Hi guys! My task is to convert a multi-model PDB file to SMILES. I've tried different programs and OpenBabel does the job the best - but still not perfect. My major concerns: -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);
Some more input data: 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. 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)? Thank you! -- View this message in context: http://forums.openbabel.org/PDB-to-SMILES-tp4659108.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
