> 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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