Re: [IMP-dev] Residue number vs residue index

[Ben Webb <>]

On 5/3/11 5:02 PM, Daniel Russel wrote:
> > 1 Residue index is sequential; you are (pretty much) guaranteed
> > that residue(our index+1) is the next residue and residue(0) is the
> > first residue in a chain.
> We don't have any explicit storage of this in IMP other than a
> Residue being the ith child of a Chain.

Ah yes, you're absolutely right, of course. It was the child indices I 
was thinking of.

> Currently this "PDB residue number" is what is called "residue index"
> in IMP. The insertion code is stored separately and not many
> operations support it as no one has cared. One can always add
> insertion code support to Selections and such when there is demand.

Makes sense. In that case it should be made clear to the user that the 
residue number/index is not unique, since it is a common mistake to 
assume it is. (I guess we should mention that we don't enforce that the 
(residue number, insertion code) tuple is unique within a chain.)

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle