Fredrik Wallner wrote: > I have a problem with some simple mol-files that describes metal salts, i.e. > Na+OH- and K+OH-. When converting to smiles with the command babel test.mol > -osmi I get the result [NaH+].[OH-] instead of the expected [Na+].[OH-] which > is what I get from ChemDraw and seems most intuitive to me. The same problem > occurs in obprop which returns a molecular weight of 41.005 instead of 39.997. > > To me, this would be a bug, but if it's somehow intended I'm wondering if > there's a setting somewhere to change the properties of Na, K, and such to > stop this from happening. > > I have attached the file test.mol for testing. I have tested myself on Open > Babel 2.2.2b4 on OSX10.6.2 and Open Babel 2.2.2 on Ubuntu Hardy LTS.
This was a bug that crept in at v2.1.1 but is not in the current version v2.2.3. Apart from upgrading, which would be best, you could replace the file atomtyp.txt with the latest version http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/data/atomtyp.txt?revision=3026 or comment out an IMPVAL line mentioning alkali metals. Chris ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
