I vote for 1 too, since we basically have it, except for optional dictionary.
On Fri, Aug 7, 2009 at 12:02 PM, Daniel Russeldrussel@gmail.com wrote: > So where do we stand? The key question is what do we want AtomType to mean? > > A couple of options: > 1) > - we use PDB atom types for AtomType > - AtomType is only guaranteed to be unique when paired with the ResidueType > or XXXType of its parent (we need LigandType or something) > - code that creates atoms must fill in element for all atoms it creates (so > add another argument to the setup_particle function) > - we could later add a function that generates a unique atom type by > combining the parent type and the atomtype > - we don't have to parse the whole dictionary unless we want to get other > information about the ligands or to fix broken names > > 2) > - we generate unique atom types by prefixing the pdb atom types with, for > example, the residue name > - AtomType is then globally unique > > I would vote for 1 but don't feel too strongly either way. We should > probably get input from Hao too. > > > On Aug 7, 2009, at 11:49 AM, Dina Schneidman wrote: > >> yes, that's of course the ultimate solution. >> I wanted to do that, however changed my mind when I saw the size of >> this dictionary. >> It seems not reasonable to load it for each PDB parsing. >> However I do think it will be nice to have it as optional. >> >> On Fri, Aug 7, 2009 at 11:47 AM, Ben Webbben@salilab.org wrote: >>> >>> On 08/07/2009 11:42 AM, Dina Schneidman wrote: >>>> >>>> Do you mean to his dictionary of chemical components? >>>> www.wwpdb.org/ccd.html >>> >>> Yes, that looks about right. Their Ligand Expo tool will even give you >>> pretty pictures of a given residue. >>> >>> Ben >>> -- >>> ben@salilab.org http://salilab.org/~ben/ >>> "It is a capital mistake to theorize before one has data." >>> - Sir Arthur Conan Doyle >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >