Add PDB writer

src/lib.rs

@@ -7,6 +7,8 @@
 mod pdb;
 
 pub use self::pdb::read_pdb::parse_pdb as parse_pdb;
+pub use self::pdb::write_pdb::write_pdb;
+
 
 pub use self::pdb::protein::Protein;
 pub use self::pdb::atom::Atom;

src/main.rs

@@ -3,12 +3,18 @@ extern crate pdbparser;
 use pdbparser::*;
 
 fn main() {
-    let my_prot = parse_pdb("tests/tests_file/5jpq.pdb", "5jpq");
+    let my_prot = parse_pdb("tests/tests_file/f2.pdb", "5jpq");
+    match write_pdb(&my_prot, "toto.pdb"){
+        Ok(_) => (),
+        Err(e) => println!("Error : {}", e),
+    };
+
+    // println!("Prot : {} \nn chain: {}\nn res: {}\nn atom: {}", my_prot.name, my_prot.get_number_chain(), my_prot.get_number_residue(), my_prot.get_number_atom());
+    // println!("Reduce protein");
+
+    // let chain_a = my_prot.select_atoms("chain a").unwrap();
+    // println!("Prot : {} \nn chain: {}\nn res: {}\nn atom: {}", chain_a.name, chain_a.get_number_chain(), chain_a.get_number_residue(), chain_a.get_number_atom());
 
-    println!("Prot : {} \nn chain: {}\nn res: {}\nn atom: {}", my_prot.name, my_prot.get_number_chain(), my_prot.get_number_residue(), my_prot.get_number_atom());
-    println!("Reduce protein");
 
-    let chain_a = my_prot.select_atoms("chain a").unwrap();
-    println!("Prot : {} \nn chain: {}\nn res: {}\nn atom: {}", chain_a.name, chain_a.get_number_chain(), chain_a.get_number_residue(), chain_a.get_number_atom());
 
 }

src/pdb/atom.rs

@@ -40,7 +40,7 @@ impl Atom {
 
     /// Get the name of the atom
     /// 
-    pub fn name(self) -> String{
+    pub fn name(&self) -> String{
         self.name.clone()
     }
 

src/pdb/mod.rs

@@ -3,5 +3,6 @@ pub mod protein;
 pub mod residue;
 pub mod read_pdb;
 pub mod chain;
+pub mod write_pdb;
 
 mod selection_atom;
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src/pdb/residue.rs

@@ -40,7 +40,7 @@ impl Residue {
         self.name.clone()
     }
 
-    /// Get the number of the residue
+    /// Get the residue ID of the residue
     /// 
     pub fn get_res_num(&self) -> u64 {
         self.res_num

src/pdb/write_pdb.rs

+use super::protein::Protein;
+
+use std::fs::File;
+use std::io::Write;
+use std::io;
+
+
+/// Write a PDB file for the `Protein`.
+/// Be careful, the protein is write with the atom numbers in its structure. Remind to use the method
+/// my_protein.refine_numerotation() before !
+pub fn write_pdb(my_prot: &Protein, file: &str) -> io::Result<()>{
+
+    let mut output_pdb = File::create(file)?;
+
+    for chain in &my_prot.lst_chain {
+        let chain_name = chain.get_name();
+        for residue in &chain.lst_res {
+            let res_name = residue.name();
+            let res_id = residue.get_res_num();
+            for atom in &residue.lst_atom {
+                let atom_name = atom.name();
+                let atom_id = atom.number;
+                let atom_coord = atom.coord;
+                output_pdb.write_fmt(format_args!("ATOM  {:>5}  {:<4}{:>3} {}{:>4}    {:>8.3}{:>8.3}{:>8.3}{:>6.2}{:>6.2}\n",
+                atom_id,
+                atom_name,
+                res_name,
+                chain_name,
+                res_id,
+                atom_coord[0],
+                atom_coord[1],
+                atom_coord[2],
+                1.0, 0.0
+                ))?;
+            }
+        }
+    }
+    Ok(())
+}
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