Hi George, On Fri, May 29, 2009 at 9:49 AM, George Oakman <[email protected]> wrote: > Hi all, > > To get at the 2D coordinates for the atoms in a molecule, I'm using > something like > > ROMol *mol = SmilesToMol(smiles); > int confid = RDDepict::compute2DCoords(*mol); > const Conformer &conf = mol->getConformer(confid); > > I can then fetch the atom coordinates using conf.getAtomPos. > > This is brilliant.
Thanks for the complement. :-) > Are there any known limitations issues with using compute2DCoords (I am > particularly thinking of cis-trans and chiral challenges)? The 2d coordinate generation *should* get the cis/trans stuff right. Chirality doesn't really show up in the 2D coordinates. > I have noticed that the distances betweem atoms comes back with a consistent > 1.5. I was just wondering if there is a reason behind the 1.5 and if I can > assume that this is static. The functions completely arbitrarily use 1.5 as the distance between bonded atoms when generating coordinates. -greg
