Hi Craig, On Wed, Nov 18, 2009 at 4:56 PM, Craig A. James <cja...@emolecules.com> wrote: > Tim, > > I've run into a problem: OpenBabel add a hydrogen to any potentially-chiral > carbon that doesn't have four bonds, for example, when it parses "ClC(Br)I" > (but not "ClC(Cl)Br" since it can't be chiral). I'm pretty sure it's the new > stereo code that's doing this, but I haven't dug into it yet.
The new stereo code doesn't need these extra hydrogens. The added hydrogens you are seeing are probably added in OBMol2Cansmi::AddHydrogenToChiralCenters (smilesformat.cpp) However, using trunk with the new stereo code, I don't see added hydrogens like Noel. > In our web interface, we allow the chemist to draw explicit "blocking" > hydrogens using Rich's ChemWriter program, and when we parse these molecules > and generate a SMILES, the SMILES writer's "keep hydrogens" option writes the > hydrogens explicitely. Any hydrogen in your drawing will also be in the > SMILES, so that when it's used as a SMARTS, the hydrogen blocks substituents > at that position. > > Unfortunately, when OpenBabel parses "ClC(Br)I", the "keep hydrogens option > writes out "Cl[CH](Br)I" because OpenBabel has added a H to the carbon, > resulting in a SMARTS that doesn't match what you intended. > > Assuming my analysis is correct, is there some way to mark or otherwise find > these added hydrogens? We don't have to remove them, I just need to know > which ones were in the user's original drawing (SD file). > > This is actually an example of a deeper question: What is the meaning of an > SD file, or any connection-table file? We often say, "It represents a > molecule." But in some cases, the correct answer is, "It represents what the > user drew," which is quite a different thing. > > Thanks, > Craig > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
