Re: [Rdkit-discuss] Fragmentation Help
Open-Source Cheminformatics and Machine Learning
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From: Paolo T. <pao...@gm...> - 2019-11-17 19:53:32
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Hi Ben, you could use SMARTS queries to do that, e.g.: from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole RDKit WARNING: [19:50:41] Enabling RDKit 2020.03.1dev1 jupyter extensions sucrose = "O1[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O[C@@]2(O[C@@H]([C@@H](O)[C@@H]2O)CO)CO" sucrose_mol = Chem.MolFromSmiles(sucrose) sucrose_mol primary_alcohol = Chem.MolFromSmarts("[CH2][OH1]") sucrose_mol.GetSubstructMatches(primary_alcohol) ((2, 3), (19, 20), (21, 22)) secondary_alcohol = Chem.MolFromSmarts("[CH1][OH1]") sucrose_mol.GetSubstructMatches(secondary_alcohol) ((4, 5), (6, 7), (8, 9), (15, 16), (17, 18)) I hope this helps, cheers p. On 16/11/2019 22:02, Ben Davidson wrote: > Hi, I am using RDKit to basically identify the oxygenated groups in > complex biomass. The ether, ester, ketone, and aldehyde getfrag > commands are amazing. I am wondering if it is possible to identify the > different types of alcohols in a molecule ie, primary, secondary, and > finally tertiary. For example in sucrose, there are 8 alcohols, 5 > secondary and 3 primary, is it possible to have RDKit identify that > for me? if you would like to see any code feel free to email me at > dav...@gm... <mailto:dav...@gm...> > Any help would be greatly appreciated. > -Ben > > > _______________________________________________ > Rdkit-discuss mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss |