Dear OpenBabel community, how do I enable a "complete protonation" of all atoms within PyBEL? A small test of the OpenBabel Windows version revealed that COO- is converted COOH, but R-NH2 is not converted to R-NH3+. As data source, I work with MOL2 files, and this shall be the output as well. For the last group, the original atom type is set to N.3, and it is not changed to N.4, although I chose a high pH of 14 to "protonate" the molecule.
If you could provide any PyBEL snippet, I would very much appreciate this! Best regards, Paul This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://disclaimer.merck.de to access the German, French, Spanish and Portuguese versions of this disclaimer. ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
