Nicer README

README.md

@@ -1,13 +1,21 @@
 # DPXRust
 
-This is a rewrite of the DPX algorithm in Rust. DPX is an algorthim for computing the depth of residues in a protein structure by finding the distance between the current residue and the nearest residue with a SASA above 0.0 [1].
+![Image of protein that has been run through DPXRust](example.png)
+*Image of 3ZYZ after being run through DPXRust colorized by DPX value*
+
+This is a rewrite of the DPX algorithm in Rust. DPX is an algorithm for computing how buried atoms in a protein structure by finding the distance between the current atom and the nearest atom with an ASA/SASA above a threshold (Defaults to 10.0 Angstroms squared) [1].
 
 ## Usage
 
+Make sure that the SASA/ASA value for each atom is in the B-factor field before running DPXRust.
+
 Example:
 ```shell
 ./DPXRust --input-path my_protein.pdb --output-path output.csv
 ```
+
+Note: DPXRust also supports mmCIF files
+
 ## Citations:
 
 [1]: Pintar A., Carugo O., Pongor S. DPX: for the analysis of the protein core. Bioinformatics. 2003;19:313–314

src/main.rs

@@ -102,8 +102,6 @@ fn main() {
 
     pdb.remove_atoms_by(|atom| atom.element() == Some(&Element::H)); // Remove all H atoms
 
-    let tree = pdb.create_atom_rtree();
-
     // First loop to build list of ASA values for each residue
     let mut asa_values : Vec<ASAData> = Vec::new();
     for residue in pdb.residues() { // Iterate over all residues in the structure