Hi Florian, The problem here isn't actually chirality (since you don't have any chiral centers specified). It's more that standard embedding can be tricky for large molecules like this. The solution is general to switch to starting the embedding from random coordinates.
ps = AllChem.ETKDGv2()ps.randomSeed = 0xf00dps.useRandomCoords = Truecids = AllChem.EmbedMultipleConfs(m,10,ps) Here's a full gist: https://gist.github.com/greglandrum/dcaed471cef37beb3c7c860be3ce1ae3 We should get something about this into the documentation. -greg On Mon, Jan 13, 2020 at 7:52 AM ジャンベール フローリアン <f-gimb...@nissan-arc.co.jp> wrote: > Dear all, > > I encountered a problem with EmbedMultipleConfs which returns empty list > for some molecules (and for another molecules a few conformations when I > don't add Hs) I think both cases are linked since problems occur with high > number of rotatable bonds (more than 25). I tried to look for a solution > but could only find these old topics > > https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/5776aafb.6070...@unito.it/ > > https://sourceforge.net/p/rdkit/mailman/message/35698188/ > which didn't help me so much, except it is a chirality problem almost for > sure. > > For example, EmbedMultipleConfs returns an empy list for this molecule. > > smiles = > 'CCCCCC1CCC(CC1)c2ccc(CCCCCOc3ccc4ccccc4c3c5c(OCCCCCc6ccc(cc6)C7CCC(CCCCC)CC7)ccc8cc(ccc58)N=Nc9ccc%10c(ccc(OCCCCCc%11ccc(cc%11)C%12CCC(CCCCC)CC%12)c%10c%13c(OCCCCCc%14ccc(cc%14)C%15CCC(CCCCC)CC%15)ccc%16ccccc%13%16)c9)cc2' > > m = Chem.MolFromSmiles(smiles) > nr = int(AllChem.CalcNumRotatableBonds(m)) > print("CalcNumRotatableBonds: ", nr) > m = Chem.AddHs(m) > ids = AllChem.EmbedMultipleConfs(m, numConfs=10, maxAttempts=500) # in my > tests, I choose numConfs at 500 at least, > print(len(ids)) > > Increasing numConfs help sometimes to find a few 3d conformations. Is it > the only solution due to the size of the number of rotatable bonds ? > > Best regards, > Florian > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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