Re: [Rdkit-discuss] Perceived bond orders of RNA PDB-files
On 04/12/2019 08:28, Illimar Hugo Rekand wrote: Hello, everyone I was wondering if there is any reason for why aromaticity and perceived bond orders are not set properly when using the MolFromPDB-function for RNA PDB files, while it works perfectly for protein PDB files? You shouldn't be perceiving bond orders from PDB files - the chemistry is already specified in the CCD: http://www.wwpdb.org/data/ccd Here's a useful library https://gitlab.ebi.ac.uk/pdbe/ccdutils Paul. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Perceived bond orders of RNA PDB-files
Hi Illimar, that's because the StandardPDBDoubleBond() function in ProximityBonds.cpp only takes into account standard amino acids, but not nucleotides. I'll submit a PR later tonight to include standard DNA and RNA bases. Cheers, p. On 04/12/2019 08:28, Illimar Hugo Rekand wrote: Hello, everyone I was wondering if there is any reason for why aromaticity and perceived bond orders are not set properly when using the MolFromPDB-function for RNA PDB files, while it works perfectly for protein PDB files? Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of Biomedicine Department of Chemistry University of Bergen ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Perceived bond orders of RNA PDB-files
Hello, everyone I was wondering if there is any reason for why aromaticity and perceived bond orders are not set properly when using the MolFromPDB-function for RNA PDB files, while it works perfectly for protein PDB files? Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of Biomedicine Department of Chemistry University of Bergen ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
