On Wed, Sep 30, 2020 at 9:45 PM Steven Pak <steven....@stonybrook.edu> wrote:
> Hello, > > I have been using RDKIT for some time now, and I could not get a certain > descriptor that would be super useful for my work. Every other descriptor > works fine, however, for some reason the following calculations always > gives me 0: > > RDKit::Descriptors::numAtomStereoCenters( rdmol ); > Does it help to add a check like this before getting stereo properties? if(!rdmol.hasProp(RDKit::common_properties::_StereochemDone)) { RDKit::MolOps::assignStereochemistry(rdmol); } > > I did convert the in-house mol information into molecular information that > is compatible with RDKIT, but for some reason it is not giving me any > information on stereocenters. > > Furthermore, when I print out the SMILES strings > from RDKit::MolToSmiles(rdmol) with explicit H turned off, it still spits > out the entire SMILE string that has [H] integrated into the string. I > would like to turn that off, unless explicit H in RDKIT may mean something > else. > MolToSmiles has the option *allHsExplicit*, but that only determines whether implicit hydrogens are always indicated in counts. So if you have a hydrogen-suppressed mol of ethane, that option decides whether you get a SMILES of "CC" or "[CH3][CH3]". But if you have an all-atom mol, then it will not suppress them. You need to first convert the hydrogen atoms to implicit before getting the SMILES. Because I often want to keep hydrogens as explicit vertices, but don't want to look at them in the SMILES string I use a wrapper function around MolToSmiles. The wrapper will create a copy and remove or add explicit hydrogen atoms, as well as call Kekulize/SetAromaticity, depending on the options passed in. Jason > > Any help would be appreciated. > > Thanks, > Steven Pak > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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