Small Fixes (#15)

* fix some clippy issues and add the repBitMask

* more field tests

* add preude

src/lib.rs

@@ -25,4 +25,9 @@
 pub mod molviewspec;
 pub mod pymolparsing;
 
-pub use crate::pymolparsing::psedata::PSEData;
+pub use self::pymolparsing::psedata::PSEData;
+
+/// Prelude module for commonly used items
+pub mod prelude {
+    pub use crate::pymolparsing::psedata::PSEData;
+}

src/molviewspec/nodes.rs

@@ -143,7 +143,7 @@ impl Node {
         println!("In the parse node!");
         println!("{:?}", self.kind);
         if self.kind == KindT::Download {
-            let mut parse_node = Node::new(KindT::Parse, Some(NodeParams::ParseParams(params)));
+            let parse_node = Node::new(KindT::Parse, Some(NodeParams::ParseParams(params)));
             self.children.get_or_insert_with(Vec::new).push(parse_node);
             self.children.as_mut().unwrap().last_mut()
         } else {

src/pymolparsing/colors.rs

@@ -24,12 +24,63 @@
 /// ```
 use once_cell::sync::Lazy;
 
-#[derive(Clone)]
+use serde_repr::{Deserialize_repr, Serialize_repr};
+
+/// Named colors.
+///
+/// See also [`crate::pymolparsing::colors::COLOR_SET`].
+///
+#[derive(Debug, Serialize_repr, Deserialize_repr, PartialEq, Clone)]
+#[repr(i32)]
+pub enum AutoColor {
+    Aquamarine = 5257,
+    Bluewhite = 5278,
+    Brown = 51,
+    Carbon = 26,
+    Cyan = 5,
+    Darksalmon = 5280,
+    Deepblue = 23,
+    Deepsalmon = 5258,
+    Deepteal = 5262,
+    Dirtyviolet = 5272,
+    Forest = 22,
+    Greencyan = 5275,
+    Grey50 = 104,
+    Grey70 = 124,
+    Hotpink = 12,
+    Hydrogen = 29,
+    Lightmagenta = 154,
+    Lightpink = 5274,
+    Lightteal = 5266,
+    Lime = 10,
+    Limegreen = 15,
+    Limon = 5276,
+    Marine = 17,
+    Olive = 18,
+    Orange = 13,
+    Paleyellow = 5256,
+    Raspberry = 5268,
+    Salmon = 9,
+    Sand = 5269,
+    Skyblue = 5277,
+    Slate = 11,
+    Smudge = 5270,
+    Splitpea = 5267,
+    Teal = 20,
+    Violet = 53,
+    Violetpurple = 5271,
+    Warmpink = 5279,
+    Wheat = 52,
+    Yellow = 6,
+    Yelloworange = 36,
+}
+
+#[derive(Clone, Debug, PartialEq)]
 pub struct Color {
-    name: &'static str, // Changed from String to &'static str,
-    r: f32,
-    g: f32,
-    b: f32,
+    pub name: &'static str, // Changed from String to &'static str,
+    pub r: f32,
+    pub g: f32,
+    pub b: f32,
 }
 
 /// Colors from Pymol

src/pymolparsing/parsing.rs

@@ -47,7 +47,7 @@
 //!  m_tmpids[m_iter.getAtm()] = m_id;
 use crate::molviewspec::nodes::{ComponentExpression, ComponentSelector};
 use crate::pymolparsing::colors::{Color, COLOR_SET};
-use crate::pymolparsing::representation::RepType;
+use crate::pymolparsing::representation::{RepBitmask, RepType};
 
 use itertools::Itertools;
 use pdbtbx::{self, Residue, PDB};
@@ -126,8 +126,10 @@ pub struct AtomInfo {
     pub elem: String,
     pub text_type: String,
     pub label: String,
+    // todo: make enum
     pub ss_type: String,
-    pub is_hydrogen: i8,
+    #[serde(deserialize_with = "int_to_bool")]
+    pub is_hydrogen: bool,
     pub custom_type: i32,
     pub priority: i32,
     pub b: f64,
@@ -137,13 +139,16 @@ pub struct AtomInfo {
     pub formal_charge: i32,
     #[serde(deserialize_with = "int_to_bool")]
     pub is_hetatm: bool,
-    pub vis_rep: i32,
+    pub vis_rep: RepBitmask,
+    // color is an index into the color vec
     pub color: i32,
     pub id: i32,
     // https://github.com/schrodinger/pymol-open-source/blob/03d7a7fcf0bd95cd93d710a1268dbace2ed77765/layer2/AtomInfo.h#L292C33-L292C77
     pub cartoon: i32, //  /* 0 = default which is auto (use ssType) */
     pub flags: i64,
-    pub is_bonded: i8,
+    #[serde(deserialize_with = "int_to_bool")]
+    pub is_bonded: bool,
+    // not sure what this is
     pub chem_flag: i32,
     // https://github.com/schrodinger/pymol-open-source/blob/03d7a7fcf0bd95cd93d710a1268dbace2ed77765/layer2/AtomInfo.cpp#L44
     pub geom: i32, // cAtomInfo*
@@ -187,7 +192,7 @@ impl AtomInfo {
     pub fn is_visible() {
         unimplemented!()
     }
-    pub fn atomInfoBrackResidue() {
+    pub fn atom_info_brack_residue() {
         // https://github.com/schrodinger/pymol-open-source/blob/03d7a7fcf0bd95cd93d710a1268dbace2ed77765/layer2/AtomInfo.cpp#L1256C6-L1256C28
         //inefficient but reliable way to find where residue atoms are located in an object
         // for purpose of residue-based operations
@@ -228,10 +233,11 @@ impl AtomInfo {
 pub struct Bond {
     pub index_1: i32,
     pub index_2: i32,
+    // todo: make enum
     pub order: i32,
     pub id: i32,
     pub stereo: i32,
-    pub unique_id: i32,
+    pub unique_id: i8,
     pub has_setting: i32,
     // todo handle arity 7 or arity 8 with specific symmetry info
     // Symmetry operation of the second atom.
@@ -295,55 +301,6 @@ pub enum ObjectType {
     CObjectCurve = 14,
 }
 
