cosmol-viewer 0.1.4.dev3__tar.gz → 0.1.5.dev1__tar.gz

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/Cargo.lock

@@ -759,7 +759,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer"
-version = "0.1.4-nightly.3"
+version = "0.1.5-nightly.1"
 dependencies = [
  "bytemuck",
  "cosmol_viewer_core",
@@ -772,7 +772,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer_core"
-version = "0.1.4-nightly.3"
+version = "0.1.5-nightly.1"
 dependencies = [
  "bytemuck",
  "eframe",
@@ -784,7 +784,6 @@ dependencies = [
  "serde",
  "serde_json",
  "serde_repr",
- "wasm-bindgen-futures",
 ]
 
 [[package]]
@@ -802,7 +801,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer_wasm"
-version = "0.1.4-nightly.3"
+version = "0.0.0"
 dependencies = [
  "base64",
  "cosmol_viewer_core",
@@ -923,9 +922,9 @@ checksum = "d8b14ccef22fc6f5a8f4d7d768562a182c04ce9a3b3157b91390b52ddfdf1a76"
 
 [[package]]
 name = "ecolor"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adf31f99fad93fe83c1055b92b5c1b135f1ecfa464789817c372000e768d4bd1"
+checksum = "084980ebede2fb1ad6c4f54285b3e489052ef2b6aa4016e4c19349417adc75c5"
 dependencies = [
  "bytemuck",
  "emath",
@@ -933,9 +932,9 @@ dependencies = [
 
 [[package]]
 name = "eframe"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b829d302a09deb4acde242262a1840ba14fadd0371980ebf713060077a1987bc"
+checksum = "4f60ee3c69cd01d5725b4ef476ed6a3a6009968c57843a2f1beb96f021e4a54b"
 dependencies = [
  "ahash",
  "bytemuck",
@@ -968,9 +967,9 @@ dependencies = [
 
 [[package]]
 name = "egui"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ab9b5d3376c79439f53a78bf7da1e3c0b862ffa3e29f46ab0f3e107430f2e576"
+checksum = "b75645894de4ca1695ab3ab7201c7953bb95c1725aafeefa6822dc901ad2a81b"
 dependencies = [
  "accesskit",
  "ahash",
@@ -986,9 +985,9 @@ dependencies = [
 
 [[package]]
 name = "egui-wgpu"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cef1fe83ba30b3d045814b2d811804f2a7e50a832034c975408f71c20df596e4"
+checksum = "acdaac35a6e0ff458aaa5776b2bda578e38334a9d1258f7795042a70372745b7"
 dependencies = [
  "ahash",
  "bytemuck",
@@ -1006,9 +1005,9 @@ dependencies = [
 
 [[package]]
 name = "egui-winit"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bb4ea8cb063c00d8f23ce11279c01eb63a195a72be0e21d429148246dab7983e"
+checksum = "4772ed5f16fa8ec2ba295e58f62b58ee83fcf49e67ec13d2b7ddf4e9a2dea34e"
 dependencies = [
  "accesskit_winit",
  "arboard",
@@ -1028,9 +1027,9 @@ dependencies = [
 
 [[package]]
 name = "egui_extras"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bdced1964ad8a02a116b1307f7b4f73dbe408c5f53dcdd488f527609f261da60"
+checksum = "550e844e608e356f4ad6843c510aa9bb5838b427e4700ed0056e9746ceeed866"
 dependencies = [
  "ahash",
  "egui",
@@ -1042,9 +1041,9 @@ dependencies = [
 
 [[package]]
 name = "egui_glow"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "668c0d4f726cc33838f0915f6b8c00af0ca0910e975ab58cf34b3e39c614552c"
+checksum = "17b94ff67a1d18933fff2519f5f57c388f932c093036c381fb9ae2853b3e1e09"
 dependencies = [
  "bytemuck",
  "egui",
@@ -1065,9 +1064,9 @@ checksum = "48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719"
 
 [[package]]
 name = "emath"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c615516cdceec867065f20d7db13d8eb8aedd65c9e32cc0c7c379380fa42e6e8"
+checksum = "0e561352ae95c22ad179fb56c38d6e6eecd86cf4925cf5c70e738dd01df9b620"
 dependencies = [
  "bytemuck",
 ]
@@ -1121,9 +1120,9 @@ dependencies = [
 
 [[package]]
 name = "epaint"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9926b9500ccb917adb070207ec722dd8ea78b8321f94a85ebec776f501f2930c"
+checksum = "a909ce8cee63e8350fb0c251ad39277a5b24f19add60787e84a3b3ab3f2bd83a"
 dependencies = [
  "ab_glyph",
  "ahash",
@@ -1139,9 +1138,9 @@ dependencies = [
 
 [[package]]
 name = "epaint_default_fonts"
-version = "0.33.0"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "66054d943c66715c6003a27a3dc152d87cadf714ef2597ccd79f550413009b97"
+checksum = "ad9649446c23368ae138716910e3e28143995691b598fbb9de16b42b0722cbcc"
 
 [[package]]
 name = "equator"
@@ -1859,9 +1858,9 @@ dependencies = [
 
 [[package]]
 name = "js-sys"
-version = "0.3.81"
+version = "0.3.82"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ec48937a97411dcb524a265206ccd4c90bb711fca92b2792c407f268825b9305"
+checksum = "b011eec8cc36da2aab2d5cff675ec18454fad408585853910a202391cf9f8e65"
 dependencies = [
  "once_cell",
  "wasm-bindgen",
@@ -3708,9 +3707,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.104"
+version = "0.2.105"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c1da10c01ae9f1ae40cbfac0bac3b1e724b320abfcf52229f80b547c0d250e2d"
+checksum = "da95793dfc411fbbd93f5be7715b0578ec61fe87cb1a42b12eb625caa5c5ea60"
 dependencies = [
  "cfg-if",
  "once_cell",
@@ -3719,25 +3718,11 @@ dependencies = [
  "wasm-bindgen-shared",
 ]
 
-[[package]]
-name = "wasm-bindgen-backend"
-version = "0.2.104"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "671c9a5a66f49d8a47345ab942e2cb93c7d1d0339065d4f8139c486121b43b19"
-dependencies = [
- "bumpalo",
- "log",
- "proc-macro2",
- "quote",
- "syn",
- "wasm-bindgen-shared",
-]
-
 [[package]]
 name = "wasm-bindgen-futures"
-version = "0.4.54"
+version = "0.4.55"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7e038d41e478cc73bae0ff9b36c60cff1c98b8f38f8d7e8061e79ee63608ac5c"
+checksum = "551f88106c6d5e7ccc7cd9a16f312dd3b5d36ea8b4954304657d5dfba115d4a0"
 dependencies = [
  "cfg-if",
  "js-sys",
@@ -3748,9 +3733,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.104"
+version = "0.2.105"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ca60477e4c59f5f2986c50191cd972e3a50d8a95603bc9434501cf156a9a119"
+checksum = "04264334509e04a7bf8690f2384ef5265f05143a4bff3889ab7a3269adab59c2"
 dependencies = [
  "quote",
  "wasm-bindgen-macro-support",
@@ -3758,22 +3743,22 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.104"
+version = "0.2.105"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9f07d2f20d4da7b26400c9f4a0511e6e0345b040694e8a75bd41d578fa4421d7"
+checksum = "420bc339d9f322e562942d52e115d57e950d12d88983a14c79b86859ee6c7ebc"
 dependencies = [
+ "bumpalo",
  "proc-macro2",
  "quote",
  "syn",
- "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.104"
+version = "0.2.105"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bad67dc8b2a1a6e5448428adec4c3e84c43e561d8c9ee8a9e5aabeb193ec41d1"
+checksum = "76f218a38c84bcb33c25ec7059b07847d465ce0e0a76b995e134a45adcb6af76"
 dependencies = [
  "unicode-ident",
 ]
@@ -3889,9 +3874,9 @@ dependencies = [
 
 [[package]]
 name = "web-sys"
-version = "0.3.81"
+version = "0.3.82"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9367c417a924a74cae129e6a2ae3b47fabb1f8995595ab474029da749a8be120"
+checksum = "3a1f95c0d03a47f4ae1f7a64643a6bb97465d9b740f0fa8f90ea33915c99a9a1"
 dependencies = [
  "js-sys",
  "wasm-bindgen",

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/Cargo.toml

@@ -1,6 +1,6 @@
 [workspace.package]
 edition = "2024"
-version = "0.1.4-nightly.3"
+version = "0.1.5-nightly.1"
 authors = ["9028 wjt@cosmol.org"]
 repository = "https://github.com/COSMol-repl/COSMol-viewer"
 homepage = "https://github.com/COSMol-repl/COSMol-viewer"
@@ -13,13 +13,13 @@ resolver = "2"
 members = ["crates/python"]
 
