[Rdkit-discuss] (no subject)

Hi RDKit community, I am currently using the Extended Reduced Graph algorithm from the RDKit package. The Smiles string I am testing with is C1C=CC2=CC=CC=C2O1. It is basically two fused aromatic rings and one of them has an Oxygen atom. When I am passing it through the ERG algorithm it is

[Rdkit-discuss] (no subject)

Dear all, The beta of the 2020.03 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1b1 I've done conda builds for Python 3.6 and 3.7 for Mac, and Linux and I'm working on the Windows builds now. These all use the beta label so that they do not

[Rdkit-discuss] (no subject)

Dear rdkit community, I would like to assign to atoms in a molecule membership to fragments like the one detected by |rdkit.Chem.Fragments.fr_Al_COO(). I was hence wondering if by any chance there was a way to |||either|: | |a) test membership like for the GetIsAromatic() type of

Re: [Rdkit-discuss] (no subject)

Very close to my current work around. Converting reaction schemes from CDX to RXN in open babel and then with rdkit to png. The issue with this route, is that openbabel tends to throw out catalysts that are central to what I'm trying to do. Using reaction smiles produces the same issue. example:

Re: [Rdkit-discuss] (no subject)

Hi Eric, as I mentioned, I do not have access to ChemDraw, so I am afraid I can't help more with that. A possible workaround is to install OpenBabel in your conda environment and use that to do a cdx->mol conversion. While it should be possible to use the openbabel or pybel module, for some

Re: [Rdkit-discuss] (no subject)

Hi Paolo, all, Thank you for responding. I tried this out this morning - though I could not find chemdraw using the combrowser. Instead I went to the registry editor grabbed the CLSID from HKEY_CLASSES_ROOT\ChemDraw.Application.15.0\CLSID. (As far as I understand this should be identical to the

Re: [Rdkit-discuss] (no subject)

Hi Eric, it looks like the GUID in rdkit/utils/chemdraw.py might be outdated. Unfortunately I don't have access to ChemDraw, so I can't test this myself, but you might be able to find the current ChemDraw GUID as follows. From a Python prompt, issue the following commands:

[Rdkit-discuss] (no subject)

Hello all, I'm trying to make use of the rdkit.utils.chemdraw to automate conversion of cdx files to png's. and other formats. However, I'm getting the following error message: ImportError: ChemDraw version (at least version 7) not found. I'm currently using windows 10 with anaconda 3 with rdkit

[Rdkit-discuss] (no subject)

Dear RDKit'ers, does anyone have experience with the Chemicalite SQLite extension? https://chemicalite.readthedocs.io/en/latest/index.html I simply tried to compile within conda with a conda cmake 3.12 and conda rdkit cmake chemicalite

Re: [Rdkit-discuss] (no subject)

Thank you so much for your help! My problem is solved :) On Tue, Jul 31, 2018 at 3:31 PM, Jason Biggs wrote: > According to http://www.rdkit.org/docs/api/rdkit.Chem.rdMolAlign-module. > html#AlignMol, the function returns the RMSD, and the probe molecule is > modified in place. Look at the

Re: [Rdkit-discuss] (no subject)

According to http://www.rdkit.org/docs/api/rdkit.Chem.rdMolAlign-module.html#AlignMol, the function returns the RMSD, and the probe molecule is modified in place. Look at the coordinates for mol2 before and after the transformation: mol = Chem.MolFromSmiles('CCCOC(=O)[O-]') >

[Rdkit-discuss] (no subject)

Hello everyone, I want to align chem B based on the 3D coordinates of chemical A and output the 3D coordinates of chemical B (alignment that center of mass of chem B is the same as chem A). I looked at the AlignMol() and Open3D align but it returns either a RMS value or a score. Is there a way

[Rdkit-discuss] (no subject)

Hello, I am writing most of my code on Java but I need to use the fingerprint function from RDkit. Is there a way to run fingerprint function on Java? Thank you so much for your help! -- Phuong Chau -- Check out the

Re: [Rdkit-discuss] (no subject)

Last week, Greg gave us a nice example of substructure matching using a SMARTS query (see below). I learned a lot from this thread, not the least of which was to use the IPythonConsole module and to enable SVG for beautiful drawings. This style is indeed much better than the old drawings. I was

