Im working on a reader for a coordinate format that splits the input into blocks of atoms and bonds. A block is either a molecule or can be more than 1 molecule.
Im not sure about how well-implented is the possibility of an OBMol holding more than 1 molecule (from the PDB reader it appears it can certainly hold more than 1). - but are there OB functions which expect to only receive 1 molecule per OBMol and are likely to fail on multiple molecule OBMols and would need the Separate function to be called Im also wondering about how such block formats are best handled - I need to be able to re-create the blocking on output ie. always splitting into the input into separate molecules which then output as 1 molecule per block is not going to work for this format (this format really needs an extra option to be able merge/split molecules into blocks as user specified) Another issue from the PDB reader is whether there are any flags which indicate eg. an OBMol contains more than 1 molecule or is a "proper" molecule in particular for PDB input from crystallographic structures there are missing atoms and residues - so it would be nice to have a flag indicating if an OBMol is a "proper" molecule or not - missing residues cause real problems because the Separate function (which as far as I can tell uses simple connectivity to determine molecules) would invalidly separate such a system into separate molecules which dont really exist physically If anybody can shed more light on these issues Id be very grateful Thanks 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
