cosmol-viewer 0.1.2.dev2__tar.gz → 0.1.2.dev4__tar.gz

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/Cargo.lock

@@ -4,9 +4,9 @@ version = 4
 
 [[package]]
 name = "ab_glyph"
-version = "0.2.30"
+version = "0.2.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1e0f4f6fbdc5ee39f2ede9f5f3ec79477271a6d6a2baff22310d51736bda6cea"
+checksum = "e074464580a518d16a7126262fffaaa47af89d4099d4cb403f8ed938ba12ee7d"
 dependencies = [
  "ab_glyph_rasterizer",
  "owned_ttf_parser",
@@ -243,7 +243,7 @@ dependencies = [
  "futures-lite",
  "parking",
  "polling",
- "rustix 1.0.7",
+ "rustix 1.0.8",
  "slab",
  "tracing",
  "windows-sys 0.59.0",
@@ -275,7 +275,7 @@ dependencies = [
  "cfg-if",
  "event-listener",
  "futures-lite",
- "rustix 1.0.7",
+ "rustix 1.0.8",
  "tracing",
 ]
 
@@ -302,7 +302,7 @@ dependencies = [
  "cfg-if",
  "futures-core",
  "futures-io",
- "rustix 1.0.7",
+ "rustix 1.0.8",
  "signal-hook-registry",
  "slab",
  "windows-sys 0.59.0",
@@ -558,9 +558,9 @@ dependencies = [
 
 [[package]]
 name = "clipboard-win"
-version = "5.4.0"
+version = "5.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "15efe7a882b08f34e38556b14f2fb3daa98769d06c7f0c1b076dfd0d983bc892"
+checksum = "bde03770d3df201d4fb868f2c9c59e66a3e4e2bd06692a0fe701e7103c7e84d4"
 dependencies = [
  "error-code",
 ]
@@ -647,7 +647,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer"
-version = "0.1.2-nightly.1"
+version = "0.1.2-nightly.4"
 dependencies = [
  "bytemuck",
  "cosmol_viewer_core",
@@ -658,12 +658,11 @@ dependencies = [
  "serde_json",
  "sha2",
  "wasm-bindgen-futures",
- "web-sys",
 ]
 
 [[package]]
 name = "cosmol_viewer_core"
-version = "0.1.2-nightly.1"
+version = "0.1.2-nightly.4"
 dependencies = [
  "bytemuck",
  "eframe",
@@ -675,7 +674,6 @@ dependencies = [
  "serde_json",
  "serde_repr",
  "wasm-bindgen-futures",
- "web-sys",
 ]
 
 [[package]]
@@ -684,22 +682,25 @@ version = "0.0.0"
 dependencies = [
  "base64",
  "cosmol_viewer_core",
+ "cosmol_viewer_wasm",
  "eframe",
  "egui_extras",
  "pyo3",
  "serde_json",
- "uuid",
- "wasm-bindgen",
 ]
 
 [[package]]
 name = "cosmol_viewer_wasm"
-version = "0.1.2-nightly.1"
+version = "0.1.2-nightly.4"
 dependencies = [
+ "base64",
  "cosmol_viewer_core",
  "eframe",
  "log",
+ "pyo3",
+ "serde",
  "serde_json",
+ "uuid",
  "wasm-bindgen",
  "wasm-bindgen-futures",
  "web-sys",
@@ -2256,7 +2257,7 @@ dependencies = [
  "concurrent-queue",
  "hermit-abi",
  "pin-project-lite",
- "rustix 1.0.7",
+ "rustix 1.0.8",
  "tracing",
  "windows-sys 0.59.0",
 ]
@@ -2468,15 +2469,15 @@ dependencies = [
 
 [[package]]
 name = "rustix"
-version = "1.0.7"
+version = "1.0.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c71e83d6afe7ff64890ec6b71d6a69bb8a610ab78ce364b3352876bb4c801266"
+checksum = "11181fbabf243db407ef8df94a6ce0b2f9a733bd8be4ad02b4eda9602296cac8"
 dependencies = [
  "bitflags 2.9.1",
  "errno",
  "libc",
  "linux-raw-sys 0.9.4",
- "windows-sys 0.59.0",
+ "windows-sys 0.60.2",
 ]
 
 [[package]]
@@ -2749,7 +2750,7 @@ dependencies = [
  "fastrand",
  "getrandom",
  "once_cell",
- "rustix 1.0.7",
+ "rustix 1.0.8",
  "windows-sys 0.59.0",
 ]
 
