My concern is that different input protonation states of the same molecule do not generate the same outputs for a given pH. E.g.: echo "NCC(=O)O" | babel -i smi -p1 -o smi [NH3+]CC(=O)O #<< The expected result
echo "[NH3+]CC(=O)[O-]" | babel -i smi -p1 -o smi [NH3+]CC(=O)[O-] #<< Carboxylate didn't get reprotonated echo "NCC(=O)O" | babel -i smi -p14 -o smi NCC(=O)[O-] #<< The expected result echo "[NH3+]CC(=O)[O-]" | babel -i smi -p14 -o smi [NH3+]CC(=O)[O-] #<< Ammonium didn't get deprotonated In these examples the parent (neutral) protonation state is handled correctly, but anything with an initial charge is not de/re-protonated to the desired pH. -- View this message in context: http://forums.openbabel.org/complete-protonation-tp3427279p3447662.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
