add support of hexa in atom number

src/main.rs

@@ -8,7 +8,7 @@ fn main() {
     println!("Nb chain : {}", toto.get_number_chain());
     println!("Nb atom : {}", toto.get_atom_index().len());
     let toto_A = toto.select_atoms("chain A").unwrap();
-    let toto_A = toto_A.select_atoms("backbone").unwrap();
+    //let toto_A = toto_A.select_atoms("backbone").unwrap();
     println!("Nb res : {}", toto_A.get_number_residue());
     println!("Nb chain : {}", toto_A.get_number_chain());
     println!("Nb atom : {}", toto_A.get_atom_index().len());

src/pdb/read_pdb.rs

@@ -24,6 +24,8 @@ fn parse_float(s: &String) -> f32 {
 
 /// Parse the string to return a i64. The `trim` is used to remove
 /// /n and spaces.
+/// In large PDB, atom number can be > 99,999. 
+/// In VMD, the atom number is in hexadecimal after 99,999
 ///
 /// # Errors  
 /// Will return 0 if the String cannot be convert and print the error
@@ -32,8 +34,13 @@ fn parse_int(s: &String) -> i64 {
     match s.trim().parse::<i64>() {
         Ok(n) => n,
         Err(e) => {
-            println!("{}", e);
-            0
+            match i64::from_str_radix(s.trim(), 16) {
+                Ok(n) => return n,
+                Err(_) => {
+                    println!("{}", e);
+                    return 0
+                }
+            }
         }
     }
 }
@@ -48,6 +55,14 @@ fn parse_int(s: &String) -> i64 {
 /// ```
 pub fn parse_pdb(f: &str) -> Protein {
     
+
+    // Allocate here to avoid multiple allocation for every call 
+    let lst_res = vec![
+        "ARG", "HIS", "HSE", "HSD", "LYS", "LYS", "ASP", "GLU", "SER", "THR", "ASN",
+        "GLN", "CYS", "SEC", "GLY", "PRO", "ALA", "VAL", "ILE", "LEU",
+        "MET", "PHE", "TYR", "TRP"
+    ];
+
     // Check if the file exist and/or can be read
     let f = match File::open(f) {
         Ok(f) => f,
@@ -71,8 +86,22 @@ pub fn parse_pdb(f: &str) -> Protein {
             let x = parse_float(&l[30..38].to_string());
             let y = parse_float(&l[38..46].to_string());
             let z = parse_float(&l[46..54].to_string());
-            protein.update_protein(chain, residue_name.clone(), residue_number as u64, atom_name.clone(), atom_number as u64, [x, y, z]);
+            if is_protein_res(residue_name, &lst_res) {
+                protein.update_protein(chain, residue_name.clone(), residue_number as u64, atom_name.clone(), atom_number as u64, [x, y, z]);
+            }
         }
     }
     protein
+}
+
+fn is_protein_res(r: &str, lst: &Vec<&str>) -> bool {
+
+    let r = r.to_uppercase();
+
+    for res in lst {
+        if r == *res {
+            return true
+        }
+    }
+    false
 }
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