Utility to get Coords (#24)

* test the conversion

* add two direfct coordinate tests

src/pymolparsing/parsing.rs

@@ -265,6 +265,16 @@ pub struct CoordSet {
     pub symmetry: Option<Vec<(((i32, i32, i32), (i32, i32, i32)), String)>>,
 }
 
+impl CoordSet {
+    /// coords are stored in a 1D vector of x,y,z,x,y,x,z,x,y,z
+    ///returns as a Vec<[x,y,z]>
+    pub fn get_coords_as_vec(&self) -> Vec<[f32; 3]> {
+        self.coord
+            .chunks(3)
+            .map(|chunk| [chunk[0], chunk[1], chunk[2]])
+            .collect()
+    }
+}
 /// Custom Value
 ///
 /// needed for the settings triplet.
@@ -422,6 +432,7 @@ impl PyObjectMolecule {
         );
         atom.unwrap()
     }
+
     /// Get unique chain names
     pub fn get_chains(&self) -> Vec<String> {
         self.atom

src/pymolparsing/psedata.rs

@@ -113,6 +113,7 @@ impl PSEData {
         // https://github.com/schrodinger/pymol-open-source/blob/master/layer1/Color.cpp#L415
         unimplemented!()
     }
+
     /// session is where all the action happens
     pub fn get_session_names(&self) -> Vec<String> {
         self.names

tests/test_pse_parsing.rs

@@ -1,5 +1,6 @@
+use itertools::assert_equal;
 use pseutils::pymolparsing::colors::Color;
-use pseutils::pymolparsing::parsing::{CustomValue, SettingsEnum};
+use pseutils::pymolparsing::parsing::{CoordSet, CustomValue, SettingsEnum};
 use pseutils::pymolparsing::representation::RepBitmask;
 use pseutils::PSEData;
 const TEST_OUTPUT_DIR: &str = "./test_temporary";
@@ -38,6 +39,17 @@ fn test_pdb_00() {
     let mols = psedata.get_molecule_data();
     assert_eq!(mols.len(), 1);
 
+    // check coordinates. theres 1 mon and 1519 atoms
+    let coord_sets: Vec<&CoordSet> = mols.iter().flat_map(|mol| mol.coord_set.iter()).collect();
+    assert_eq!(coord_sets.len(), 1);
+
+    let coords_01 = coord_sets[0].get_coords_as_vec();
+    assert_eq!(coords_01.len(), 1519);
+
+    let coords_01_atom_01 = coords_01;
+    assert_equal(coords_01_atom_01[0], [50.873, 32.978, 2.387]);
+    assert_equal(coords_01_atom_01[1518], [52.372, 15.397, -15.323]);
+
     let atom01 = mols[0].get_atom(0);
     assert!(atom01.x() == 50.87300109863281);
     assert!(atom01.y() == 32.97800064086914);