[BioPython] Reassigning parent ids in Bio.PDB-structures?

[Christian Meesters]

> > breakpoints = [1254, 5444,
> >                 6690, 10888,
> >                 10889, 16332,
> >                 16333, 21776,
> >                 21776, 27220,
> >                 27221, 32665]
> 
> I'm assuming this is "breaks" later on.
Absolutely - that's the pain with copy & paste for demos ... sorry.

> As the reason, I think this is what is happening: Given an atom, then 
> atom.parent will be a residue object, and atom.parent.parent will be a 
> chain object.  Note all the atoms in a single amino acid residue will 
> share share the same .parent, and all the atoms in a single chain will 
> share the same .parent.parent
> 
> i.e. You have renamed Chain "A" to "A", and then later renamed this 
> chain to "B", and then again to "C".  You didn't ever split up the chain 
> into sub chains.
Mh, makes sense. 
> 
> To be honest, I would be tempted to write a quick and dirty script which 
> parsed the raw PDB file, and rewrote the chain field based on the atom 
> sequence number - without the overhead of the PDB parser.
Yes, would have been too easy ;-). Only wanted to add this functionality
to a larger application and make it easy to use. There is no strict need
to do so, but it would have been nice.
However, thanks for the input.

Christian