On 09/07/2012 20:59, Jeff Janes wrote: > If I make a file foo.smi with just this in it: > > [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1ccccc1c2=O > > And then make and use an index file: > > ~/openbabel/bin/obabel foo.smi -ofs > ~/openbabel/bin/obabel foo.fs -ocan -sfoo.smi -at5 -aa --title "" > > I find that the structure is only 0.7 similar to itself.
The problem is the [N-]=[N+]= structure, which could also be written [N]#[N]= . When indexing, dative bonds like these are converted into the second form. So when searching the target should also be in this form. obabel foo.smi -O foo1.smi -b 1 molecule converted obabel foo.fs -ocan -sfoo1.smi -at5 -aa --title "" [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1ccccc1c2=O 1 1 molecule converted It has proved difficult to find a suitable user interface for this that does not interfere with other features, especially as the charged form is the more common one. Originally the target molecule was also automatically converted; this may be a better way. In the meantime I will add a note to the documentation. Chris ------------------------------------------------------------------------------ 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
