Re: [Rdkit-discuss] 2019.09.1 RDKit Release

On 25/10/2019 16:20, Greg Landrum wrote: Dear all, I'm pleased to announce that the next version of the RDKit - 2019.09 - is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2019_09_1 Binaries have

Re: [Rdkit-discuss] how to set the stereochemistry of a molecule

thank you very much Hongbin for the detailed answer and for pointing the information. So, it is possible to manually change the tag  from CW to CCW? kind regards Alfredo ⁣Enviado desde BlueMail ​ En 30 de octubre de 2019 01:32, en 01:32, Greg Landrum escribió: >Hongbin has the answer here

Re: [Rdkit-discuss] how to set the stereochemistry of a molecule

On Wed, Oct 30, 2019 at 10:16 AM Alfredo Quevedo wrote: > thank you very much Hongbin for the detailed answer and for pointing the > information. > So, it is possible to manually change the tag from CW to CCW? > Yes, Atoms have a SetChiralTag() method that you can use for this.

Re: [Rdkit-discuss] how to set the stereochemistry of a molecule

thank you Greg for the hint, Kind regards Alfredo ⁣Enviado desde BlueMail ​ En 30 de octubre de 2019 07:03, en 07:03, Greg Landrum escribió: >On Wed, Oct 30, 2019 at 10:16 AM Alfredo Quevedo > >wrote: > >> thank you very much Hongbin for the detailed answer and for pointing >the >>

Re: [Rdkit-discuss] Stereochemistry in rdkit

Hi Greg, Thank you for the answer. I used to use the stereochemistry assignment the way you describe, but someone complained that in one of the molecules they knew the stereochemistry was incorrect. It was suggested that we use the stereochemistry we have in db, so I changed that to setting

[Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by 'Du'

Hi RDKitters, I'm trying to use rdkit to generate molecular fingerprints (such as AP or ECFP) on molecules that have non-interactive pseudoatoms ('dummy atoms', denoted by Du). I attached a sample PDB file containing the dummy atoms on positions 21-24. Reading this file

Re: [Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by 'Du'

Hi Jenke, I have put together a small gist showing a slightly hacky way to round-trip a molecule containing dummy atoms through a PDB block (assuming that your molecules do not contain astatine). If your dummy atoms are called "DU" rather than " *", you may just change the replace()

Re: [Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by 'Du'

Thanks Paolo, this works brilliantly. Let's hope astatine inhibitors won't gain in popularity  Best, Jenke From: Paolo Tosco Sent: 30 October 2019 13:25 To: SCHEEN Jenke ; RDKit Discuss Subject: Re: [Rdkit-discuss] fingerprint a molecule with pseudoatoms

Re: [Rdkit-discuss] Incorrect Aromaticity?

It is aromatic according to the RDKit aromaticity model described here: https://www.rdkit.org/docs/RDKit_Book.html#aromaticity The O and N each contribute 2 electrons. Each of the carbons shared with the 6-member ring contribute one electron. The carbonyl is sp2 and contributes zero electrons.

Re: [Rdkit-discuss] Incorrect Aromaticity?

You've specified that the ring is aromatic in your smiles input. Did you mean "C1CCC2C(C1)OC(N2)=O"? *dan nealschneider* | senior developer [image: Schrodinger Logo] On Wed, Oct 30, 2019 at 12:00 PM Hao wrote: > Hello, > > It seems like RDKit is making my

Re: [Rdkit-discuss] Stereochemistry in rdkit

On Wed, Oct 30, 2019 at 10:28 AM Lukas Pravda wrote: > > Thank you for the answer. I used to use the stereochemistry assignment the > way you describe, but someone complained that in one of the molecules they > knew the stereochemistry was incorrect. > Do you mean the R/S labels were incorrect

[Rdkit-discuss] Incorrect Aromaticity?

Hello, It seems like RDKit is making my molecule aromatic when I don't think it should it. Here's the original smiles: c1ccc2c(c1)OC(N2)=O. A snippet of the workflow: [image: image.png] As you can see it makes the 5 membered ring aromatic. My chemistry isn't strong, so if someone can elucidate

Re: [Rdkit-discuss] Incorrect Aromaticity?

@Dan The issue I meant was in the first line, where it writes the 5 membered ring as aromatic. Thanks for the response Ivan. I thought each atom in an aromatic ring must contribute but I guess not. Very cool! On Wed, Oct 30, 2019 at 3:08 PM Ivan Tubert-Brohman <