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.
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
