Dear Jan, I was using 2020.03.3 I can't get to install the version 2020.03.4 which you are using. I work with command line Anaconda on Open SUSE 15.1 Linux and installing using: conda install -q -y -c conda-forge rdkit gives me version 2018.09
while installing with: conda install -c rdkit rdkit gets me to version 2020.03.3 I will try reinstalling Anaconda from scratch, I think and see what happens then The structure in your notebook looks good to me Thank you so much! Wojtek Plonka +48885756652 wojtekplonka.com <http://www.wojtekplonka.com> fb.com/wojtek.plonka On Sun, Jul 12, 2020 at 3:40 PM Jan Halborg Jensen <jhjen...@chem.ku.dk> wrote: > The 3D structure of the first molecule looks fine to me: > > https://colab.research.google.com/drive/1V-KkS4tMfbD5UNIs5tyQewZnYtq7yQ7i?usp=sharing > > What version of RDKit are you using? > > On 12 Jul 2020, at 07.00, Wojtek Plonka <plon...@plonkaw.com> wrote: > > Dear Greg, All, > > (I tried sending the message some time ago, but I think it did not go > through) > > I'm trying to convert some molecules which I have as SMILES strings only > to 3D. > I use a methodology similar to the below script, except this example saves > to SDF at different stages of conversion for test purposes. > > What happens is that I get very bad 3D structures, CH3 groups with insane > geometry, crazy bond lengths between heavy atoms for some molecules, even > as the EmbedMolecule and MMFFOptimizeMolecule report success. The problems > seem to be gone when I remove the chirality data from SMILES (as far as > little I understand and like SMILES at all:) ) The script has 3 molecules > to process, I'd greatly appreciate it if any of you could take a look at > the SDF with any 3D molecule viewer file it produces. The first and second > one are processed, the third fails, but this is OK. The problem is the > geometry I get for the first molecule. > > Any suggestions what I might be doing wrong? > > I tried playing with parameters of EmbedMolecule and MMFFOptimizeMolecule, > also using UFF optimization, no success. I can fix my molecules by running > MM3 calculations in external software, but I'd love to avoid that. > > Here is the code: > > from rdkit import Chem > from rdkit.Chem import AllChem > > > myuglymols = [ > 'C[C@@]12OC(=O)[C@]3(O)CC[C@H]4[C@@H](C[C@@H](O)[C@ > @]5(O)CC=CC(=O)[C@]45C)[C@@]45O[C@@]13[C@@H](C4=O)[C@]1(C)C[C@H]2OC(=O)[C@ > @H]1CO5', > > 'C[C]12OC(=O)[C]3(O)CC[CH]4[CH](C[CH](O)[C]5(O)CC=CC(=O)[C]45C)[C]45O[C]13[CH](C4=O)[C]1(C)C[CH]2OC(=O)[CH]1CO5' > , > 'CC1=CC(=O)[C@@H](O)[C@]2(C)[C@H]3[C@]4(O)OC[C@@]33[C@@H](C[C@ > @H]12)OC(=O)C[C@H]3C(=C)[C@H]4O' > ] > > w = Chem.SDWriter('uglymols.sdf') > > for smiles in myuglymols: > m = Chem.MolFromSmiles(smiles) > if (m): > mold = m > m.SetProp('State','MolFromSmiles') > w.write(m) > Chem.SanitizeMol(m) > m.SetProp('State','SanitizeMol') > w.write(m) > try: > print (smiles) > m= Chem.AddHs(m) > > # > print(AllChem.EmbedMolecule(m,randomSeed=42,useRandomCoords=True,useSmallRingTorsions=True, > useMacrocycleTorsions=True)) > print(AllChem.EmbedMolecule(m)) > m.SetProp('State','SanitizeMol') > w.write(m) > opt = AllChem.MMFFOptimizeMolecule(m,maxIters=10000, > ignoreInterfragInteractions=False,mmffVariant='MMFF94') > m.SetProp('State','MMFFOptimizeMolecule') > m.SetProp('Optimized',str(1-opt)) > w.write(m) > print(opt) > except Exception as e: > print ('Failed') > m = mold > m.SetProp('Optimized','Error') > w.write(m) > w.flush() > w.close() > > Thank you very much! > > Wojtek Plonka > +48885756652 > wojtekplonka.com > <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.wojtekplonka.com%2F&data=02%7C01%7Cjhjensen%40chem.ku.dk%7Cc9707731a2bb4cbe0cb908d826288afa%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637301302871312100&sdata=wqIefe2q8aJZjp4DHjHwAxgVPZuJT%2F9C275sYbdvOJU%3D&reserved=0> > fb.com/wojtek.plonka > <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffb.com%2Fwojtek.plonka&data=02%7C01%7Cjhjensen%40chem.ku.dk%7Cc9707731a2bb4cbe0cb908d826288afa%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637301302871312100&sdata=0JJKbq4i%2FytGSx%2Bui6aUfdrheILCwJKOSPxTLRGXat4%3D&reserved=0> > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=02%7C01%7Cjhjensen%40chem.ku.dk%7Cc9707731a2bb4cbe0cb908d826288afa%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637301302871342085&sdata=blIHAuotiLkpcDk8h6kZGCA%2B78ffGzPOfobpZ%2BQXtPQ%3D&reserved=0 > > >
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