Re: [Rdkit-discuss] Trying to repeat Greg's C++ blog example

st program work like charm . All the best, Markus On Wed, Oct 13, 2021 at 2:28 PM Markus Metz wrote: > Dear all: > I would like to repeat Greg's example here: > > https://greglandrum.github.io/rdkit-blog/tutorial/technical/2021/07/24/setting-up-a-cxx-dev-env.html > > Working on

[Rdkit-discuss] Trying to repeat Greg's C++ blog example

Dear all: I would like to repeat Greg's example here: https://greglandrum.github.io/rdkit-blog/tutorial/technical/2021/07/24/setting-up-a-cxx-dev-env.html Working on Centos 7.6 and the 2021.03.5 rdkit release I followed all the steps and used the exact same input files. I have set the env

[Rdkit-discuss] MD5 checksum error

Dear all: I searched the mailing list here and came up with a very similar issue: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08044.html However, this helped me only so much. I am trying to compile rdkit from source and I followed the steps outlined in the manual: bash

Re: [Rdkit-discuss] sd file format question

Several points: A) Sorry, I forgot. I am using rdkit 2020.03 B) the attached piperidine.sdf file is input i used to generate the molblock. I copy and pasted the content. C) I also noticed that babel adds the missing charge in after writing out the piperidine example as sdf file and converting it

[Rdkit-discuss] sd file format question

Hello everybody:I have a question to the sd file format.When I write charged molecules via rdkit I noticed that the charge definition in the atom block is not written.The charge is written at the end of the entry.So far this worked perfectly fine for me.Now, I am using a program which reads the

Re: [Rdkit-discuss] visualize substructure matches in Molecule Grid Image

ts=hit_ats, change it to > highlightAtomLists=[hit_ats] instead. > > Kangway > From: Markus Metz mailto:metm...@gmail.com>> > Sent: Tuesday, September 29, 2020 2:33 PM > To: rdkit-discuss@lists.sourceforge.net > <mailto:rdkit-discuss@lists.sourceforge.net&

[Rdkit-discuss] visualize substructure matches in Molecule Grid Image

Dear all:I am looking for some advice.Is there a way to highlight substructure matches in molecules displayed as Molecule Grid Image.I found the highlightAtomLists and highlightBondLists options but the does not seem to work.Does anybody know how I can accomplish this? Please see below for an

Re: [Rdkit-discuss] A question of molecule structure

Dear Gao: Your question is a tautomer related issue. May be this might help you: https://rdkit.blogspot.com/2020/01/trying-out-new-tautomer.html https://github.com/rdkit/rdkit/issues/2908

[Rdkit-discuss] AllChem.ReplaceSubstructs question

Hello: I am puzzled by the output from ReplaceSubstructs as it can produce two fragments. So I went and tried the examples in the manual and I observed this: The example in the intro manual with the recursive smarts pattern works as expected. repl = Chem.MolFromSmiles('OC') patt =

Re: [Rdkit-discuss] rdkit.ML.Scoring?

Awesome, thanks very much! Markus On Wed, Nov 6, 2019 at 7:49 AM Greg Landrum wrote: > Hi Markus, > > try: from rdkit.ML.Scoring import Scoring > > We could make this a bit easier to discover... > > -greg > > > On Wed, Nov 6, 2019 at 4:18 PM Markus Metz wrote:

[Rdkit-discuss] rdkit.ML.Scoring?

Hello all: I just came across the description of this package on rdkit.org. However, it seems there is not much to import. When I type from rdkit.ML.Scoring import 'tab' in a jupyter notebook I am getting Scoring __doc__ __file__ __name__ __package__ Can you please clarify if and maybe when this

Re: [Rdkit-discuss] Transparent background for 2D molecule images

wrote: > On 11/20/2017 05:01 PM, Markus Metz wrote: > > Here is a code snippet: > ... > > Hmm. Now that I look at it, what I have running is > > def _to_rdk_svg( self, mol ) : > assert isinstance( mol, rdkit.Chem.rdchem.Mol ) > dr = rdkit.Chem.Draw.

[Rdkit-discuss] Transparent background for 2D molecule images

Hello: I am interested in plotting 2D molecules without background color, that is transparent. When I searched the user list I thought I found a solution here: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg07282.html I might have completely misunderstood this email

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

Hello: Just started to play with the new rdkit version in Jupyter and wanted to display a mol. The mol is displayed but an error is also thrown. Please see attached notebook. Best, Markus displaykekulizerror.ipynb Description: Binary data

[Rdkit-discuss] Two rdkit versions, always one is used

And of course it would probably help to let you know that I am working on centos 6. In addition I checked the environment variables in my virtual environment but could not find anything obviously wrong. Markus -- Forwarded message -- From: Markus Metz <metm...@gmail.com>

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

Hello all: I just installed the newest rdkit version via conda in a virtual env called 09217. This went without any problems. In addition I have an older rdkit version installed in a virtual env called 092016. Now, when I run a jupyter notebook in the 092017 env and display the rdkit version it

[Rdkit-discuss] create 2D structure image with text

Dear all: I was wondering if somebody could tell me if it is possible to create a 2D picture drawing of a molecule combined with some text, let's say some SAR data? Any suggestions would be highly appreciated. All the best, Markus

[Rdkit-discuss] mmpdb installation on windows using mingw

Hello Christian: I am trying to install your program and get the following error message: $ mmpdb help-analysis Traceback (most recent call last): File "C:/Users/---/Anaconda3/envs/my-rdkit-env/Scripts/mmpdb", line 8, in signal.signal(signal.SIGPIPE, signal.SIG_DFL) # Allow the output

Re: [Rdkit-discuss] Another Can't kekulize mol observation

tAtomWithIdx(nbrIdx).SetNumExplicitHs(1) > scaffold = edit_mol.GetMol() > > scaffold_smiles = Chem.MolToSmiles(scaffold) > print(scaffold_smiles) > > This produces: > > c1ccc(cc1)-c1n[nH]c(n1)-c1c1 > > > I hope that helps > -greg > > > On Thu, Apr 27, 2017 at

Re: [Rdkit-discuss] Another Can't kekulize mol observation

cc1)-c1nnc(n1)-c1c1',False)` >> (reference: http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfi >> les-module.html#MolFromSmiles) >> >> 2. Manually Kekulize it: >> `Chem.MolFromSmiles('c1ccc(cc1)-C1=NN=C(N1)-c1c1')` >> . This indicate the H is on the 4'N. >&g

[Rdkit-discuss] Another Can't kekulize mol observation

Hello all: I obtained this smiles string: c1ccc(cc1)-c1nnc(n1)-c1c1 by removing atoms from the n1 in parentheses. Using: mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nnc(n1)-c1c1") throws an error: Can't kekulize mol. Using mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nncn1-c1c1") works fine.

Re: [Rdkit-discuss] generating scaffold trees

Dear Axel and all: I have come across an older discussion about Ansgar Schuffenhauer's work on scaffolds: -- Axel Pahl

Re: [Rdkit-discuss] Molecule representation

Dear Stephane: Thank you very much. I will give it a try. Cheers, Markus On Tue, Mar 7, 2017 at 3:39 PM, Stéphane Téletchéa < stephane.teletc...@univ-nantes.fr> wrote: > Le 07/03/2017 à 19:00, Markus Metz a écrit : > > Does anybody have a suggestion how I might chang

[Rdkit-discuss] Molecule representation

Dear all: I am wondering if it is possible to depict 2D structures as ball and stick. I have some very simple fragments and I would like to use them for axis annotation in a heatmap. Currently I generate the png files via MolToFile and read them in again. Changing size did not help. I also tried

Re: [Rdkit-discuss] Getting Started: labeling sidechain by number of core atom it was attached to

Hello Greg: Duh! I guess I sat too long in front of the screen. As always, thank you very much for your help! Markus On Wed, Feb 22, 2017 at 7:50 PM, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Markus, > > > On Thu, Feb 23, 2017 at 1:41 AM, Markus Metz <met

[Rdkit-discuss] Getting Started: labeling sidechain by number of core atom it was attached to

Dear all: According to the example it is possible to use the option labelByIndex=True in ReplaceCore. Converting the sidechains from mol to smiles with isomericSmiles=True labels the sidechains with 1 and 5. Where do these numbers come from? I included the atom indices in the mol drawing but the

Re: [Rdkit-discuss] How to determine if atoms are part of the same ring?

Dear Andrew: Thank you very much for your input. I was able to refine and correct my approach with your suggestions. Cheers, Markus On Wed, Feb 8, 2017 at 12:23 PM, Andrew Dalke <da...@dalkescientific.com> wrote: > On Feb 8, 2017, at 19:22, Markus Metz <metm...@gmai

[Rdkit-discuss] How to determine if atoms are part of the same ring?

Dear RDKit community: I am facing the situation that I would like to attach indices to atoms in a molecule defined by a substructure. The substitution pattern is of importance. Therefore I needed to include the wildcards atoms in my substructure. If I get the atom indices of this substructure,

[Rdkit-discuss] postgres installation observation

Hello all: In the process of installing the latest rdkit version I noticed that when I try and install postgres with conda install -c rdkit rdkit-posgresql I am getting the warning that rdkit will be downgraded. Is there a way to update this? Thank you very much in advance. Markus

[Rdkit-discuss] Another Can't kekulize mol question

Hello all: This might be another FAQ but here it goes. I am wondering if there is a convenient way to output those structures throwing errors. BTW, the molecules were sanitized. As always, any input is highly appreciated. Markus

Re: [Rdkit-discuss] (no subject)

rawing code to use SVG for the rendering: > > from rdkit.Chem.Draw import IPythonConsole > IPythonConsole.ipython_useSVG=True > > It really does make the drawings a lot better. > > I hope this helps, > -greg > > > > > > > On Wed, Sep 21, 2016 at 8:47 PM

[Rdkit-discuss] 2D alignment question

== Trying to post my message again as there seems to be a problem with my first attempt. == 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

[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

Re: [Rdkit-discuss] AllChem.DeleteSubstructs question

Hello: Greg's suggestions worked out. Best, Markus On Fri, Sep 16, 2016 at 1:44 PM, Greg Landrum <greg.land...@gmail.com> wrote: > Glad to hear it. Would you mind replying to the list as well so that the > thread is closed? > > Best, > -greg > > > On Fri, Sep 16

[Rdkit-discuss] AllChem.DeleteSubstructs question

Hello everybody: I am working on a script which removes the cores based on a given pattern and I am wondering how I can accomplish that if two matches are present in the parent molecule two outputs are generated with each matching pattern deleted once. ReplaceSubstructs seems to have an option

[Rdkit-discuss] substructure search with brics framents on cdk2 cmpds fails partially

Hello all: I am trying to use the brics algorithm to fragment my compounds, filter the fragments and try to group the original compounds by selected fragments. As test I used the cdk2 data set provided by rdkit. Here is a sample code partly cannibalizing Greg's and others' example code: This

[Rdkit-discuss] m.GetProp('property'): KeyError: 'property'

Dear all: I spend some time searching the rdkit website and its mailing list. But I was not able to find anything regarding my issue. I am a newbie. So bear with me if this is a FAQ. I am trying to extract the properties for molecules from an sd file. This worked fine with the id. But not so for