Re: [Rdkit-discuss] Restraining torsions whilst generating conformers
Dear Bruce, How about to use the defined core which has your desired torsions? Here are examples to generate restricted conformers with user defined cores. https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock http://rdkit.blogspot.com/2019/01/more-on-constrained-embedding.html Thanks, Taka 2020年4月26日(日) 1:11 Bruce Milne : > Hi, > > Is it possible to add torsional restraints whilst > using AllChem.EmbedMultipleConfs() to generate conformers? I did look at > this some time back but ended up moving on to another project and never > found out if it could be done. I asked a similar thing in this group at the > time (about avoiding the generation of cis-peptide bonds) but I don't think > it got an answer. > > I suspect that it may not be possible with AllChem.EmbedMultipleConfs() > but if anyone knows of an alternative for generating partially constrained > structures it would be good to know. > > Cheers, > Bruce > > -- > Prof. Dr. Bruce F. Milne > CFisUC > Department of Physics > University of Coimbra > Rua Larga > 3004 - 516 Coimbra > Portugal > > https://orcid.org/-0002-5522-4808 > https://publons.com/researcher/2905148/bruce-milne/ > https://www.linkedin.com/in/brucemilne > > A/h = S/k > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] MolLogP
Dear all, Lipinski's rule of 5 indicates logP <5. Is rdkit.Chem.Crippen.MolLogP() the suitable function to calculate this logP? JM -- Jean-Marc Nuzillard Institut de Chimie Moléculaire de Reims, CNRS UMR 7312 Faculté des Sciences Exactes et Naturelles, Bâtiment 18 BP 1039 51687 REIMS Cedex 2 France Tel : 03 26 91 82 10 Fax : 03 26 91 31 66 http://www.univ-reims.fr/icmr http://eos.univ-reims.fr/LSD/CSNteam.html ORCID : -0002-5120-2556 http://www.univ-reims.fr/LSD/ http://www.univ-reims.fr/LSD/JmnSoft/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Restraining torsions whilst generating conformers
Hi, Is it possible to add torsional restraints whilst using AllChem.EmbedMultipleConfs() to generate conformers? I did look at this some time back but ended up moving on to another project and never found out if it could be done. I asked a similar thing in this group at the time (about avoiding the generation of cis-peptide bonds) but I don't think it got an answer. I suspect that it may not be possible with AllChem.EmbedMultipleConfs() but if anyone knows of an alternative for generating partially constrained structures it would be good to know. Cheers, Bruce -- Prof. Dr. Bruce F. Milne CFisUC Department of Physics University of Coimbra Rua Larga 3004 - 516 Coimbra Portugal https://orcid.org/-0002-5522-4808 https://publons.com/researcher/2905148/bruce-milne/ https://www.linkedin.com/in/brucemilne A/h = S/k ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Complications with ConstrainedEmbed
I have a follow up question on ConstrainedEmbed. You pass the molecule to embed and the substructure core into this function and get back the embedded and aligned molecule. In rare cases there will be multiple substructure matches (e.g. in the case of symmetry). How would one go about generating alignment for all of these matches rather than (presumably) just the first? Tim On 18/04/2020 11:56, Paolo Tosco wrote: Hi Tim, mol.GetSubstructMatch(query) will give you indices in mol that match query. Also note that |rdFMCS.||MCSResult| has a |queryMol |property that encode the MCS query, so you don't need to rebuild the query molecule out of the SMARTS pattern. p. On 18/04/2020 10:27, Tim Dudgeon wrote: I also updated the Jupyter notebook with the solution. Out of interest, I now need to get the atom indices of the part of the molecule that matched. As Jupyter is nicely highlighting this that must already be present in the molecule somehow, but I can't find out how. I look at molecule and atom properties but can't find anything that suggests "highlight me". How is this encoded? Tim On 17/04/2020 19:02, Paolo Tosco wrote: Hi Tim, I’ll take a look later and get back to you. Cheers, p. On 17 Apr 2020, at 18:55, Tim Dudgeon wrote: I'm wanting to use AllChem.ConstrainedEmbed() to generate a conformer of a molecule tethered to a molecule that should always have some MCS. I found some code on the internet that mostly works, but I don't fully understand. It generally works as planned, but for a small number of examples it fails. Can someone guide me to what is wrong. Here is an example (good and bad): https://github.com/tdudgeon/jupyter_mpro/blob/master/tethering.ipynb ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] ?????? Why this substructure query by SMARTS failed
Hi Greg and Andreas, Thanks for your help to look into my question. However, I made a wrong judgement about the mismatch between the SMARTS and the SMILES structure. They actually match well!!! Sorry for my wrong question The problem roots from my test of the PAINS KNIME workflow(http://www.myexperiment.org/workflows/4748.html). I want to have a Python script that do the same as the workflow. After the KNIME test, I tried to implemented the PAINS filter with RDkit in Python. I exported the PAINS SMARTS patterns and query SMILES to csv files, and wrote a short Python script. However, the script only identified 350 SMILES that match PAINS, which is very different from the 753(it is 824 when I run with Knime 4.1.2) reported by the KNIME workflow. After discussion with my colleague, we found that the reason for the difference is related to whether hydrogen addition to the query molecule is executed. This is actually implemented by Greg in his test script(https://github.com/rdkit/rdkit/blob/master/Data/Pains/test_data/run_tests.py) In short, we have a Python script now that can do the same thing as KNIME workflow. And we'd like to share with the community. https://github.com/zhentg/GShare/blob/master/CADD/PAINS_filter.py Python=3.7.6 RDkit=2019.09.3 Best regards Zhenting 4/25/2020 -- -- ??:"Greg Landrum"https://lists.sourceforge.net/lists/listinfo/rdkit-discuss___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
