[Rdkit-discuss] Substructure matching misbehaving with bridged atoms?

2023-03-15 Thread James Wallace
I've been using the substructure match with query molecules to do an R-Group decomposition. This works well, except in the case where the query molecule contains a 'bridged atom in a ring. Take this example (I've replaced the irrelevant part with a Y atom for confidentiality) FC1=CC=C(N2CC3CC2CN3S

Re: [Rdkit-discuss] substructure matching

2020-07-21 Thread Jan Halborg Jensen
I get both to be True using version 2020.03.04 On 21 Jul 2020, at 14.08, Quoc-Tuan DO mailto:quoctuan...@greenpharma.com>> wrote: Hello, I am not very familiar with smiles/smarts and find the following results quite puzzling: >>> patt = >>> Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c23.c1

Re: [Rdkit-discuss] substructure matching

2020-07-21 Thread Ivan Tubert-Brohman
Hi Quoc-Tuan, I can't reproduce your observations; I get True in both cases. Which version of RDKit are you using? One thing to note is that you are parsing a SMARTS with MolFromSmiles. I wouldn't recommend that in general, although it appears that in this case RDKit is lenient enough to accept "

[Rdkit-discuss] substructure matching

2020-07-21 Thread Quoc-Tuan DO
Hello, I am not very familiar with smiles/smarts and find the following results quite puzzling: >>> patt = Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c23.c1ccc(cc1)C~C2NC~Cc3c23') >>> mol = Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C

Re: [Rdkit-discuss] substructure matching

2020-07-10 Thread Quoc-Tuan DO
Hello, I am not very familiar with smiles/smarts and find the following results quite puzzling: >>> patt = Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c23.c1ccc(cc1)C~C2NC~Cc3c23') >>> mol = Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C2)NCCc5c