2010/9/14 Gonçalo C. Justino <jose.just...@ist.utl.pt>: > Quoting Geoffrey Hutchison <ge...@geoffhutchison.net>: > >> >> Hi Gonçalo, >> >> I'm CC'ing the mailing lists here. It's definitely a bug, so I >> appreciate the bug report. I know that we haven't supported the TB >> specification because there aren't any working examples of what the >> results should be.... It's otherwise pretty easy for us to add it. > > What do you mean by "there aren't any working examples of what the > results should be" ? Is it experimental results that are lacking ?
It simply means the TB3-TB20 tags are not documented and their meaning is unknown. Examples (i.e. 2D/3D structure + smiles), would allow us to determine the meaning but I have never seen a smiles with TB or OH tag. a...@tb0](b)(c)(d)e means viewing from a to e, bcd are clockwise a...@tb1](b)(c)(d)e means viewing from a to e, bcd are counter-clockwise The 20 available tags probably alternate like this with a different axis. With 5 ligands, there are 10 possible axis combinations: ae ad ac ab be bd bc ce cd de However, the order remains unknown. For the 30 octahedral combinations a similar reasoning can be followed. Since the documentation is lacking and no known (open) implementation exists, we could just specify the meaning in the OpenSMILES specification. Ideally the definition would be identical to the original daylight definition though. Tim > Gonçalo > > > > >> As for the octahedral vs. square-planar 3D coordinates, I'll take a >> look. Certainly we'd like to get v2.3 released in the next few >> weeks, so fixing bugs like this are important. >> >> Thanks very much, >> -Geoff > > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Blueobelisk-SMILES mailing list > blueobelisk-smi...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-smiles > ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
