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.
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?