On Mon, Feb 22, 2010 at 11:31:56AM -0500, Geoffrey Hutchison wrote: > > 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.
in this format you can have multiple blocks in a file as in the SDF format however (which I think is unlike the SDF format) in a single block there can be multiple molecules - where molecules are not separated (which sounds like they are in the CDX format) > > > 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? yes - in the case of Xray structures in the PDB you have missing heavy atoms and residues so in general PDB proteins are not "proper" molecules - the molecule is defined by the SEQRES record but not all atoms implied by this record actually exist as ATOM records > > I think it might be more helpful if you told us more about this particular > format. > its the Desmond MD program format David ------------------------------------------------------------------------------ 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
