[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [IMP-dev] Atom::create



it does. update your version

On Thu, Aug 6, 2009 at 10:43 PM, Keren Lasker<> wrote:
> 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()?
>>>>> _______________________________________________
>>>>> IMP-dev mailing list
>>>>> 
>>>>> https://salilab.org/mailman/listinfo/imp-dev
>>>>
>>>> _______________________________________________
>>>> IMP-dev mailing list
>>>> 
>>>> https://salilab.org/mailman/listinfo/imp-dev
>>>
>>> _______________________________________________
>>> IMP-dev mailing list
>>> 
>>> https://salilab.org/mailman/listinfo/imp-dev
>>>
>> _______________________________________________
>> IMP-dev mailing list
>> 
>> https://salilab.org/mailman/listinfo/imp-dev
>
> _______________________________________________
> IMP-dev mailing list
> 
> https://salilab.org/mailman/listinfo/imp-dev
>