Hi guys! I'm using Open Babel 2.3.1 in a GNU/Linux (2.6.32-5-amd64) machine with debian OS. openbabel generate erroneous structures when the option "-p" to add hydrogens appropriate for a certain pH is activated and the output is SMILES or canonical SMILES. An example is provided with 3 files: http://forums.openbabel.org/file/n4655151/test.zip test.zip
*test1_2D.sdf* file contains an exemple input molecule. If I execute: /obabel -isdf test1_2D.sdf -osmi -O test1.smi/ The *test1.smi* output is correct. But if I execute: /obabel -isdf test1_2D.sdf -p 7 -osmi -O test1_obcharged.smi/ The output *test1_obcharged.smi*contains a wrong positive charge in a carbon atom. The same problem appears with similar molecules. Please, does anybody know why is this happens and how can we solve this issue? Many thanks! -- View this message in context: http://forums.openbabel.org/erroneous-structures-when-the-option-p-is-activated-tp4655151.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
