Re: [Rdkit-discuss] Hydrogens not recognised as Dummy Atoms?

Tubert-Brohman Sent: 08 July 2021 19:02:10 To: Adelene LAI Cc: rdkit-discuss Subject: Re: [Rdkit-discuss] Hydrogens not recognised as Dummy Atoms? Hi Adelene, You can't match an atom that doesn't exist as a node in the molecular graph, so if you really want to match a hydrogen, you'll have to add

[Rdkit-discuss] Hydrogens not recognised as Dummy Atoms?

Hi RDKit Community, I've observed that hydrogens are not recognised as dummy atoms when trying to do substructure matching. Is there a way to make them so? Ideally without adding explicitHs. - smi = 'CCOCCOCCCO' mol = Chem.MolFromSmiles(smi) #with dummy atom q1s = 'CCOCCOCCCO*' q1m =

[Rdkit-discuss] RDKit Error capturing: Chem.WrapLogs unexpected result

Hi RDKit Community, I'm trying to run a script in the command line without having any RDKit warnings or errors show up in the CL. Instead, I want them written into a log.txt from rdkit import Chem from contextlib import redirect_stderr Chem.WrapLogs() with open('log.txt', 'w') as f:

Re: [Rdkit-discuss] Removing hydrogen atoms without neighbors

Hi Navid, Could you give an example? Are you trying to remove disconnected H-atoms from the mol object? A Doctoral Researcher Environmental Cheminformatics UNIVERSITÉ DU LUXEMBOURG Campus Belval | Luxembourg Centre for Systems Biomedicine 6, avenue du Swing, L-4367 Belvaux T +356 46 66 44

Re: [Rdkit-discuss] Simple question about double bond stereo in molblock output

Hi James, Interesting problem! You are right that the bond you are interested in has STEREONONE, but I am not sure that STEREONONE necessarily translates to having a bond stereo value of 0. (philosophical question?) https://gist.github.com/adelenelai/0e2c4c90f33bac9197d7a11495b4f164 Like

Re: [Rdkit-discuss] Partial substructure match?

URG Campus Belval | Luxembourg Centre for Systems Biomedicine 6, avenue du Swing, L-4367 Belvaux T +356 46 66 44 67 18 [github.png] adelenelai From: Rajarshi Guha Sent: Friday, November 20, 2020 4:16:11 PM To: Gustavo Seabra Cc: Dan Nealschneider; Adelene LAI; RDK

Re: [Rdkit-discuss] Partial substructure match?

Hi Dan and Gustavo, MCSS sounds good, but depends on the goal. >From the way Gustavo wrote, it sounds like a Query-Target substructure search >- he has a list of targets and one specific query, and he wants to compare >matching rate amongst the members of the list. If so, I would try query

[Rdkit-discuss] A postdoc position at the intersection of cheminformatics and life cycle assessment

[github.png] adelenelai From: Wang Zhanyun (IfU, ESD) Sent: Thursday, November 12, 2020 9:58 AM To: Adelene LAI Subject: A postdoc position at the intersection of cheminformatics and life cycle assessment Dear Adelene, Hope this email finds you well

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

ably the way to go, but you might also be able to use the InchiKey and the Inchi auxiliary information together as a compound hash key. -P. On Sun, Oct 25, 2020 at 10:53 AM Adelene LAI mailto:adelene@uni.lu>> wrote: Hi Gustavo, (Sorry, forgot to reply all before...) Your deduplica

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

YSTEMS BIOMEDICINE 6, avenue du Swing, L-4367 Belvaux T +356 46 66 44 67 18 [github.png] adelenelai From: Gustavo Seabra Sent: Sunday, October 25, 2020 2:27:15 PM To: Adelene LAI Subject: Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key Actually, I was

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

Hi Gustavo, https://gist.github.com/adelenelai/59a8794e1f030941c19bcb50aa8adf3f In the gist above, I tried doing some further investigating. It seems for the example you gave, the rdkit functions indeed give the same

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

] adelenelai From: David Cosgrove Sent: Thursday, October 22, 2020 12:46:54 PM To: Adelene LAI Cc: Greg Landrum; Paolo Tosco; rdkit-discuss Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry? Hi Adelene, In SMILES, there’s no way

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

66 44 67 18 [github.png] adelenelai From: Paolo Tosco Sent: Wednesday, October 21, 2020 10:56:24 AM To: Adelene LAI Cc: Greg Landrum; rdkit-discuss Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry? Hi Adelene, Greg, I have updated my

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

20 6:15:58 AM To: Adelene LAI Cc: rdkit-discuss Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry? Paolo's gist includes a vocabulary mistake[1] that I think is confusing things here. In the RDKit the stereochemistry of a double bond can be unspecified, unknown, or known. U

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

] adelenelai From: Paolo Tosco Sent: Tuesday, October 20, 2020 1:52:12 PM To: Adelene LAI Cc: rdkit-discuss Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry? Hi Adelene, this gist https://gist.github.com/ptosco

[Rdkit-discuss] How to preserve undefined stereochemistry?

Hi RDKit Community, Is there a way to preserve undefined stereochemistry aka unspecified stereochemistry when doing MolFromSmiles? I'm working with a bunch of molecules, some with stereochemistry defined, some without. If stereochemistry is undefined in the SMILES, I would like it to stay

[Rdkit-discuss] Advanced Substructure Matching question

Hello, I'm trying to understand the example below. https://www.rdkit.org/docs/GettingStartedInPython.html#advanced-substructure-matching Why is it when checking for "all_carbon" that the substructure with indices 6,11,17,5,4 is filtered out? Isn't atom 4 also a carbon? Or does it have