[Rdkit-discuss] SMARTS and ring closure

2020-01-17 Thread Jean-Marc Nuzillard
Dear all, I would like to write a SMARTS chain that matches any compound with a decalin ring system, whatever bond multiplicity. I wrote it as 'C1~C~C2~C~C~C~C~C2~C~C1' with ~ standing for "any bond". The C1-C1 and C2-C2 bonds have the "default type", which is single or aromatic. The code m1

Re: [Rdkit-discuss] [EXTERNAL] SMARTS and ring closure

2020-01-17 Thread Richard Hall
I think this will do it pattern = Chem.MolFromSmarts('C1~C~C2~C~C~C~C~C~2~C~C~1') you need to ring closure bonds to be set to any as well hope that helps Rich From: Jean-Marc Nuzillard Sent: 17 January 2020 09:54 To: RDKit Discuss Subject: [EXTERNAL] [Rdkit-discuss] SMARTS and ring closure D

Re: [Rdkit-discuss] SMARTS and ring closure

2020-01-17 Thread Brice Hoffmann
Dear Jean-Marc, adding '~' between C and ring number seems to work: 'm1 = Chem.MolFromSmiles('C1(=C12)2') m2 = Chem.MolFromSmiles('C1CCC=C(C12)2') pattern = Chem.MolFromSmarts('C~1~C~C~2~C~C~C~C~C~2~C~C~1') print(m1.HasSubstructMatch(pattern)) print(m2.HasSubstructMatch(pattern)) retu

Re: [Rdkit-discuss] RD Kit Cartridge Postgresql upgrade

2020-01-17 Thread Tim Dudgeon
The latest cartridge containers for informaticsmatters/rdkit-cartridge-debian are based on PostgreSQL version 11. This can/will change with different RDKit major version builds as the base Debian packages change and I have little control over this. I'd like to do this better but building all c