Re: [Rdkit-discuss] Fwd: What is correct treatment of bond stereochemistry defined by hydrogen
Yeah, it would be great if you could create an issue for the general problem that removeHs() should not remove H atoms that are contributing to the definition of a stereo bond On Fri, 6 Apr 2018 at 18:49, Dan Nealschneider < dan.nealschnei...@schrodinger.com> wrote: > Thanks, Greg- > > >> >>> What is the correct treatment of bond stereochemistry at centers for >>> which a hydrogen is required in order to specify the bond stereochemistry? >>> For example, an imine with a hydrogen substituent (trivial example, >>> F/C=N/[H]). >>> >> >> In these cases the H cannot be implicit. The double bond stereochemistry >> is always defined relative to atoms bonded to the double-bonded atoms (more >> complex to write than it actually is) and there’s just no way to do this if >> either of those atoms is implicit. >> > > Ok. It sounds like the correct treatment for my schrodinger/rdkit > translation layer is to leave these hydrogens explicit. > > >> I notice that when I use the smiles constructor, or if I read from an SDF >>> file using the SDMolSupplier, the C=N bond in the example shown above is >>> not recognized as having stereochemistry. However, if I use >>> removeHydrogens=False in the SDMolSupplier, the bond *is* recognized as >>> Z. >>> >> >> I need to confirm it (I’m on my phone at the moment), but I think this is >> a bug: removeHs() should not remove atoms that determine stereochemistry. >> This might be something I can get fixed before the next release. >> > > Reading from SMILES in RDKit also loses this hydrogen: > > Python 3.6.2 (default, Sep 26 2017, 17:33:28) > [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin > >>> import rdkit.Chem > >>> rdkit.__version__ > '2017.03.1' > >>> m = rdkit.Chem.MolFromSmiles('F/C=N/[H]') > >>> rdkit.Chem.MolToSmiles(m, isomericSmiles=True) > 'N=CF' > > Would it be useful for me to file a bug report? > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Fwd: What is correct treatment of bond stereochemistry defined by hydrogen
Thanks, Greg- > >> What is the correct treatment of bond stereochemistry at centers for >> which a hydrogen is required in order to specify the bond stereochemistry? >> For example, an imine with a hydrogen substituent (trivial example, >> F/C=N/[H]). >> > > In these cases the H cannot be implicit. The double bond stereochemistry > is always defined relative to atoms bonded to the double-bonded atoms (more > complex to write than it actually is) and there’s just no way to do this if > either of those atoms is implicit. > Ok. It sounds like the correct treatment for my schrodinger/rdkit translation layer is to leave these hydrogens explicit. > I notice that when I use the smiles constructor, or if I read from an SDF >> file using the SDMolSupplier, the C=N bond in the example shown above is >> not recognized as having stereochemistry. However, if I use >> removeHydrogens=False in the SDMolSupplier, the bond *is* recognized as >> Z. >> > > I need to confirm it (I’m on my phone at the moment), but I think this is > a bug: removeHs() should not remove atoms that determine stereochemistry. > This might be something I can get fixed before the next release. > Reading from SMILES in RDKit also loses this hydrogen: Python 3.6.2 (default, Sep 26 2017, 17:33:28) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin >>> import rdkit.Chem >>> rdkit.__version__ '2017.03.1' >>> m = rdkit.Chem.MolFromSmiles('F/C=N/[H]') >>> rdkit.Chem.MolToSmiles(m, isomericSmiles=True) 'N=CF' Would it be useful for me to file a bug report? -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Fwd: What is correct treatment of bond stereochemistry defined by hydrogen
Hi Dan, On Fri, 6 Apr 2018 at 00:24, Dan Nealschneider < dan.nealschnei...@schrodinger.com> wrote: > > What is the correct treatment of bond stereochemistry at centers for which > a hydrogen is required in order to specify the bond stereochemistry? For > example, an imine with a hydrogen substituent (trivial example, F/C=N/[H]). > In these cases the H cannot be implicit. The double bond stereochemistry is always defined relative to atoms bonded to the double-bonded atoms (more complex to write than it actually is) and there’s just no way to do this if either of those atoms is implicit. I notice that when I use the smiles constructor, or if I read from an SDF > file using the SDMolSupplier, the C=N bond in the example shown above is > not recognized as having stereochemistry. However, if I use > removeHydrogens=False in the SDMolSupplier, the bond *is* recognized as > Z. > I need to confirm it (I’m on my phone at the moment), but I think this is a bug: removeHs() should not remove atoms that determine stereochemistry. This might be something I can get fixed before the next release. *At core, I have 2 questions:* Is RDKit able to represent stereochemistry > about this bond if the hydrogen is implicit? > Nope. Not at the moment. -greg -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss