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Re: [IMP-dev] Atom::create



> That said, creating a single coordinate in PDB format is kind of an odd end
> goal, and if you just want to do that, printf seems the right way to go :-)
it is, but I don't want to worry about field width, alignments, etc.
and therefore it makes sense to use existing functionality.

>
> Without such methods, you can't do much better although Chain and Residue
> and Atom all inherit from Hierarchy and so the casts are not needed. Nor are
> the separate creation of the Particles:
>
>>  m = IMP.Model()
>>       chain = IMP.atom.Chain.create(IMP.Particle(m), 'A')
>>       residue = IMP.atom.Residue.create(IMP.Particle(m))
>>       atom = IMP.atom.Atom.create(IMP.Particle(m), IMP.atom.AT_CA)
>>       xyz = IMP.core.XYZ.create(ap)
>>       residue.add_child(atom)
>>       chain.add_child(residue)
>>       print atom.get_pdb_string()
>
>
> On Aug 7, 2009, at 11:24 AM, Dina Schneidman wrote:
>
>>> atom = IMP::atom::Atom::create(p,IMP::atom::AT_CA)
>>> connecting this atom to a molecule ( with residue and chain of course)
>>
>> I tried to do the same thing now, i.e. print single coordinate in PDB
>> format.
>> something that normally should take 2 lines of code and ended up with 14
>> lines.
>>       m = IMP.Model()
>>       rp = IMP.Particle(m)
>>       ap = IMP.Particle(m)
>>       cp = IMP.Particle(m);
>>       chain = IMP.atom.Chain.create(cp, 'A')
>>       residue = IMP.atom.Residue.create(rp)
>>       atom = IMP.atom.Atom.create(ap, IMP.atom.AT_CA)
>>       xyz = IMP.core.XYZ.create(ap)
>>       hcd = IMP.atom.Hierarchy.cast(cp)
>>       hrd = IMP.atom.Hierarchy.cast(rp)
>>       had = IMP.atom.Hierarchy.cast(ap)
>>       hcd.add_child(hrd)
>>       hrd.add_child(had)
>>       print atom.get_pdb_string()
>>
>> Is there a way to make it simpler?
>> Am I the only one who thinks it should be simpler?
>>
>> Dina
>>
>>> 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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