Re: [Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate

I don’t know if this is the issue but Are the order of atoms the same between the pdb file and the smiles string? --- Sent from Workspace ONE Boxer On July 16, 2022 at 8:14:51 PM PDT, He, Amy wrote: Dear RDKit experts, I am new to RDKit and I have a si

Re: [Rdkit-discuss] deprotection of dimthyl acetal?

. Brian From: Kangway Chuang Sent: Wednesday, March 2, 2022 7:31 PM To: Bennion, Brian Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] deprotection of dimthyl acetal? Hi Brian, The Deprotect function will apply any number of deprotections

[Rdkit-discuss] deprotection of dimthyl acetal?

Hello All, I have poking about the docs and some emails trying to find a way to deprotect a group compounds. The docs describe the DeprotectData module but I am not making the connection to how that will operate on my molecules. my tentative smarts is here [CX4;H3][O][C:1][O][CX4;H3]>>[C:1]=[O]

[Rdkit-discuss] proper technical term for generating virtual compounds with rdkit and smarts

hello I have a paper in review and is intended for a large audience that has synthetic chemists, biologist and comp chem. One reviewer had issues with the term in-silico syntheses. I used rdkit and smarts reactions to generate large libraries of compounds for our research project. Is there a be

Re: [Rdkit-discuss] changes in chirality in rdkit?

Ok Greg. thank you for the sneak preview. brian From: Greg Landrum Sent: Tuesday, July 14, 2020 11:36 PM To: Bennion, Brian Cc: Rafal Roszak ; RDKit Discuss Subject: Re: [Rdkit-discuss] changes in chirality in rdkit? Hi Brian, I think you&#x

Re: [Rdkit-discuss] changes in chirality in rdkit?

first image. [cid:image001.png@01D659C1.FD411770] The second string after RDKit processing is shown in the second image here. [cid:image002.png@01D659C1.FD411770] -Original Message- From: Rafal Roszak Sent: Tuesday, July 14, 2020 1:25 AM To: Bennion, Brian Cc: Bennion, Brian via

[Rdkit-discuss] changes in chirality in rdkit?

hello, I am "translating" smiles strings output in a csv file from another program into RDKit canonical strings with this code. If there is something that I am doing incorrectly I would appreciate the input. thanks brian bennion The original smiles string "OC[C@@H]1O[C@H](Cn2c(N33)nnc2[C@

Re: [Rdkit-discuss] trying to figure out what an rdkit warning means

n rdkit is doing, if its not just using rdkit as well. Brian From: Greg Landrum Sent: Friday, June 12, 2020 7:06 AM To: Bennion, Brian Cc: rdkit-discuss Subject: Re: [Rdkit-discuss] trying to figure out what an rdkit warning means On Thu, Jun 11, 2020 at 4:04

Re: [Rdkit-discuss] trying to figure out what an rdkit warning means

'InChI=1S/C25H28O2/c1-20(2)8-7-9-21(3)18-19-27-24-15-13-23(14-16-24)25(26)17-12-22-10-5-4-6-11-22/h4-6,8,10-18H,7,9,19H2,1-3H3/b17-12+,21-18+' Best, -greg On Thu, Jun 11, 2020 at 3:46 AM Bennion, Brian via Rdkit-discuss mailto:rdkit-discuss@lists.sourceforge.net>> wrote: Hell

[Rdkit-discuss] trying to figure out what an rdkit warning means

Hello, Below I show a smiles string from MOE and the smiles string calculated from RDKit and the InChI string calculated by RDkit(2020_1). The error on conversion to inchi string is confusing me after entering both smiles strings into a viewer I don't see any undefined stereo center. O=C(/C=C/c

Re: [Rdkit-discuss] Any known papers on reverse engineering fingerprints into structures? --> We have just published a preprint to this!

Thank you for the link. I will look at it! --- Sent from Workspace ONE Boxer On May 14, 2020 at 11:25:49 PM PDT, Tuan Le wrote: Hi Brian, I was working on a study to deduce molecular structures given ECFP fingerprints and came across your open question

Re: [Rdkit-discuss] Open-source business models and the RDKit

One of the goals of ATOM is to fund work that will be open sourced. I think any of the partners can choose to hire consultants for the work. https://atomscience.org/ Atom atomscience.org Transforming drug discovery. The Accelerating Therapeutics for Opportunities in

