________________________________ Da: Francesca Magarotto - francesca.magarot...@studio.unibo.it <francesca.magarot...@studio.unibo.it> Inviato: mercoledì 28 luglio 2021 09:43 A: Gabriele Macari <gabriele.mac...@outlook.it> Oggetto: R: [Rdkit-discuss] Generating 3D molecules for docking
Hi, thanks a lot for your reply and your help with the code. As for the conversion from SMILES to mol (m = Chem.MolFromSmiles) is it possible to use not a single SMILE like in the example but a whole file with thousands of smiles? However, doing some research I found this https://github.com/rdkit/rdkit/discussions/3647, so unfortunately it seems to me that it's not possible to obtain the Tripos Mol2 file I need to perform the virtual screening with Dock6.9... Maybe there's something I'm not considering. Every other opinions or suggestions would be very appreciated. Thanks to all for your patience and your kindness, regards. ________________________________ Da: Gabriele Macari <gabriele.mac...@outlook.it> Inviato: mercoledì 28 luglio 2021 09:10 A: Francesca Magarotto - francesca.magarot...@studio.unibo.it <francesca.magarot...@studio.unibo.it> Oggetto: Re: [Rdkit-discuss] Generating 3D molecules for docking Hi Francesca, I faced a similar issue some time ago. Starting from a SMILES file you can embed a conformation to your molecule (e.g. calculate its 3D coordinate), minimize it and then save the mol object in PDB format (I'm pretty sure you can also save the molecule in mol2 format, check the RDKiT starter guide for confirmation). Now the code: from rdkit import Chem, DataStructs from rdkit.Chem import AllChem m = Chem.MolFromSmiles('O=C(NCc1ncccc1F)c1coc(CCNCCc2nc3ccccc3[nH]2)n1') m2 = Chem.AddHs(m) AllChem.EmbedMolecule(m2) AllChem.MMFFOptimizeMolecule(m2) with open('output/path/3dmolecule.pdb','w') as fo: fo.write(Chem.MolToPDBBlock(m2)) Hoe it helps, Gabriele Il 28/07/2021 06:27, Francesca Magarotto - francesca.magarot...@studio.unibo.it<mailto:francesca.magarot...@studio.unibo.it> ha scritto: Hi, thanks for your reply. The only problem is that I have smiles file, I can download from ZINC15 in sdf but again I don’t download only the molecules I chose from the cluster analysis. I really don’t know what to do because I’m a thesis student (still not graduated) and it’s the very first time with all of this. If it’s not possible to do this kind of thing I need to tell to my supervisor. Thanks to all. ________________________________ Da: Gustavo Seabra <gustavo.sea...@gmail.com><mailto:gustavo.sea...@gmail.com> Inviato: martedì 27 luglio 2021 22:21 A: Francesca Magarotto - francesca.magarot...@studio.unibo.it<mailto:francesca.magarot...@studio.unibo.it> <francesca.magarot...@studio.unibo.it><mailto:francesca.magarot...@studio.unibo.it> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net><mailto:rdkit-discuss@lists.sourceforge.net> Oggetto: Re: [Rdkit-discuss] Generating 3D molecules for docking Hi Francesca, As far as I know (someone please correct me if I'm wrong), RDKit can read but cannot save the files in Mol2 format. But if you have the file in SDF format, you can convert them to Mol2 using OpenBabel. The command would be something like: $ obabel -isdf sdf_file.sdf -omol2 -Omol2_file.mol2 -m The -m tells obabel to split the multimolecule file into individual molecules. -- Gustavo Seabra. On Tue, Jul 27, 2021 at 1:37 PM Francesca Magarotto - francesca.magarot...@studio.unibo.it<mailto:francesca.magarot...@studio.unibo.it> <francesca.magarot...@studio.unibo.it<mailto:francesca.magarot...@studio.unibo.it>> wrote: Hi, after a cluster analysis using a dataset of compounds from ZINC15 (in smiles format) I have picked a subset for virtual screening. However, I have a problem. The program Dock6 reads only TRIPOS mol2 format: is it possible to convert the molecules I chose for virtual screening with RDKit? In ZINC15 the molecules are also provided in mol2 format, but in this case I download all of them and not only the ones I selected after cluster analysis. I don't know what to do. Thanks, regards. _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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