Residue Name and Serial Number in Atom struct about pdbtbx

[DocKDE]

Yes, that's a good idea, thanks! Your code doesn't quite compile like this but I was able to make it work.
Some minor points: To insert a PointWithData into the RTree object the point needs to be an array and the pos method returns a tuple. That's why I constructed this manually from the x, y and z fields.
I was aware of the atomic_radius method, in fact I somewhat stole the idea (as you may have recognized). However, I saw the need to implement several different values for the radius variable in order to check for different levels of "closeness" of all the atoms. What I needed most was a way to check for atoms that are so close that their Lennard-Jones-Potential term will explode in a MM calculation and the atomic radius that's currently defined in pdbtbx is too large for this. For this specific use case I used something completely arbitrary but implementing several radii for several purposes might be worthwhile somewhere down the road.
Otherwise, I'm currently in the process of refactoring what I have to make use of what you wrote as much as possible so I'll make use of the methods you provided as well as I can but it takes a while to change everything. For now I'm trying to get it to work first and then make it more streamlined.
Thanks again for your great work and the help! I really appreciate it!

[douweschulte]

Maybe the easiest would be to add the residue information to your points in the Rtree. Would the following code work for your use case? In this way you will have all information you need while the structures will remain as minimalistic as possible.

PointWithData::new(((residue.name(), residue..serial_number()), atom), atom.pos())

For your information the technically the residue.serial_number() could occur multiple times, if this is a problem you should also use the residue.insertion_code(). Using this you should be able to rewrite your example to the following:

for residue in &pdb.residues() {
    for atom in &residue.atoms() {
        // The radius code can be simplified (see https://docs.rs/pdbtbx/0.6.1/pdbtbx/struct.Atom.html#method.atomic_radius)
        // Also if you feel the name could be better let me know, I am thinking about renaming it to vdw_radius and including other radii as well
        let contacts = tree.locate_within_distance(atom.pos(), atom.atomic_radius());
        for (other_residue, other_atom) in contacts {
            if other_atom < atom // Internally uses the serial number, available since v0.6.0
                // This is how testing for residue equality could look 
                && other_residue.0 != residue.name() 
                && other_residue.1 != residue.serial_number()
                // And the protein backbone
                && !(other_residue.0 == Some("C")
                    && residue.name() == Some("N")
                    && other_residue.1 + 1 == residue.serial_number())
            {
                table.add_row(row![
                    bByFd =>
                    other_atom.serial_number(),
                    other_atom.name(),
                    other_residue.0,
                    atom.serial_number(),
                    atom.name(),
                    residue.name(),
                    format!("{:.2}", atom.distance(other_atom))]);
            }
        }
    }
}

I also took the liberty to change some functions to ones I built into pdbtbx, use whatever you like, but I try to include such functions for general use. So if you find yourself define a couple functions like that, please report them so I can include them in the library.
Please let me know if this works for you, otherwise I will think about something else.

Edit: I took the liberty to colour your code example (by adding rust after the triple quotes to mark the start of the code block)