Dear Igor, On Tue, Aug 5, 2008 at 10:29 PM, Greg Landrum <[email protected]> wrote: > > On Tue, Aug 5, 2008 at 10:17 PM, Igor Filippov [Contr] > <[email protected]> wrote: >> >> Great, I got it to work - there is one small problem though. >> When I get SMILES string there is always an extra property with the >> value of "0", doesn't exist in the SD output and I'm not sure where it's >> coming from: >> [H]Oc1c2c3c(cc1)CC1([H])N(C)CCC33C1([H])C=CC([H])(O[H])C3([H])O2 0 72 >> 0.94463 >> ^^^ >> this zero after SMILES and before "72". > > That's the slot for the molecule name (it's "_Name" property). If the > molecule doesn't have a name, the Smiles writer dumps the sequence > number of the molecule. So in your example above, that was the first > molecule (sequence number zero) in the file.
> ... snip .... > I have to do some investigating to see how much I will break if I > modify the SmilesWriter to not generate names automatically; if it > doesn't cause too many problems I will do that. If there are problems > associated with switching off the automatically generated names, I > will instead add an option to suppress names on-demand. I just checked in a change to the SmilesWriter that is a bit of a compromise and that, I think makes sense: if you provide an empty nameHeader argument to its constructor, names will not be written to the output regardless of whether or not the molecules have names. Please give it a try and let me know what you think. -greg
