Hi Greg, Thanks. Now I understand it.
Best regards, Dr. Xiaobo Li Postdoctoral Research Associate Andrew I. Cooper Group University of Liverpool / Materials Innovation Factory Department of Chemistry Crown Street Liverpool, L69 7ZD United Kingdom From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 20 February 2019 07:37 To: Li, Xiaobo [xiaoboli] <xiaobo...@liverpool.ac.uk> Cc: Rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Why this doesn't work? HasStructMatch function The middle ring in your system is considered to be aromatic. You can see this by looking at the output SMILES: In [3]: m=Chem.MolFromSmiles('CN(C(C=CC=C1)=C1C2=O)C3=C2C=CC=C3') In [4]: Chem.MolToSmiles(m) Out[4]: 'Cn1c2ccccc2c(=O)c2ccccc21' Given this, you need either the ~ bond (which matches anything) instead of -, or you could avoid specifying the bond order in your query. In SMARTS a bond that's not specified is either single or aromatic: In [5]: s=Chem.MolFromSmarts('c1ccccc1[#6](c2ccccc2)=[#8]') In [6]: m.HasSubstructMatch(s) Out[6]: True Best, -greg On Tue, Feb 19, 2019 at 11:56 PM Jason Biggs <jasondbi...@gmail.com<mailto:jasondbi...@gmail.com>> wrote: Change your pattern to use ~ as an unspecified bond instead of - for a single bond: >m=Chem.MolFromSmiles('CN(C(C=CC=C1)=C1C2=O)C3=C2C=CC=C3') >s=Chem.MolFromSmarts('c1ccccc1~[#6](~c2ccccc2)=[#8]') >m.HasSubstructMatch(s) True Jason On Tue, Feb 19, 2019 at 4:42 PM Li, Xiaobo [xiaoboli] <xiaobo...@liverpool.ac.uk<mailto:xiaobo...@liverpool.ac.uk>> wrote: Dear all, Why the output is False? m=Chem.MolFromSmiles('CN(C(C=CC=C1)=C1C2=O)C3=C2C=CC=C3') s=Chem.MolFromSmarts('c1ccccc1-[#6](-c2ccccc2)=[#8]') m.HasSubstructMatch(s) Output: False m [cid:image001.png@01D4C93D.34643F00] s [cid:image002.png@01D4C93D.34643F00] Best regards, Xiaobo Li _______________________________________________ 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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