-/// Named colors.
-///
-/// See also [`crate::pymolparsing::colors::COLOR_SET`].
-///
-#[derive(Debug, Serialize_repr, Deserialize_repr, PartialEq, Clone)]
-#[repr(i32)]
-pub enum AutoColor {
-    Aquamarine = 5257,
-    Bluewhite = 5278,
-    Brown = 51,
-    Carbon = 26,
-    Cyan = 5,
-    Darksalmon = 5280,
-    Deepblue = 23,
-    Deepsalmon = 5258,
-    Deepteal = 5262,
-    Dirtyviolet = 5272,
-    Forest = 22,
-    Greencyan = 5275,
-    Grey50 = 104,
-    Grey70 = 124,
-    Hotpink = 12,
-    Hydrogen = 29,
-    Lightmagenta = 154,
-    Lightpink = 5274,
-    Lightteal = 5266,
-    Lime = 10,
-    Limegreen = 15,
-    Limon = 5276,
-    Marine = 17,
-    Olive = 18,
-    Orange = 13,
-    Paleyellow = 5256,
-    Raspberry = 5268,
-    Salmon = 9,
-    Sand = 5269,
-    Skyblue = 5277,
-    Slate = 11,
-    Smudge = 5270,
-    Splitpea = 5267,
-    Teal = 20,
-    Violet = 53,
-    Violetpurple = 5271,
-    Warmpink = 5279,
-    Wheat = 52,
-    Yellow = 6,
-    Yelloworange = 36,
-}
-
 /// PyObject
 ///
 /// General Object-Level settings object
@@ -356,12 +313,10 @@ pub struct PyObject {
     pub object_type: ObjectType, // cObject_t
     pub name: String,
     pub color: i32, // represents a pointer into an array of colors.
-    //
     // https://github.com/schrodinger/pymol-open-source/blob/03d7a7fcf0bd95cd93d710a1268dbace2ed77765/layer1/Rep.h
     // https://github.com/schrodinger/pymol-open-source/blob/03d7a7fcf0bd95cd93d710a1268dbace2ed77765/modules/pymol/constants.py#L155-L177
     // https://github.com/schrodinger/pymol-open-source/blob/03d7a7fcf0bd95cd93d710a1268dbace2ed77765/modules/pymol/viewing.py#L51C1-L53C71
-    pub vis_rep: i32, //
-
+    pub vis_rep: RepBitmask, //
     pub extent_min: [f32; 3],
     pub extent_max: [f32; 3],
     pub extent_flag: i32,
@@ -376,7 +331,7 @@ pub struct PyObject {
 impl PyObject {
     /// get_color - note this currently works if there are
     /// no custom colors.
-    pub fn get_color(self) -> Color {
+    pub fn get_color(&self) -> Color {
         COLOR_SET
             .get(self.color as usize)
             .expect("Index within bounds")
@@ -612,30 +567,14 @@ impl<'de> Deserialize<'de> for PymolSessionObjectData {
         D: Deserializer<'de>,
     {
         let value = Value::deserialize(deserializer)?;
-
-        // Debug print
-        // println!("Deserialized value: {:?}", value);
-
-        // Try to deserialize as PyObjectMolecule
         match from_value::<PyObjectMolecule>(value.clone()) {
             Ok(molecule) => return Ok(PymolSessionObjectData::PyObjectMolecule(molecule)),
             Err(_) => {} // If it fails, we'll try the next option
         }
-
-        // println!(
-        //     "Did not serialize as a molecule. Not trying as a session: {:?}",
-        //     value
-        // );
-
-        // If that fails, try to deserialize as SessionSelector
-        match from_value::<SessionSelectorList>(value.clone()) {
-            Ok(selection) => return Ok(PymolSessionObjectData::SessionSelectorList(selection)),
-            Err(_) => {} // If it fails, we'll return an error
+        if let Ok(selection) = from_value::<SessionSelectorList>(value.clone()) {
+            return Ok(PymolSessionObjectData::SessionSelectorList(selection));
         }
-
-        // If both fail, return a generic error
-        // Err(String::from("We are unable to serialize this Value"));
-        Err(panic!("Problem opening the file"))
+        Err(serde::de::Error::custom("Failed to deserialize value"))
     }
 }
 

