> -problems with bond order (e.g. it makes non-aromatic ring out of aromatic > one) > -problems with charges (e.g. it converts charged group like NH3+ to radical > NH3);
Can you post the PDB file? Since PDB does not usually contain bond orders, Open Babel needs to perceive aromaticity, etc. and this is impossible to debug without seeing your file. > 1. My PDB contains ALL hydrogens (polar+non-polar), but it seems that Babel > takes only polar hydrogens into account. Is it possible to make it > considering non-polar hydrogens as well? It should solve the problem with > aromaticity. If possible, I’d avoid PDB for your file format. By its nature PDB files typically do not contain hydrogens, so at the moment there’s no way to say “all hydrogens are specified, I promise." > 2. I have a generic SMILES representation for all PDB compounds (i.e. with > undefined protonation state). Is it possible to make some consensus (i.e. > protonation state from PDB and core SMILES structure from this initial > SMILES file)? I’m not entirely sure what you mean. Do you want to search through the PDB file for fragment matching a SMILES/SMARTS to see what the protonation states are? -Geoff ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