@@ -3915,9 +3916,9 @@ dependencies = [
 
 [[package]]
 name = "zbus"
-version = "5.8.0"
+version = "5.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "597f45e98bc7e6f0988276012797855613cd8269e23b5be62cc4e5d28b7e515d"
+checksum = "4bb4f9a464286d42851d18a605f7193b8febaf5b0919d71c6399b7b26e5b0aad"
 dependencies = [
  "async-broadcast",
  "async-executor",
@@ -3972,9 +3973,9 @@ dependencies = [
 
 [[package]]
 name = "zbus_macros"
-version = "5.8.0"
+version = "5.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e5c8e4e14dcdd9d97a98b189cd1220f30e8394ad271e8c987da84f73693862c2"
+checksum = "ef9859f68ee0c4ee2e8cde84737c78e3f4c54f946f2a38645d0d4c7a95327659"
 dependencies = [
  "proc-macro-crate",
  "proc-macro2",

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/Cargo.toml

@@ -1,6 +1,6 @@
 [workspace.package]
 edition = "2024"
-version = "0.1.2-nightly.1"
+version = "0.1.2-nightly.4"
 authors = ["9028 wjt@cosmol.org"]
 repository = "https://github.com/COSMol-repl/COSMol-viewer"
 homepage = "https://github.com/COSMol-repl/COSMol-viewer"
@@ -13,10 +13,11 @@ resolver = "2"
 members = ["crates/python"]
 
 [workspace.dependencies]
-cosmol_viewer = { version = "0.1.2-nightly.1", path = "cosmol_viewer"}
-cosmol_viewer_core = { version = "0.1.2-nightly.1", path = "crates/core" }
+cosmol_viewer = { version = "0.1.2-nightly.4", path = "cosmol_viewer"}
+cosmol_viewer_core = { version = "0.1.2-nightly.4", path = "crates/core" }
 
 eframe = { version = "0.32.0", features = ["wayland","x11"] }
+pyo3 = { version = "0.25.1", features = ["extension-module", "abi3-py37"] }
 egui-winit = { version = "0.32.0", features = ["wayland","x11"] }
 egui_extras = { version = "0.32.0" }
 serde = { version = "1.0.219" , features = ["derive"] }

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.1.2.dev2
+Version: 0.1.2.dev4
 Summary: Molecular visualization tools
 Author-email: 95028 <wjt@cosmol.org>
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/crates/core/Cargo.toml

@@ -13,7 +13,6 @@ glam = { version = "0.30.3" , features = ["serde"] }
 egui_extras.workspace = true
 serde.workspace = true
 bytemuck = "1.23.1"
-web-sys = "0.3.77"
 serde_repr = "0.1"
 wasm-bindgen-futures = "0.4.50"
 once_cell = "1.21.3"

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/crates/core/src/lib.rs

@@ -67,12 +67,10 @@ impl eframe::App for App {
     }
 }
 
-#[cfg(not(target_arch = "wasm32"))]
 pub struct NativeGuiViewer {
     pub app: Arc<Mutex<Option<App>>>,
 }
 
-#[cfg(not(target_arch = "wasm32"))]
 impl NativeGuiViewer {
     pub fn render(scene: &Scene) -> Self {
         use std::{
@@ -80,17 +78,22 @@ impl NativeGuiViewer {
             thread,
         };
 
+        #[cfg(not(target_arch = "wasm32"))]
         use eframe::{
             NativeOptions,
             egui::{Vec2, ViewportBuilder},
         };
 
+        let viewport_size = scene.viewport.unwrap_or([800, 500]);
+
         let app: Arc<Mutex<Option<App>>> = Arc::new(Mutex::new(None));
         let app_clone = Arc::clone(&app);
 
         let scene = Arc::new(Mutex::new(scene.clone()));
-
+        #[cfg(not(target_arch = "wasm32"))]
         thread::spawn(move || {
+            use std::process;
+
             use eframe::{EventLoopBuilderHook, run_native};
             let event_loop_builder: Option<EventLoopBuilderHook> =
                 Some(Box::new(|event_loop_builder| {
@@ -98,24 +101,21 @@ impl NativeGuiViewer {
                     {
                         use egui_winit::winit::platform::windows::EventLoopBuilderExtWindows;
                         event_loop_builder.with_any_thread(true);
-                        println!("Running on windows")
                     }
                     #[cfg(feature = "wayland")]
                     {
                         use egui_winit::winit::platform::wayland::EventLoopBuilderExtWayland;
                         event_loop_builder.with_any_thread(true);
-                        println!("Running on wayland")
                     }
                     #[cfg(feature = "x11")]
                     {
                         use egui_winit::winit::platform::x11::EventLoopBuilderExtX11;
                         event_loop_builder.with_any_thread(true);
-                        println!("Running on X11")
                     }
                 }));
 
             let native_options = NativeOptions {
-                viewport: ViewportBuilder::default().with_inner_size(Vec2::new(800.0, 500.0)),
+                viewport: ViewportBuilder::default().with_inner_size(Vec2::new(viewport_size [0] as f32, viewport_size[1] as f32)),
                 depth_buffer: 24,
                 event_loop_builder,
                 ..Default::default()
@@ -130,6 +130,7 @@ impl NativeGuiViewer {
                     Ok(Box::new(AppWrapper(app.clone())))
                 }),
             );
+            process::exit(0);
         });
 