[Rdkit-discuss] boron compound not recognized by RDkit

Hello, Awhile back I had noticed that rdkit has issues with boron containing compounds. One is below, and I admit it is a strange one. I read in an sdf file and write it out after calculating a formal charge on the molecule. It seems to be read into rdkit ok but writing errored out with "ValueEr

[Rdkit-discuss] boron atom/element support in RDkit

Hello Does RDkit support boron in SMILES strings? We have a number of compounds for which rdkit parsing is not successful. The commonality is that there is a B or b listed in the string. Thank you for any help. Brian Bennion LLNL

Re: [Rdkit-discuss] problems with EmbedMol

Hello Greg and Jan, This is a real newbie question, but what is the use case for this function? Is it used to generate all possible connections (limited by some distance) between 3 or more atoms given in a smiles string? Brian From: Greg Landrum Sent: Wedn

[Rdkit-discuss] UFFTYPE error in MMFF minimization

Hello In order to bypass errors in UFF typing I am using MMFF94 as a minimization forcefield. However errors about UFF atom type are still occurring for Boron. staring MMFF94 minimization CHEMBL2374533 [15:59:34] UFFTYPER: Unrecognized atom type: B_1 (26) [15:59:34] UFFTYPER: Unrecognized atom t

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

Hello Jacob, Have you received any offline replies to this post? brian From: Jacob D Durrant Sent: Thursday, October 12, 2017 10:21:46 PM To: rdkit-discuss@lists.sourceforge.net Subject: [Rdkit-discuss] Question about pKa prediction using RDKit I've been strug

Re: [Rdkit-discuss] UFF atom type errors

together. Brian From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: Friday, October 06, 2017 10:27 PM To: Bennion, Brian Cc: Guillaume GODIN ; RDKit Discuss (rdkit-discuss@lists.sourceforge.net) Subject: Re: [Rdkit-discuss] UFF atom type errors Yeah, those atom types that you are seeing are

Re: [Rdkit-discuss] nitrogen valence issues

. Bran -Original Message- From: Chris Earnshaw [mailto:cgearns...@gmail.com] Sent: Thursday, October 05, 2017 08:46 To: Bennion, Brian Cc: RDKit Discuss (rdkit-discuss@lists.sourceforge.net) Subject: Re: [Rdkit-discuss] nitrogen valence issues Hi Some

Re: [Rdkit-discuss] UFF atom type errors

r that RDKIT is >classifying He as He1 and then as He for which there is no formal UFF atom >type. Is this presumption correct? Brian From: Guillaume GODIN [mailto:guillaume.go...@firmenich.com] Sent: Thursday, October 05, 2017 22:59 To: Bennion, Brian ; RDKit Discuss (rdkit-discuss@lists.sou

[Rdkit-discuss] UFF atom type errors

Hello, As part of my workflow, I am attempting to generate a starting 3D structure from a 2D representation loaded from an sdf file. On certain structures I receive the following UFF errors when attempting to minimize the structure. [20:50:43] UFFTYPER: Unrecognized atom type: He1 (0) [20:50:43]

Re: [Rdkit-discuss] nitrogen valence issues

is also incorrect. The file is on a remote server so I will repost with attachment if I continue to have problems. Brian From: Chris Earnshaw Sent: Thursday, October 5, 2017 12:04:02 AM To: Bennion, Brian; RDKit Discuss (rdkit-discuss@lists.sourceforge.net

[Rdkit-discuss] nitrogen valence issues

Hello, After looking at the email list and seeing that this error has cropped up several times for aromatic/aliphatic heterocyclic nitrogens I still haven't been able to resolve the valence =4 error for one of the azo groups in a molecule that has 7. The first couple of azo groups seem to be in

[Rdkit-discuss] troubles going from 2D to 3D

Hello All, I am parsing a set of 2D sd files in rdkit in order to generate a 3D structure. The code is below and is based on what I could find on the list for errors in generating 3D coordinates. Temp.mol is the downloaded molfile from chembl for compound CHEMBL500809. I must be doing someth

Re: [Rdkit-discuss] list of failed chembl ids

Thank you Andrew for the explanation. I was just commenting to my summer intern that you might weigh in. Brian From: Andrew Dalke [mailto:da...@dalkescientific.com] Sent: Tuesday, August 08, 2017 15:21 To: RDKit Discuss (rdkit-discuss@lists.sourceforge.net) Subject: Re: [Rdkit-discuss] list of

