On Feb 22, 2010, at 11:50 AM, David Osguthorpe wrote: > 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)
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. -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
