate on this: the new 3D descriptors are currently available in github and will be in the next release, but they aren't in the 2017.03 release. On Thu, Jul 13, 2017 at 7:43 PM, Paul Emsley wrote: > On 13/07/17 18:19, Abhik Seal wrote: > > Hello > > I

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