On Feb 21, 2010, at 6:24 PM, David Osguthorpe wrote: > Im also wondering about how such block formats are best handled
I tend to suggest the principal of least surprise. Let's use "fragment" to imply an isolated molecular fragment, and "database" to represent a whole file. There are definitely file formats which serve as molecular databases -- multiple block records, each may contain multiple fragments. SDF is a good example. There are also formats like PDB which contain one record, which may or may not contain multiple fragments. The ChemDraw CDX format sounds a bit similar to what you describe. It's a binary blob, which stores individual molecular fragments as separate "blocks." So the Open Babel import treats these as separate records. PDB, on the other hand, thinks one file = one record, so you get one OBMol which may have multiple fragments -- if you want them separated, you call OBMol::Separate. > residues - so it would be nice to have a flag indicating if an OBMol is a > "proper" > molecule or not You gave an example, but I'm not sure I have the same intuition of a "proper" molecule. Do you mean a system where all atoms and connectivity are determined? I think it might be more helpful if you told us more about this particular format. Cheers, -Geoff ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
