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Re: [IMP-dev] Atom::create



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 Lasker<> 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 <> 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()?
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