src/pymolparsing/representation.rs

@@ -47,6 +47,7 @@ pub enum RepType {
 }
 
 bitflags! {
+     #[derive(Debug)]
     pub struct RepBitmask: u32 {
         const CYL             = 1 << 0;
         const SPHERE          = 1 << 1;

tests/test_molview_spec.rs

@@ -206,7 +206,7 @@ fn test_moviewspec_01_common_actions_selectors() {
     };
     // State is the base model
     let mut state = State::new();
-    let mut structure = state
+    let structure = state
         .download("https://files.wwpdb.org/download/1cbs.cif")
         .expect("Create a Download node with a URL")
         .parse(structfile)

tests/test_pse_parsing.rs

@@ -1,5 +1,6 @@
-use pseutils::pymolparsing::colors::Color;
+use pseutils::pymolparsing::colors::{Color, COLOR_SET};
 use pseutils::pymolparsing::parsing::{CustomValue, SettingsEnum};
+use pseutils::pymolparsing::representation::RepBitmask;
 use pseutils::PSEData;
 const TEST_OUTPUT_DIR: &str = "./test_temporary";
 
@@ -30,32 +31,43 @@ fn test_load_pse_data_molecule_selection() {
 #[test]
 fn test_pdb_00() {
     let psedata: PSEData = PSEData::load("tests/data/example.pse").unwrap();
-    let names = psedata.get_session_names();
-    print!("{:?}", names);
     // this has a Molecule and a selection
+    let names = psedata.get_session_names();
     assert_eq!(names.len(), 2);
 
     let mols = psedata.get_molecule_data();
     assert_eq!(mols.len(), 1);
+
     let atom01 = mols[0].get_atom(0);
     assert!(atom01.x() == 50.87300109863281);
     assert!(atom01.y() == 32.97800064086914);
     assert!(atom01.z() == 2.38700008392334);
 
     let chains = mols[0].get_chains();
-    println!("Chains: {:?}", chains);
     let residues = mols[0].get_residues_by_chain(chains[0].clone());
-    println!("Residues: {:?}", residues);
-
     let residue = mols[0].create_residue(chains[0].clone(), residues[0]);
-    println!("Residue: {:?}", residue);
-
     let chain = mols[0].create_chain(chains[0].clone());
-    println!("Chain: {:?}", chain);
 
     // Check symmetry code
     let (unit, sym) = mols[0].get_unit_cell_symmetry();
-    println!("{:?},{:?}", unit, sym);
+
+    // Check the pymol object fields
+    let pyobj = &mols[0].object;
+    let color = &pyobj.get_color();
+    assert_eq!(
+        *color,
+        Color {
+            name: "carbon",
+            r: 0.2,
+            g: 1.0,
+            b: 0.2
+        }
+    );
+
+    let vis_rep = &pyobj.vis_rep;
+    assert!(vis_rep.contains(RepBitmask::CYL));
+    // check the name
+    assert_eq!(&pyobj.name, "1pdb");
 
     // Move on to PDB, baby!
     let pdb = mols[0].to_pdb();
@@ -158,11 +170,10 @@ fn test_colors() {
         [0.0, 1.0, 1.0], // cyan - 999
     ];
 
-    let mut name = String::from("c000");
     for a in 0..1000 {
         let set1 = (a as f32 / A_DIV) as usize;
         // sprintf(color->Name,"c%03d",a);
-        name = format!("c{:03}", a);
+        let name = format!("c{:03}", a);
         let f = 1.0 - (a as f32 - (set1 as f32 * A_DIV)) / A_DIV;
         let r = f * spectrum_c[set1][0] + (1.0 - f) * spectrum_c[set1 + 1][0];
         let g = f * spectrum_c[set1][1] + (1.0 - f) * spectrum_c[set1 + 1][1];
@@ -205,10 +216,9 @@ fn test_colors() {
 
     // complementary spectra separated by white (w000-w999)
 
-    let mut name = String::from("w000");
     for a in 0..1000 {
         let set1 = (a as f32 / W_DIV) as usize;
-        name = format!("w{:03}", a);
+        let name = format!("w{:03}", a);
         let f = 1.0 - (a as f32 - (set1 as f32 * W_DIV)) / W_DIV;
         let r = f * spectrum_w[set1][0] + (1.0 - f) * spectrum_w[set1 + 1][0];
         let g = f * spectrum_w[set1][1] + (1.0 - f) * spectrum_w[set1 + 1][1];