[Rdkit-discuss] Substructure search using RDKit PostgreSQL cartridge

Dear user, I am trying to perform a substructure search using smiles notation under the ChEMBL database I have already loaded into my postgreSQL database. I am here providing two sample molecules in smiles format as read by the RDKit cartrigde into the database: Molecule 1:

Re: [Rdkit-discuss] Molecule does not have substructure match with its fragments

Hi Larissa, A '*' atom in a SMILES is translated into an atom with atomic number zero. In a normal substructure match this will only match other atoms of atomic number zero. If you want to turn it into a query feature, the easiest way is with the function Chem.AdjustQueryProperties(). Here's an

Re: [Rdkit-discuss] MCS search

HI Colin, On Mon, May 28, 2018 at 2:48 PM Colin Bournez wrote: > Hi everybody, > > Here is my piece of code to run a MCS : > > from rdkit import Chem > from rdkit.Chem import rdFMCS > mol1 = Chem.MolFromSmiles('CN1CCN(Cc2ccc(C=O)cc2)CC1') > mol2 =