On Jun 16, 2023, at 03:15, S Joshua Swamidass <swamid...@gmail.com> wrote: > In graph theory, a planar graph is a graph that can be embedded in the plane, > i.e., it can be drawn on the plane in such a way that its edges intersect > only at their endpoints. In other words, it can be drawn in such a way that > no edges cross each other.
Years ago at http://www.dalkescientific.com/writings/diary/archive/2012/05/18/nonplanar_compounds.html I did a search of a subset of 28.5 million PubChem structures and found 224 topologically non-planar examples, like https://pubchem.ncbi.nlm.nih.gov/compound/50919058 . I also gave some literature citations, like "Synthesis of the first topologically non-planar molecule" (1981) at https://www.sciencedirect.com/science/article/abs/pii/0040403981800779 . > On Jun 15, 2023, at 22:50, S Joshua Swamidass <swamid...@gmail.com> wrote: > > Have any other libraries adopted your approach? It's clever. It isn't my approach. It depends on which part you consider clever. I've been told some of the ideas can be traced back to Bernhard Rohde's PhD thesis, citation 20 in the paper ("who employed a stable numbering for equivalence classes instead of a sequential index"). Rohde is also thanked in the acknowledgements. And Rohde has/had his own in-house library at Novartis which included canonicalization. I wouldn't be surprised if NextMove has their own implementation, given how Roger Sayle is a co-author of the paper. > the covalent bonds of proteins of arbitrary size are a planar graph too, even > though most (all?) proteins have a 3D structure. FWIW, due to disulfide bonds in cystines, proteins can be topologically non-planar. https://academic.oup.com/nar/article/47/D1/D367/5223942?login=false give PDB entry 1AOC as an example, with their database entry at https://knotprot.cent.uw.edu.pl/view/1aoc/A/ . Best regards, Andrew da...@dalkescientific.com _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