         Self { app: app_clone }

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/crates/core/src/scene.rs

@@ -2,8 +2,11 @@ use std::collections::HashMap;
 
 use serde::{Deserialize, Serialize};
 
-use crate::{shader::CameraState, utils::{self, ToMesh}, Shape};
-
+use crate::{
+    Shape,
+    shader::CameraState,
+    utils::{self, ToMesh},
+};
 
 #[derive(Deserialize, Serialize, Clone)]
 pub struct Scene {
@@ -12,6 +15,7 @@ pub struct Scene {
     pub named_shapes: HashMap<String, Shape>,
     pub unnamed_shapes: Vec<Shape>,
     pub scale: f32,
+    pub viewport: Option<[usize; 2]>,
 }
 
 impl Scene {
@@ -30,6 +34,7 @@ impl Scene {
             named_shapes: HashMap::new(),
             unnamed_shapes: Vec::new(),
             scale: 1.0,
+            viewport: None,
         }
     }
 
@@ -46,12 +51,6 @@ impl Scene {
         }
     }
 
-    pub fn delete_shape(&mut self, id: &str) {
-        if self.named_shapes.remove(id).is_none() {
-            panic!("Sphere with ID '{}' not found", id);
-        }
-    }
-
     pub fn update_shape<S: Into<Shape>>(&mut self, id: &str, shape: S) {
         let shape = shape.into();
         if let Some(existing_shape) = self.named_shapes.get_mut(id) {
@@ -60,4 +59,18 @@ impl Scene {
             panic!("Shape with ID '{}' not found", id);
         }
     }
-}
+
+    pub fn delete_shape(&mut self, id: &str) {
+        if self.named_shapes.remove(id).is_none() {
+            panic!("Sphere with ID '{}' not found", id);
+        }
+    }
+
+    pub fn set_viewport(&mut self, width: usize, height: usize) {
+        self.viewport = Some([width, height]);
+    }
+
+    pub fn set_background_color(&mut self, background_color: [f32; 3]) {
+        self.background_color = background_color;
+    }
+}

cosmol_viewer-0.1.2.dev4/crates/core/src/shapes/mod.rs

@@ -0,0 +1,6 @@
+mod sphere;
+pub use sphere::Sphere;
+mod stick;
+pub use stick::Stick;
+mod molecules;
+pub use molecules::Molecules;

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/crates/core/src/shapes/molecules.rs

@@ -64,16 +64,16 @@ impl AtomType {
 
     pub fn radius(&self) -> f32 {
         match self {
-            AtomType::H  => 1.20,
-            AtomType::C  => 1.70,
-            AtomType::N  => 1.55,
-            AtomType::O  => 1.52,
-            AtomType::F  => 1.47,
-            AtomType::P  => 1.80,
-            AtomType::S  => 1.80,
+            AtomType::H => 1.20,
+            AtomType::C => 1.70,
+            AtomType::N => 1.55,
+            AtomType::O => 1.52,
+            AtomType::F => 1.47,
+            AtomType::P => 1.80,
+            AtomType::S => 1.80,
             AtomType::Cl => 1.75,
             AtomType::Br => 1.85,
-            AtomType::I  => 1.98,
+            AtomType::I => 1.98,
             AtomType::Unknown => 1.5,
         }
     }
@@ -163,11 +163,8 @@ impl Molecules {
         }
     }
 
-    pub fn clickable(mut self, val: bool) -> Self {
-        self.interaction.clickable = val;
-        self
-    }
-
+    /// Centers the molecule by translating all atoms so that the geometric center
+    /// is at the origin (0.0, 0.0, 0.0).
     pub fn centered(mut self) -> Self {
         if self.atoms.is_empty() {
             return self;
@@ -207,8 +204,13 @@ impl Molecules {
 
