A colleague has pointed out to me the likely problem with the depictions. Mol files can have either 2D or 3D coordinates. I'm guessing that 3D mol files are not interpreted correctly by the drawing program you used to view the structures; it must have set the z coordinate to 0 without any warning.
There is native nitro normalisation for the opposite direction using the "-b" option. To specify arbitary transformations the process is a bit more roundabout. You need to add the transformation to the file at (on my computer) C:\Users\noel\AppData\Roaming\OpenBabel-2.3.2\data\plugindefines.txt (or copy this file to your current directory and edit it there). At the following to the end: OpTransform rsc # ID. Commandline option to invoke is --nodative * # There is no datafile; the transforms are at the end of the entry Apply RSC normalisations TRANSFORM [N:1](=O)=[O:2] >> [N+:1](=O)[O-:2] Once you have done this, you have extended Open Babel with new functionality. "obabel -L ops" will list "rsc" as a new option. "obabel -L rsc" will give the help text. To use it, use "--rsc" as follows: > obabel -:CCN(=O)(=O) --rsc -osmi CC[N+](=O)[O-] I think you can add as many transformations as you want, or list them in a separate file and give the filename. - Noel On 10 December 2013 17:43, daya <d...@rsc.org> wrote: > Thanks for the reply Noel, > Ah, I didn't know about the "--gen2d" option - sounds like I should have > used that. I'll try it out... > And it looks like I misunderstood the --unique option... > How does the nitro normalisation work? That would definitely be something > we're interested in... > Thanks again, Aileen > > > > > -- > View this message in context: > http://forums.openbabel.org/Converting-CIFs-to-mols-using-OpenBabel-tp4657031p4657043.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
