Re: [Rdkit-discuss] Embedding of molecules with incorrect stereochistry assignment

, Hao On Thu, Jan 19, 2023 at 7:09 AM Gianmarco Ghiandoni wrote: > Hi all, > > Anyone can help with this matter? > > Thanks, > > On Tue, 17 Jan 2023 at 13:03, Gianmarco Ghiandoni > wrote: > >> Hi all, >> >> I have come across an issue while

Re: [Rdkit-discuss] Cannot get the desired result from AllChem.ReplaceSubstructs

d try using Python strings' replace() > method on SMILES. I believe esters can be represented in two ways (left to > right and right to left), so keep that in mind. You can always use > GetSubstructMatches later to see if any ester was left behind. > Regards. > > On Sun, May 15, 2022

Re: [Rdkit-discuss] Cannot get the desired result from AllChem.ReplaceSubstructs

tructs. You can probably create a reaction SMARTS string for > converting a generic ester to a generic disulfide ( > https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html). > > On Sun, May 15, 2022 at 12:31 AM Ming Hao wrote: > >> Hi All, >> >> I w

[Rdkit-discuss] Cannot get the desired result from AllChem.ReplaceSubstructs

Hi All, I want to replace the ester structure ('COC(C)=O') with disulfide ('CSSC') [image: image.png] Here is what I did, but it does not work. It seems to need specified methods to replace the original structure with the new one, not just put individual SMILES there.

[Rdkit-discuss] Job Openings at Reverie Labs

/transformers-for-drug-discovery/ We have openings which can found on https://www.reverielabs.com/careers for: - Computational Chemists - Cheminformatics/ Molecular Data Scientists - Machine Learning Engineers Best, Hao Shen ___ Rdkit-discuss mailing list

Re: [Rdkit-discuss] File Formats with Partial Charges

Oh! I didn't realize atom properties were so cleanly integrated into sdfs. This is great - I will try things out and hopefully it works smoothly. Thanks a lot! On Wed, Oct 27, 2021 at 8:53 PM Patrick Walters wrote: > Hi Hao, > > As a long-time file format geek. I feel the nee

[Rdkit-discuss] File Formats with Partial Charges

software) 3. visualization Thanks, Hao ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Are Partial Charge Calculations Dependent on Conformers?

that there aren't really other RDKit descriptors that rely on conformers. In the future, I'll be using QM to generate partial charges as you have suggested. Best, Hao On Wed, Jun 30, 2021 at 11:07 PM Greg Landrum wrote: > Hi Hao, > > The reference for how the Gasteiger charges is c

[Rdkit-discuss] Are Partial Charge Calculations Dependent on Conformers?

in range(mol.GetNumAtoms())] print(mmff_partial_charges) print(contribs) Thanks, Hao ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] What should be the citation reference for this rdMolAlign.GetCrippenO3A() in RDKit?

://doi.org/10.1021/ci990307l > > Cheers, > p. > > On Fri, Apr 9, 2021 at 4:47 PM Ming Hao wrote: > >> Hello, >> >> Currently, I am using the method: rdMolAlign.*GetCrippenO3A**()* in >> RDKit for comparing two 3D small molecule conformations. >

[Rdkit-discuss] What should be the citation reference for this rdMolAlign.GetCrippenO3A() in RDKit?

Hello, Currently, I am using the method: rdMolAlign.*GetCrippenO3A**()* in RDKit for comparing two 3D small molecule conformations. I want to know what is the proper citation for this method? Is this: Open3DALIGN: an open-source software aimed at unsupervised ligand alignment Paolo

[Rdkit-discuss] The difference between rdkit.Chem.Descriptors and rdkit.Chem.rdMolDescriptors

lt;https://www.rdkit.org/docs/GettingStartedInPython.html#descriptor-calculation>" only mentioned rdkit.Chem.Descriptors, could you please explain the key difference between two packages? Thanks Hao ___ Rdkit-discuss mailing list Rdkit-discuss@lists

Re: [Rdkit-discuss] Define identical atoms in SMARTS pattern

oducts and check that [#X:1] == [#X:2]. With some modifications this also allows you to run reactions with molecules that require the same R-groups! Best, Hao On Fri, Jul 24, 2020 at 10:19 AM Ivan Tubert-Brohman < ivan.tubert-broh...@schrodinger.com> wrote: > Hi Jan, > > I don't think

[Rdkit-discuss] rdkit: get reasonable conformation of a small molecule with tri-phosphate from a smiles

Hello, Recently, I countered such a question. I can not get the good conformation for a small molecule with tri-phosphate, like below: https://www.rcsb.org/ligand/ET9 NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@ @H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C3=C)c2N1 The most difficult part I think is that

Re: [Rdkit-discuss] Question about ECFP fingerprints when using multiprocessing and chiralty

Thanks a bunch Greg for the very helpful explanation! Things make more senses now. On Wed, May 20, 2020 at 12:51 AM Greg Landrum wrote: > Hi Hao, > > Good question! I had to do a bit of digging to figure that out > > Here's what's going on: > The Morgan fingerprint code uses

[Rdkit-discuss] Question about ECFP fingerprints when using multiprocessing and chiralty

46, 283, 389, 650, 786, 807, 1057, 1113, 1171, 1844, 1917] Thanks and hope everyone is staying healthy! Hao ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Incorrect Aromaticity?

. The carbonyl is sp2 and > contributes zero electrons. The total is 6, which satisfies the 4n+2 rule. > > Ivan > > On Wed, Oct 30, 2019 at 3:00 PM Hao wrote: > >> Hello, >> >> It seems like RDKit is making my molecule aromatic when I don't think it >> should

[Rdkit-discuss] Incorrect Aromaticity?

what I'm seeing, that would be very helpful. Thanks! Hao ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss