You probably want to try tunning query parameters: https://github.com/greglandrum/rdkit_blog/blob/master/notebooks/Tuning%20substructure%20queries.ipynb
Sincerely/Atenciosamente, Luan Carvalho Martins luancarvalhomart...@gmail.com On Wed, Sep 16, 2020 at 12:59 PM Rafael da Fonseca Lameiro < rafael.lame...@alumni.usp.br> wrote: > Hi all, I was applying the code from the ConstrainedEmbed tutorial > <http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html> > and found a problem when trying to embed a molecule with an aromatic atom > that is not in the core. As an example, 1-aminopropan-2-one > and 2-acetylpyridine: > [image: image.png] > > > from rdkit import Chem > from rdkit.Chem import AllChem, rdFMCS > > m1 = Chem.MolFromSmiles("CC(CN)=O") > m2 = Chem.MolFromSmiles("CC(C1=CC=CC=N1)=O") > AllChem.EmbedMolecule(m1, useRandomCoords=True) > > mols = [m1, m2] > res = rdFMCS.FindMCS(mols, threshold=0.8, completeRingsOnly=False) > p = Chem.MolFromSmarts(res.smartsString) > > print(m1.HasSubstructMatch(p)) # True > print(m2.HasSubstructMatch(p)) # True > > core1 = > AllChem.DeleteSubstructs(AllChem.ReplaceSidechains(Chem.RemoveHs(m1), p), > Chem.MolFromSmiles('*')) > core1.UpdatePropertyCache() > > print(m1.HasSubstructMatch(core1)) # True > print(m2.HasSubstructMatch(core1)) # False > > Of course, when I try: > > m3 = Chem.AddHs(m2, addCoords=True) > Chem.AllChem.ConstrainedEmbed(m3, core1, ignoreSmoothingFailures=True, > useTethers=True) > > I get ValueError("molecule doesn't match the core") > > For some reason, after p is converted to core1, it stops matching the > aromatic N. If the N in m2 is not aromatic, the program works. > In some cases, I was able to match m2 to the core, but the core is missing > the N atom. > Any thoughts on how to solve this? I am actually reading the scaffold m1 > from a .mol file, so I need that aromatic N there. Maybe there is a way to > add information on m1 that states that its N should be aromatic. > > Thank you in advance > -- > Rafael da Fonseca Lameiro > MSc Organic and Biological Chemistry > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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