WebAug 3, 2024 · [Updated 10.03.2024 by Charles T Hoyt to demonstrate the use of his chembl_downloader] [Updated 19.12.2024 to use new functionality from the 2024.09 RDKit release] Over the last couple of releases we’ve added a number of RDKit features which allow useage of more advanced substructure query features and more control over the … WebNov 5, 2024 · You can also see it without involving DeleteSubstructs, by starting from different SMILES representations of the same molecule: >>> m1 = Chem.MolFromSmiles ('FC12C3CCCC1C32F') >>> m2 = Chem.MolFromSmiles ('C12C3CCCC1C32') >>> m3 = Chem.MolFromSmiles ('C1CC2C3C (C1)C23') >>> Chem.MolToSmiles (m2) == …
Thread: [Rdkit-discuss] How to get substructure matches
WebNov 5, 2024 · You can also see it without involving DeleteSubstructs, by starting from different SMILES representations of the same molecule: >>> m1 = … WebJan 23, 2024 · Now I have the bond of the carbon to proton selected in the molecule and the carbon to R-group in my fragment. These bonds can be aligned onto each other to position the 3D-fragment correctly versus the molecule. This can be conveniently done using the AlignMol function available in rdkit. AlignMol(fragment,mol,atomMap=( … helen tatton
Thread: [Rdkit-discuss] GetSubstructMatch bug? + mol depiction …
WebMar 6, 2024 · $\begingroup$ If I'm using params.removeHs=False for searching with structure 2, then HasSubstructMatch(pattern) only finds structure 2 (as in your example). Why are structures 1 and 3 not found as well? Maybe because of the explicit non-aromatic extra carbon in search structure 2? What do I have to change that by drawing structure 2 … WebMar 6, 2024 · $\begingroup$ If I'm using params.removeHs=False for searching with structure 2, then HasSubstructMatch(pattern) only finds structure 2 (as in your example). Why are structures 1 and 3 not found … WebSep 1, 2024 · matches: a matching vector of the type returned by mol.GetSubstructMatch(…) replaceDummies: toggles replacement of atoms that match dummies in the query. ... (the default behavior), the first operation that failed (as defined in rdkit.Chem.SanitizeFlags) is returned. Zero is returned on success. helen tallman