should not just the function get_name of the element table should handle UNKNOWN_ELEMENT ? On Aug 6, 2009, at 10:36 PM, Dina Schneidman wrote:
> the right way to determine the element is from element field in pdb, > since from atom type it can be ambiguous. if the element is not > determined and stored when the pdb is read than the information is > lost. I suggest just to fix the writer. > > On Thu, Aug 6, 2009 at 7:12 PM, Keren Laskerkerenl@salilab.org > wrote: >> yes - probably should not be stored, but still doing something like: >> atom = IMP::atom::Atom::create(p,IMP::atom::AT_CA) >> connecting this atom to a molecule ( with residue and chain of >> course) >> and then writing the molecule as pdb, results in a error unknown >> element in >> get_element. >> On Aug 6, 2009, at 7:05 PM, Daniel Russel wrote: >> >>> It should get it from the aromtype for all properly initialized atom >>> types. If it isn't currently doing that blame Dina :-) we should >>> be able to >>> fix it easily. >>> >>> I'm not sure there is a reason to store the element in the >>> particle rather >>> than just look it up from the atomtype when get_element is called. >>> Is there? >>> >>> >>> >>> On Aug 6, 2009, at 6:31 PM, Keren Lasker kerenl@salilab.org wrote: >>> >>>> seems that now element is needed for writing atoms in pdb format. >>>> Would not it make sense to set the value of element in >>>> Atom::create()? >>>> _______________________________________________ >>>> 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 >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev