[IMP-dev] Residue number vs residue index

[Daniel Russel <>]

It was pointed out that the thing we call a "residue index" in imp appears to be more commonly referred to as a "residue number" (that is, the number  of the residue as stored in the pdb file). Given that there are a number of classes involved and it may involve a lot of outside code, it is unclear how to best deal with it.

The things affected include
- IMP::atom::Residue::get_index() and set_index()
- IMP::atom::get_residue_index()
- IMP::atom::Selection (the residue_indexes and residue_index arguments and functions)
- IMP::atom::Fragment, various functions
- IMP::atom::Domain, various functions

Possible actions are:
1) improve the documentation to say residue index= residue number as we tend to use the name index for such things in IMP
2) provide new functions which use number instead of index in their names and hide the old ones from the docs (but support them indefinitely, as they are all very simple)
3) provide new functions and deprecated the old ones
4) remove all such functions :-)

Thoughts?