On Mon, Mar 01, 2010 at 12:39:37PM -0500, Geoffrey Hutchison wrote: > > > My suggestion is that each block should be treated as one OBMol. There are > already mechanisms to separate fragments in an OBMol (i.e., using Separate). > This would be in keeping with the principal of least surprise. > > > 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 > > This is true, we don't have such a flag and it would probably be useful for > some formats. >
Hi geoff, I think you are right - it would ensure there are no problems if the molecules are separated - which is sort of what the second question was leading to - all the molecule separation functions Ive seen (all connectivity based) would of course separate such PDB structures so it would be useful to be able to suppress this in the Separate method Ive been very impressed with OpenBabel and would like to be able to use it as the basis for handling molecules - however I do deal with solvated protein molecular simulations so Im still figuring out if it can really handle eg. 100,000 atom systems - or indeed 10,000 water molecules as the OBMol overhead may be too much for 10,000 3 atom proper OBMol molecules (also of course all the connectivity etc. information is just duplicated in this case) 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