         // 1. 原子 -> Sphere
         for (i, pos) in self.atoms.iter().enumerate() {
-            let radius = self.atom_types.get(i).unwrap_or(&AtomType::Unknown).radius() * 0.2;
-            let color = self.atom_types.get(i).unwrap_or(&AtomType::Unknown).color();
+            let radius = self
+                .atom_types
+                .get(i)
+                .unwrap_or(&AtomType::Unknown)
+                .radius()
+                * 0.2;
+            let color = self.style.color.unwrap_or(self.atom_types.get(i).unwrap_or(&AtomType::Unknown).color());
 
             let mut sphere = Sphere::new(*pos, radius);
             sphere.interaction = self.interaction;
@@ -234,14 +236,14 @@ impl Molecules {
         }
 
         // 2. 键 -> Stick
-        for (i, bond) in self.bonds.iter().enumerate() {
+        for (_i, bond) in self.bonds.iter().enumerate() {
             let [a, b] = *bond;
             let pos_a = self.atoms[a as usize];
             let pos_b = self.atoms[b as usize];
 
-            let mut stick = Stick::new(pos_a, pos_b, 0.1); // or radius by bond type
-            stick.interaction = self.interaction;
-            stick = stick.color([0.7, 0.7, 0.7]);
+            let mut stick = Stick::new(pos_a, pos_b, 0.1);
+            // stick.interaction = self.interaction;
+            stick = stick.color(self.style.color.unwrap_or([0.7, 0.7, 0.7]));
 
             let mesh = stick.to_mesh(1.0);
 
@@ -271,3 +273,9 @@ impl Molecules {
         }
     }
 }
+
+impl VisualShape for Molecules {
+    fn style_mut(&mut self) -> &mut VisualStyle {
+        &mut self.style
+    }
+}

cosmol_viewer-0.1.2.dev4/crates/core/src/shapes/sphere.rs

@@ -0,0 +1,173 @@
+use serde::{Deserialize, Serialize};
+
+use crate::{
+    Shape,
+    scene::Scene,
+    utils::{Interaction, MeshData, VisualShape, VisualStyle},
+};
+
+use once_cell::sync::Lazy;
+use std::collections::HashMap;
+use std::sync::Mutex;
+
+#[derive(Clone)]
+struct SphereMeshTemplate {
+    vertices: Vec<[f32; 3]>,
+    normals: Vec<[f32; 3]>,
+    indices: Vec<u32>,
+}
+
+static SPHERE_TEMPLATE_CACHE: Lazy<Mutex<HashMap<u32, SphereMeshTemplate>>> =
+    Lazy::new(|| Mutex::new(HashMap::new()));
+
+fn get_or_generate_sphere_mesh_template(quality: u32) -> SphereMeshTemplate {
+    let mut cache = SPHERE_TEMPLATE_CACHE.lock().unwrap();
+
+    if let Some(template) = cache.get(&quality) {
+        return template.clone(); // 直接返回已有的
+    }
+
+    let lat_segments = 10 * quality;
+    let lon_segments = 20 * quality;
+
+    let mut vertices = Vec::new();
+    let mut normals = Vec::new();
+    let mut indices = Vec::new();
+
+    for i in 0..=lat_segments {
+        let theta = std::f32::consts::PI * (i as f32) / (lat_segments as f32);
+        let sin_theta = theta.sin();
+        let cos_theta = theta.cos();
+
+        for j in 0..=lon_segments {
+            let phi = 2.0 * std::f32::consts::PI * (j as f32) / (lon_segments as f32);
+            let sin_phi = phi.sin();
+            let cos_phi = phi.cos();
+
+            let nx = sin_theta * cos_phi;
+            let ny = cos_theta;
+            let nz = sin_theta * sin_phi;
+
+            vertices.push([nx, ny, nz]); // 单位球
+            normals.push([nx, ny, nz]);
+        }
+    }
+
+    for i in 0..lat_segments {
+        for j in 0..lon_segments {
+            let first = i * (lon_segments + 1) + j;
+            let second = first + lon_segments + 1;
+
+            indices.push(first);
+            indices.push(first + 1);
+            indices.push(second);
+
+            indices.push(second);
+            indices.push(first + 1);
+            indices.push(second + 1);
+        }
+    }
+
+    let template = SphereMeshTemplate {
+        vertices,
+        normals,
+        indices,
+    };
+
+    cache.insert(quality, template.clone());
+
+    template
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone, Copy)]
+pub struct Sphere {
+    pub center: [f32; 3],
+    pub radius: f32,
+    pub quality: u32,
+
+    pub style: VisualStyle,
+    pub interaction: Interaction,
+}
+
+impl Into<Shape> for Sphere {
+    fn into(self) -> Shape {
+        Shape::Sphere(self)
+    }
+}
+
+impl Sphere {
+    pub fn new(center: [f32; 3], radius: f32) -> Self {
+        Self {
+            center,
+            radius,
+            quality: 2,
+            style: VisualStyle {
+                opacity: 1.0,
+                visible: true,
+                ..Default::default()
+            },
+            interaction: Default::default(),
+        }
+    }
+
+    pub fn set_center(mut self, center: [f32; 3]) -> Self {
+        self.center = center;
+        self
+    }
+
+    pub fn set_radius(mut self, radius: f32) -> Self {
+        self.radius = radius;
+        self
+    }
+
+    // pub fn clickable(mut self, val: bool) -> Self {
+    //     self.interaction.clickable = val;
+    //     self
+    // }
+
+    pub fn to_mesh(&self, scale: f32) -> MeshData {
+        let template = get_or_generate_sphere_mesh_template(self.quality);
+
+        let [cx, cy, cz] = self.center;
+        let r = self.radius;
+
+        let transformed_vertices: Vec<[f32; 3]> = template
+            .vertices
+            .iter()
+            .map(|v| {
+                [
+                    (v[0] * r + cx) * scale,
+                    (v[1] * r + cy) * scale,
+                    (v[2] * r + cz) * scale,
+                ]
+            })
+            .collect();
+
+        let transformed_normals: Vec<[f32; 3]> = template
+            .normals
+            .iter()
+            .map(|n| n.map(|x| x * scale)) // 你可以不乘 scale，如果只用于方向
+            .collect();
+
+        let base_color = self.style.color.unwrap_or([1.0, 1.0, 1.0]);
+        let alpha = self.style.opacity.clamp(0.0, 1.0);
+        let color = [base_color[0], base_color[1], base_color[2], alpha];
+
+        let colors = vec![color; transformed_vertices.len()];
+
+        MeshData {
+            vertices: transformed_vertices,
+            normals: transformed_normals,
+            indices: template.indices.clone(),
+            colors: Some(colors),
+            transform: None,
+            is_wireframe: self.style.wireframe,
+        }
+    }
+}
+
+impl VisualShape for Sphere {
+    fn style_mut(&mut self) -> &mut VisualStyle {
+        &mut self.style
+    }
+}

