Thread: [Rdkit-discuss] Number of sp3 atoms
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From: Chris S. <sw...@ma...> - 2020-05-31 13:24:14
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Hi, I’ve written a Jupyter notebook to calculate a variety of calculated properties of molecules (MWt, TPSA, HAC, HBD/A etc.) I’d like to include the number of sp3 atoms, is there an easy way to do this? Cheers, Chris |
From: Andrew D. <da...@da...> - 2020-05-31 15:10:25
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On May 31, 2020, at 15:23, Chris Swain via Rdkit-discuss <rdk...@li...> wrote: > I’d like to include the number of sp3 atoms, is there an easy way to do this? I don't easily see a function for that. There's rdMolDescriptors.CalcFractionCSP3() which "returns the fraction of C atoms that are SP3 hybridized". You can do it yourself by looking at the atom's hybridization: >>> mol = Chem.MolFromSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C") >>> sum((a.GetHybridization() == Chem.HybridizationType.SP3) for a in mol.GetAtoms()) 3 Cheers, Andrew da...@da... |
From: Jean-Marc N. <jm....@un...> - 2020-05-31 16:23:00
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Le 31/05/2020 à 16:52, Andrew Dalke a écrit : > On May 31, 2020, at 15:23, Chris Swain via Rdkit-discuss <rdk...@li...> wrote: >> I’d like to include the number of sp3 atoms, is there an easy way to do this? > I don't easily see a function for that. There's rdMolDescriptors.CalcFractionCSP3() which "returns the fraction of C atoms that are SP3 hybridized". > > You can do it yourself by looking at the atom's hybridization: > > >>>> mol = Chem.MolFromSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C") >>>> sum((a.GetHybridization() == Chem.HybridizationType.SP3) for a in mol.GetAtoms()) > 3 > > Cheers, > > Andrew > da...@da... > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss Yes, but >>> mol = Chem.MolFromSmiles("O=COC") >>> sum((a.GetHybridization() == Chem.HybridizationType.SP3) for a in mol.GetAtoms()) 1 because the two oxygen atoms are SP2. Best regards, Jean-Marc -- Jean-Marc Nuzillard Directeur de Recherches au CNRS Institut de Chimie Moléculaire de Reims CNRS UMR 7312 Moulin de la Housse CPCBAI, Bâtiment 18 BP 1039 51687 REIMS Cedex 2 France Tel : 03 26 91 82 10 Fax : 03 26 91 31 66 http://www.univ-reims.fr/icmr http://eos.univ-reims.fr/LSD/CSNteam.html http://www.univ-reims.fr/LSD/ http://www.univ-reims.fr/LSD/JmnSoft/ |