 [workspace.dependencies]
-cosmol_viewer = { version = "0.1.4-nightly.3", path = "cosmol_viewer"}
-cosmol_viewer_core = { version = "0.1.4-nightly.3", path = "crates/core" }
+cosmol_viewer = { version = "0.1.5-nightly.1", path = "cosmol_viewer"}
+cosmol_viewer_core = { version = "0.1.5-nightly.1", path = "crates/core" }
 
-eframe = { version = "0.33.0", features = ["wayland","x11"] }
 pyo3 = { version = "0.27.1", features = ["extension-module", "abi3-py37"] }
-egui-winit = { version = "0.33.0", features = ["wayland","x11"] }
-egui_extras = { version = "0.33.0" }
+eframe = { version = "0.33.2", features = ["wayland","x11"] }
+egui-winit = { version = "0.33.2", features = ["wayland","x11"] }
+egui_extras = { version = "0.33.2" }
 serde = { version = "1.0.228" , features = ["derive"] }
 serde_json = "1.0.145"
 base64 = "0.22.1"

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.1.4.dev3
+Version: 0.1.5.dev1
 Summary: Molecular visualization tools
 Author-email: 95028 <wjt@cosmol.org>
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/Cargo.toml

@@ -12,9 +12,8 @@ serde_json.workspace = true
 egui_extras.workspace = true
 serde.workspace = true
 glam = { version = "0.30.8" , features = ["serde"] }
-bytemuck = "1.23.2"
+bytemuck = "1.24.0"
 serde_repr = "0.1.20"
-wasm-bindgen-futures = "0.4.54"
 once_cell = "1.21.3"
 image = "0.25.8"
 

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/lib.rs

@@ -1,7 +1,5 @@
 mod shader;
-use std::{
-    sync::{Arc, Mutex},
-};
+use std::sync::{Arc, Mutex};
 
 pub mod parser;
 pub mod utils;
@@ -14,16 +12,16 @@ use eframe::{
 
 use shader::Canvas;
 
-pub use crate::utils::Shape;
+pub use crate::utils::{Logger, RustLogger, Shape};
 pub mod shapes;
 use crate::{scene::Scene, utils::Frames};
 
 pub mod scene;
 use image::{ImageBuffer, Rgba};
 
-pub struct AppWrapper(pub Arc<Mutex<Option<App>>>);
+pub struct AppWrapper<L: Logger>(pub Arc<Mutex<Option<App<L>>>>);
 
-impl eframe::App for AppWrapper {
+impl<L: Logger> eframe::App for AppWrapper<L> {
     fn update(&mut self, ctx: &egui::Context, frame: &mut eframe::Frame) {
         if let Some(app) = &mut *self.0.lock().unwrap() {
             app.update(ctx, frame);
@@ -31,36 +29,41 @@ impl eframe::App for AppWrapper {
     }
 }
 
-pub struct App {
-    canvas: Canvas,
+pub struct App<L: Logger> {
+    canvas: Canvas<L>,
     gl: Option<Arc<eframe::glow::Context>>,
     pub ctx: egui::Context,
     screenshot_requested: bool,
     screenshot_result: Option<(Arc<egui::ColorImage>, egui::TextureHandle)>,
+    logger: L,
 }
 
-impl App {
-    pub fn new(cc: &eframe::CreationContext<'_>, scene: Scene) -> Self {
+impl<L: Logger> App<L> {
+    pub fn new(cc: &eframe::CreationContext<'_>, scene: Scene, logger: L) -> Self {
+        logger.log("Creating new viewer app...");
         let gl = cc.gl.clone();
-        let canvas = Canvas::new(gl.as_ref().unwrap().clone(), scene).unwrap();
+        let canvas = Canvas::new(gl.as_ref().unwrap().clone(), scene, logger).unwrap();
         App {
             gl,
             canvas,
             ctx: cc.egui_ctx.clone(),
             screenshot_requested: false,
             screenshot_result: None,
+            logger,
         }
     }
 
-    pub fn new_play(cc: &eframe::CreationContext<'_>, scene: Frames) -> Self {
+    pub fn new_play(cc: &eframe::CreationContext<'_>, scene: Frames, logger: L) -> Self {
+        logger.log("Creating new viewer app...");
         let gl = cc.gl.clone();
-        let canvas = Canvas::new_play(gl.as_ref().unwrap().clone(), scene).unwrap();
+        let canvas = Canvas::new_play(gl.as_ref().unwrap().clone(), scene, logger).unwrap();
         App {
             gl,
             canvas,
             ctx: cc.egui_ctx.clone(),
             screenshot_requested: false,
             screenshot_result: None,
+            logger,
         }
     }
 