Re: [Rdkit-discuss] (no subject)

Hello: Greg and Curt your comments are very much appreciated. Thanks for getting back to me! Best, Markus On Wed, Sep 21, 2016 at 8:31 PM, Greg Landrum wrote: > Hi Markus, > > Curt's instincts are dead on: the problem here is the rings. > > I'll show the fix and then

Re: [Rdkit-discuss] (no subject)

Hi Markus, Curt's instincts are dead on: the problem here is the rings. I'll show the fix and then explain what's going on. You just need to add one line to your code: core = "[a]12[a][a][a][a][a]1[a][a][a]2" pattern = Chem.MolFromSmarts(core) Chem.GetSSSR(pattern)

Re: [Rdkit-discuss] (no subject)

Hi Markus, I suspect the problem is that your SMARTS query is not as specific as you might think. For example, RDKit does not understand how many rings there are in your SMARTS query. Each [a] could be an atom arbitrarily connected to many other rings that wouldn't be a part of the substructure

[Rdkit-discuss] (no subject)

Hello all: I am trying to perform a 2D alignment of molecules by using a pattern for which I am using Compute2DCoords. If I use a smarts string matching napthalene the 2D depiction is as one would expect. However, if I am switching to a 5,6 aromatic smarts pattern the matched benzoxazol the 2D

[Rdkit-discuss] (no subject)

Hi RDKitters, I am preparing a set of compounds for a virtual screening. While the majority are achiral compounds, there are also some racemic structures in the dataset. For the virtual screen, I would like to enumerate the enantiomers from these racemates, e.g. from CC1N1 -

Re: [Rdkit-discuss] (no subject)

Cc: RDKit Discuss rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] (no subject) Hi Axel,   On Mon, Oct 21, 2013 at 4:58 PM, chemis...@gmx.de wrote:   I am a medicinal chemist and am using RDKit and the Postgresql cartridge with much success in a small startup project

[Rdkit-discuss] (no subject)

Hi, I am a medicinal chemist and am using RDKit and the Postgresql cartridge with much success in a small startup project as the backbone for the chemical / biological database and for cheminformatics (Lipinski and such, substructure and similarity searches, ...). I have just upgraded from

Re: [Rdkit-discuss] (no subject)

Hi Axel, On Mon, Oct 21, 2013 at 4:58 PM, chemis...@gmx.de wrote: I am a medicinal chemist and am using RDKit and the Postgresql cartridge with much success in a small startup project as the backbone for the chemical / biological database and for cheminformatics (Lipinski and such,

Re: [Rdkit-discuss] (no subject)

Hi, There was a recent thread on the topic here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02766.html -greg On Wednesday, December 26, 2012, Huw Jones wrote: Hi there, Just a quick question. I read that in February there was no support for an RDKit PosrgreSQL

Re: [Rdkit-discuss] (no subject)

On Sat, Jul 28, 2012 at 7:51 AM, Huw Jones huwdjo...@gmail.com wrote: My question is am I using the wrong PIL or an outdated PIL (I did update the PIL installed on my MacOS however that did not resolve the issue) or something. The hack I used to fix the issue with no structures being generated

Re: [Rdkit-discuss] (no subject)

On Sat, Jul 28, 2012 at 12:10 PM, Gianluca Sforna gia...@gmail.com wrote: On Sat, Jul 28, 2012 at 7:51 AM, Huw Jones huwdjo...@gmail.com wrote: My question is am I using the wrong PIL or an outdated PIL (I did update the PIL installed on my MacOS however that did not resolve the issue) or

[Rdkit-discuss] (no subject)

Hi there, I have recently installed RDKit on my Mac using the excellent guide at: http://edc.github.com/homebrew-rdkit/ I had one issue though. When initially trying to create depictions using: from rdkit import Chem from rdkit.Chem import Draw mol = Chem.MolFromSmiles('c1ccncc1CC(=O)O')

[Rdkit-discuss] (no subject)

Hello, I would like to know if there is someone who uses utility Cinfony with RDKit. I use version 0.9 of Cinfony and an old version of RDKit (May 2008). There is no problem when using both programs. But I cannot arrive to install version Q2009P25, RDKit module is not found when I loaded.