> atom by atom, and then call `ConnectTheDots()` to add bonds Not surprisingly, for a general-purpose library, Open Babel has a general-purpose bond perception algorithm. As you note, it will ensure oxygen atoms have a maximum of two bonds. This ensures PDB and other crystallography files with disordered atoms still retain “normal” valency.
> How should I then approach this SMARTS matching problem? My system has regular > water molecules and I have only coordinates and atomic numbers, so a priori I > don't know which oxygen atoms belong to H3O+ and which hydrogen atoms are > bridging hydrogen in H5O2+. I would say *that* is your key problem, not SMARTS. You can certainly adapt the ConnectTheDots code - it simply loops through all atoms and checks where the distance between atoms is smaller than the sum of the covalent radii. Those are “bonds.” (OB’s code will sort along the Z axis and adds a few additional checks for performance reasons, but that’s the basics of the algorithm.) You’ll need a special-purpose bond detection algorithm for your needs. You might find larger hydrogen-bonded clusters beyond H5O2, for example. I’ve found systems with unusual bond distances. That’s part of chemistry. -Geoff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