@@ -93,7 +96,7 @@ fn color_image_to_rgba_bytes(image: &egui::ColorImage) -> Vec<u8> {
     image.pixels.iter().flat_map(|c| c.to_array()).collect()
 }
 
-impl eframe::App for App {
+impl<L: Logger> eframe::App for App<L> {
     fn update(&mut self, ctx: &egui::Context, _frame: &mut eframe::Frame) {
         #[cfg(not(target_arch = "wasm32"))]
         egui_extras::install_image_loaders(ctx);
@@ -141,16 +144,16 @@ impl eframe::App for App {
 }
 
 pub struct NativeGuiViewer {
-    pub app: Arc<Mutex<Option<App>>>,
+    pub app: Arc<Mutex<Option<App<RustLogger>>>>,
 }
 
 impl NativeGuiViewer {
     pub fn render(scene: &Scene, width: f32, height: f32) -> Self {
+        use std::time::Duration;
         use std::{
             sync::{Arc, Mutex},
             thread,
         };
-        use std::time::Duration;
 
         #[cfg(not(target_arch = "wasm32"))]
         use eframe::{
@@ -160,14 +163,14 @@ impl NativeGuiViewer {
 
         // let viewport_size = scene.viewport.unwrap_or([800, 500]);
 
-        let app: Arc<Mutex<Option<App>>> = Arc::new(Mutex::new(None));
+        let app: Arc<Mutex<Option<App<RustLogger>>>> = 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};
+            use std::process;
             let event_loop_builder: Option<EventLoopBuilderHook> =
                 Some(Box::new(|event_loop_builder| {
                     #[cfg(target_family = "windows")]
@@ -200,7 +203,7 @@ impl NativeGuiViewer {
                 native_options,
                 Box::new(move |cc| {
                     let mut guard = app_clone.lock().unwrap();
-                    *guard = Some(App::new(cc, scene.lock().unwrap().clone()));
+                    *guard = Some(App::new(cc, scene.lock().unwrap().clone(), RustLogger));
                     Ok(Box::new(AppWrapper(app_clone.clone())))
                 }),
             );
@@ -260,7 +263,14 @@ impl NativeGuiViewer {
         }
     }
 
-    pub fn play(frames: Vec<Scene>, interval: f32, loops: i64, width: f32, height: f32, smooth: bool) {
+    pub fn play(
+        frames: Vec<Scene>,
+        interval: f32,
+        loops: i64,
+        width: f32,
+        height: f32,
+        smooth: bool,
+    ) {
         use std::{
             sync::{Arc, Mutex},
             thread,
@@ -279,7 +289,7 @@ impl NativeGuiViewer {
             egui::{Vec2, ViewportBuilder},
         };
 
-        let app: Arc<Mutex<Option<App>>> = Arc::new(Mutex::new(None));
+        let app: Arc<Mutex<Option<App<RustLogger>>>> = Arc::new(Mutex::new(None));
         let app_clone = Arc::clone(&app);
 
         #[cfg(not(target_arch = "wasm32"))]
@@ -319,14 +329,13 @@ impl NativeGuiViewer {
                 native_options,
                 Box::new(move |cc| {
                     let mut guard = app_clone.lock().unwrap();
-                    *guard = Some(App::new_play(cc, frames));
+                    *guard = Some(App::new_play(cc, frames, RustLogger));
                     Ok(Box::new(AppWrapper(app_clone.clone())))
                 }),
             );
             process::exit(0);
         });
 
-        loop {
-        }
+        loop {}
     }
 }

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/parser/sdf.rs

@@ -1,3 +1,5 @@
+pub use crate::utils::{Logger, RustLogger};
+
 #[derive(Debug, Clone)]
 pub struct Atom {
     pub atom: String,
@@ -24,6 +26,10 @@ pub struct ParserOptions {
 }
 
 pub fn parse_sdf(sdf: &str, options: &ParserOptions) -> MoleculeData {
+    _parse_sdf(sdf, options, RustLogger)
+}
+
+pub fn _parse_sdf(sdf: &str, options: &ParserOptions, logger: impl Logger) -> MoleculeData {
     let lines: Vec<&str> = sdf.lines().collect();
     if lines.len() > 3 && lines[3].len() > 38 {
         let version = lines[3][34..39].trim();

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/scene.rs

@@ -1,9 +1,12 @@
+use crate::utils::Logger;
 use std::collections::HashMap;
 
 use serde::{Deserialize, Serialize};
 
 use crate::{
-    shader::CameraState, utils::{self, InstanceData, Interpolatable, IntoInstanceGroups, ShapeKind, ToMesh}, Shape
+    Shape,
+    shader::CameraState,
+    utils::{self, InstanceData, Interpolatable, IntoInstanceGroups, ShapeKind, ToMesh},
 };
 