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/crates/core/src/shapes/stick.rs

@@ -10,11 +10,11 @@ use crate::{
 pub struct Stick {
     pub start: [f32; 3],
     pub end: [f32; 3],
-    pub radius: f32,
+    pub thickness_radius: f32,
     pub quality: u32,
 
     pub style: VisualStyle,
-    pub interaction: Interaction,
+    interaction: Interaction,
 }
 
 impl Into<Shape> for Stick {
@@ -28,7 +28,7 @@ impl Stick {
         Self {
             start,
             end,
-            radius,
+            thickness_radius: radius,
             quality: 6,
             style: VisualStyle {
                 opacity: 1.0,
@@ -39,25 +39,25 @@ impl Stick {
         }
     }
 
-    pub fn radius(mut self, radius: f32) -> Self {
-        self.radius = radius;
+    pub fn set_thickness(mut self, thickness: f32) -> Self {
+        self.thickness_radius = thickness;
         self
     }
 
-    pub fn start(mut self, start: [f32; 3]) -> Self {
+    pub fn set_start(mut self, start: [f32; 3]) -> Self {
         self.start = start;
         self
     }
 
-    pub fn end(mut self, end: [f32; 3]) -> Self {
+    pub fn set_end(mut self, end: [f32; 3]) -> Self {
         self.end = end;
         self
     }
 
-    pub fn clickable(mut self, val: bool) -> Self {
-        self.interaction.clickable = val;
-        self
-    }
+    // fn clickable(mut self, val: bool) -> Self {
+    //     self.interaction.clickable = val;
+    //     self
+    // }
 
     pub fn to_mesh(&self, scale: f32) -> MeshData {
         let mut vertices = Vec::new();
@@ -66,7 +66,7 @@ impl Stick {
         let mut colors = Vec::new();
 
         let segments = 20 * self.quality;
-        let r = self.radius;
+        let r = self.thickness_radius;
 
         let start = glam::Vec3::from_array(self.start);
         let end = glam::Vec3::from_array(self.end);

{cosmol_viewer-0.1.2.dev2 → cosmol_viewer-0.1.2.dev4}/crates/core/src/utils.rs

@@ -1,7 +1,7 @@
 use glam::Mat4;
 use serde::{Deserialize, Serialize};
 
-use crate::shapes::{molecules::Molecules, sphere::Sphere, stick::Stick};
+use crate::shapes::{Molecules, Sphere, Stick};
 
 #[derive(Serialize, Deserialize, Debug, Clone, Default, Copy)]
 pub struct VisualStyle {