Merge branch 'master' of gitlab.inria.fr:pnoel/pdbparser

src/lib.rs

+//! # pdbparser
+//! 
+//! `pdbparser` is a library to manipulate protein structure. It can parse, create and filter PDB files.
+//! 
+
 mod pdb;
 
 pub use self::pdb::read_pdb::parse_pdb as parse_pdb;

src/main.rs

@@ -4,7 +4,7 @@ use pdbparser::*;
 
 fn main() {
     //let tutu = open_pdb_file("src/tests/f2_adn.pdb");
-    let tutu = parse_pdb("src/tests_file/5jpq.pdb");
+    let tutu = parse_pdb("src/tests_file/f2.pdb");
     println!("Nb res : {}", tutu.get_number_residue());
     println!("Nb chain : {}", tutu.get_number_chain());
 }

src/pdb/atom.rs

@@ -35,10 +35,10 @@ impl Atom {
     /// let h1 = pdbparser::Atom::new(String::from("HT1"), 1, [1.0, 5.0, 2.0]);
     /// let h2 = pdbparser::Atom::new(String::from("HT1"), 1, [11.0, 17.0, 5.0]);
     /// 
-    /// assert_eq!(15.905973, h1.compute_distance(h2));
+    /// assert_eq!(15.905973, h1.compute_distance(&h2));
     /// 
     /// ````   
-    pub fn compute_distance(&self, a: Atom) -> f32 {
+    pub fn compute_distance(&self, a: &Atom) -> f32 {
         (
         (self.coord[0] - a.coord[0]).powi(2) + 
         (self.coord[1] - a.coord[1]).powi(2) +

src/pdb/protein.rs

@@ -50,7 +50,7 @@ impl<'a> Protein {
                 return true
             }
         }
-        return false
+        false
     }
 
     /// Return a mutable reference of a chaine with its name. Return None if the
@@ -147,6 +147,27 @@ impl<'a> Protein {
         n
     }
 
+    /// Return the number of atom in the protein
+    ///
+    /// # Examples
+    /// 
+    /// ````
+    /// use pdbparser;
+    /// 
+    /// let my_prot = pdbparser::parse_pdb("src/tests_file/f2.pdb");
+    /// assert_eq!(1085, my_prot.get_number_atom());
+    /// ````
+    pub fn get_number_atom(&self) -> u64 {
+        let mut n: u64 = 0;
+        for chain in self.lst_chain.iter() {
+            for res in chain.lst_res.iter() {
+                for _ in res.lst_atom.iter() {
+                    n += 1;
+                }
+            }
+        }
+        n
+    }
 
     /// Function that add information on the protein (used in the parsing)
     /// /!\Change this to a macro!

src/pdb/read_pdb.rs

@@ -4,9 +4,7 @@ use std::io::BufReader;
 use std::process;
 
 use super::protein::Protein;
-use super::chain::Chain;
-use super::residue::Residue;
-use super::atom::Atom;
+
 
 /// Parse the string to return a f32. The `trim` is used to remove
 /// /n and spaces.
@@ -40,7 +38,14 @@ fn parse_int(s: &String) -> i64 {
     }
 }
 
-
+/// Parse the pdb file and return a protein structure
+/// 
+/// # Examples
+/// ```
+/// use pdbparser;
+/// let my_prot = pdbparser::parse_pdb("src/tests_file/f2.pdb");
+/// assert_eq!(66, my_prot.get_number_residue());
+/// ```
 pub fn parse_pdb(f: &str) -> Protein {
     
     // Check if the file exist and/or can be read
@@ -66,7 +71,7 @@ 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.clone(), residue_name.clone(), residue_number as u64, atom_name.clone(), atom_number as u64, [x, y, z]);
+            protein.update_protein(chain, residue_name.clone(), residue_number as u64, atom_name.clone(), atom_number as u64, [x, y, z]);
         }
     }
     protein

src/tests/test.rs

-extern crate pdbparser;
-
-use pdbparser::Atom;
-
-#[test]
-fn test_atom() {
-    Atom::new();
-    assert_eq!("rr", "rr");
-}
\ No newline at end of file

tests/test.rs

+extern crate pdbparser;
+
+#[test]
+fn test_parse_f2() {
+    use pdbparser;
+    let my_prot = pdbparser::parse_pdb("src/tests_file/f2.pdb");
+    assert_eq!(1, my_prot.get_number_chain());
+    assert_eq!(66, my_prot.get_number_residue());
+    assert_eq!(1085, my_prot.get_number_atom());
+}
+