Not everything was merged to the OB 2.3.2 release branch if it fiddled with the API. I have a feeling that this was the case here, but I'd have to go back and doublecheck. Without checking, I think that the underlying cause is that the SMARTS internals are exposed in the API (by accident or whatever) and so any work to correct things can cause the API to change.
- Noel On 7 August 2013 14:59, Craig James <cja...@emolecules.com> wrote: > Does anybody remember disabling chirality features for SMARTS matching > somewhere around version 2.3.2? I have a vague memory that using '@' for a > tetrahedral center was just broken and gave wrong answers prior to Tim's > work, so it was disabled and SMARTS were matched as though they had no > chiral markings. I tested earlier versions (pre-2.3.2), and they use the > '@' markings correctly. I also tested the latest dev branch and it works > correctly. But the official 2.3.2 release seems to ignore the '@' flag. > > wrong: OpenBabel 2.3.2: > > $ echo "C[C@H](Br)Cl" | babel -s"C[C@H](Br)Cl" -i smi -o can > C[C@H](Br)Cl > 1 molecule converted > > $ echo "C[C@H](Br)Cl" | babel -s"C[C@@H](Br)Cl" -i smi -o can > C[C@H](Br)Cl > 1 molecule converted > > correct: OpenBabel 2.3.x-dev (HEAD) > > $ echo "C[C@H](Br)Cl" | obabel -s"C[C@H](Br)Cl" -i smi -o can > C[C@H](Br)Cl > 1 molecule converted > [radon:emi] ~ $ echo "C[C@H](Br)Cl" | obabel -s"C[C@@H](Br)Cl" -i smi -o can > 0 molecules converted > > I'm in the middle of deploying a new version of some of our internal > software, and ran into this while testing. Normally I like to use the > production version, but in this case I'll probably want to use the fixed > version. I tried to dig through the source to find something, but there are > so many changes in the stereo code I couldn't pinpoint anything. > > Thanks, > Craig > > ------------------------------------------------------------------------------ > Get 100% visibility into Java/.NET code with AppDynamics Lite! > It's a free troubleshooting tool designed for production. > Get down to code-level detail for bottlenecks, with <2% overhead. > Download for free and get started troubleshooting in minutes. > http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