[Rdkit-discuss] list of failed chembl ids

Hello, If anyone is interested, the list of chembl ids for compounds that had such crazy 2D sd files are listed below. Several are just different formulations of the same parent compound. 181880 450200 1198593 1201364 1977677 1992520 2146259 2146289 2146290 2299271 3182693 3184182 3187332 31888

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

smiles strings. Brian From: Peter S. Shenkin [mailto:shen...@gmail.com] Sent: Monday, August 07, 2017 14:26 To: Bennion, Brian Cc: Chris Swain ; rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds That molecule's SMIL

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

The carbocations are in small heterocyclic molecules. see CHEMBL3815233 Brian From: Chris Swain Sent: Monday, August 7, 2017 11:46:30 AM To: rdkit-discuss@lists.sourceforge.net Subject: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds

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

From: Bennion, Brian Sent: Monday, August 07, 2017 11:39 To: 'Konrad Koehler' Subject: RE: [Rdkit-discuss] using rdkit to read in chembl23 1.7 million compounds Hello Konrad, Thank you for your response. For the handful of compounds i looked at: multiple ringed compounds that had

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

Hello, This might be a nit picky question. I am attempting to read in the smiles string for the 1.7 million non-biological compounds in the latest chembl23 release. As it turns out 382 compounds fail to be read by RDkit. The errors are either kekulization failure or valence errors. Has anyone

[Rdkit-discuss] mass replacement of External R-groups with many substituents

Hello All, I have looked around the email list and studied the daylight guide as well as the opensmiles website in hopes of solving my problem. External r-groups is a proposed extension but that is all I could find. It is possible that I have made it too complicated though. In discussions wit

[Rdkit-discuss] [SOLVED?]RE: protonating proper tertiary amines

x27;t AddH's to the copy of the molecule i send out for other functions. This seems to solve the issue. Thanks for the help. brian From: Greg Landrum [greg.land...@gmail.com] Sent: Wednesday, August 31, 2016 7:49 PM To: Bennion, Brian Cc: rdk

Re: [Rdkit-discuss] protonating proper tertiary amines

test10=moleculeH.GetAtomWithIdx(i[1]).GetDegree() moleculeStrings2=rdkit.Chem.MolToSmiles(moleculeH,isomericSmiles=True) print "test3-10: ",test3,test7,test8,test9,test10,moleculeStrings2 From: Greg Landrum [greg.land...@gmail.com] Sent: Wednesday,

Re: [Rdkit-discuss] protonating proper tertiary amines

ndrum [greg.land...@gmail.com] Sent: Wednesday, August 31, 2016 11:01 AM To: Bennion, Brian Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] protonating proper tertiary amines hmm, perplexing. How about we try something simple. Instead of doing real molecules that may be propri

Re: [Rdkit-discuss] protonating proper tertiary amines

print "No tertiary nitrogen matches" return(molecule,tertNHnum) return (moleculeH,tertNHnum) ## ________ From: Greg Landrum [greg.land...@gmail.com] Sent: Monday, August 29, 2016 10:41 PM To: Bennion, Brian Cc: rdkit-discuss@lists.sourceforge.net Sub

[Rdkit-discuss] protonating proper tertiary amines

Hello, I have seemed to hit a wall with what seems like a simple task. First, I have ~9800 compounds that have a primary amine for a reaction that I am completing in rdkit. About 250 of those compounds have a tertiary alkylamine that is most likely protonated at pH 7.4. The dataset is a set of

Re: [Rdkit-discuss] Molecular properties + pickling

This is not a bug nor a feature per se. You need to set the compounds as PropteryMOl Ie Ketone = [x for x in supplAlkylKetones if x is not None] for i in range(len(Ketone)): Ketone[i] = PropertyMol(Ketone[i]) From: Maciek Wójcikowski [mailto:mac...@wojcikowski.pl] Sent: Friday, March 18, 2

Re: [Rdkit-discuss] compatibiltiy between parallel python and rdkit

ts. Brian From: Christos Kannas [chriskan...@gmail.com] Sent: Monday, March 02, 2015 10:46 AM To: Bennion, Brian Cc: RDKit Subject: Re: [Rdkit-discuss] compatibiltiy between parallel python and rdkit Hi Brian, This is due to the way all parallel Python packages handle message transf

[Rdkit-discuss] compatibiltiy between parallel python and rdkit

Hello, I am relatively new to rdkit but have found it to be very useful in creating compounds with the reaction functions. Currently my project involves taking a handful of scaffolds and creating shrubbery for these scaffolds based on available precursor compounds. I found that creating more