This may be related to a longstanding bug that has yet to be fixed. See: http://sourceforge.net/tracker/index.php?func=detail&aid=3203137&group_id=40728&atid=428740
This essentially makes the -p option unusable if you are expecting charges in the output format. Quoting green69 <gcinci...@gmail.com> on Fri, 15 Jun 2012 03:53:36 -0700 (PDT): > 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 > > _____________________________________________________ Dr. Douglas R. Houston Lecturer Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ 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