 #[derive(Deserialize, Serialize, Clone)]
@@ -71,7 +74,6 @@ impl InstanceGroups {
     }
 }
 
-
 impl Scene {
     pub fn _get_meshes(&self) -> Vec<utils::MeshData> {
         self.named_shapes
@@ -136,13 +138,13 @@ impl Scene {
 }
 
 impl Interpolatable for Scene {
-    fn interpolate(&self, other: &Self, t: f32) -> Self {
+    fn interpolate(&self, other: &Self, t: f32, logger: impl Logger) -> Self {
         let named_shapes = self
             .named_shapes
             .iter()
             .map(|(k, v)| {
                 let other_shape = &other.named_shapes[k];
-                (k.clone(), v.interpolate(other_shape, t))
+                (k.clone(), v.interpolate(other_shape, t, logger))
             })
             .collect();
 
@@ -150,7 +152,7 @@ impl Interpolatable for Scene {
             .unnamed_shapes
             .iter()
             .zip(&other.unnamed_shapes)
-            .map(|(a, b)| a.interpolate(b, t))
+            .map(|(a, b)| a.interpolate(b, t, logger))
             .collect();
 
         Self {

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/shader/canvas.rs

@@ -17,31 +17,38 @@ use crate::scene::StickInstance;
 use crate::shapes::Sphere;
 use crate::shapes::Stick;
 use crate::utils::Frames;
-use crate::utils::Interpolatable;
+use crate::utils::{Interpolatable, Logger};
 
-pub struct Canvas {
+pub struct Canvas<L: Logger> {
     shader: Arc<Mutex<Shader>>,
     camera_state: CameraState,
     frames: Option<Frames>,
     interpolate_enabled: bool,
+    logger: L,
 }
 
-impl Canvas {
-    pub fn new<'a>(gl: Arc<eframe::glow::Context>, scene: Scene) -> Option<Self> {
+impl<L: Logger> Canvas<L> {
+    pub fn new<'a>(gl: Arc<eframe::glow::Context>, scene: Scene, logger: L) -> Option<Self> {
         Some(Self {
             shader: Arc::new(Mutex::new(Shader::new(&gl, scene)?)),
             camera_state: CameraState::new(1.0),
             frames: None,
             interpolate_enabled: false,
+            logger,
         })
     }
 
-    pub fn new_play<'a>(gl: Arc<eframe::glow::Context>, frames: Frames) -> Option<Self> {
+    pub fn new_play<'a>(gl: Arc<eframe::glow::Context>, frames: Frames, logger: L) -> Option<Self> {
+        if frames.frames.is_empty() {
+            logger.error("No frames provided");
+            return None;
+        }
         Some(Self {
             shader: Arc::new(Mutex::new(Shader::new(&gl, frames.frames[0].clone())?)),
             camera_state: CameraState::new(1.0),
             interpolate_enabled: frames.smooth,
             frames: Some(frames),
+            logger,
         })
     }
 
@@ -100,7 +107,11 @@ impl Canvas {
             } else {
                 // 这里是原先的插值 / 非插值逻辑
                 if self.interpolate_enabled {
-                    frames.frames[frame_a_index].interpolate(&frames.frames[frame_b_index], t)
+                    frames.frames[frame_a_index].interpolate(
+                        &frames.frames[frame_b_index],
+                        t,
+                        self.logger,
+                    )
                 } else {
                     frames.frames[frame_a_index].clone()
                 }

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/shapes/molecules.rs

@@ -6,7 +6,9 @@ use crate::{
     parser::sdf::MoleculeData,
     scene::{InstanceGroups, SphereInstance},
     shapes::{sphere::Sphere, stick::Stick},
-    utils::{Interaction, Interpolatable, IntoInstanceGroups, MeshData, VisualShape, VisualStyle},
+    utils::{
+        Interaction, Interpolatable, IntoInstanceGroups, Logger, MeshData, VisualShape, VisualStyle,
+    },
 };
 
 use std::{collections::HashMap, str::FromStr};
@@ -102,7 +104,29 @@ pub struct Molecules {
 }
 
 impl Interpolatable for Molecules {
-    fn interpolate(&self, other: &Self, t: f32) -> Self {
+    fn interpolate(&self, other: &Self, t: f32, logger: impl Logger) -> Self {
+        // 检查原子数量是否匹配
+        if self.atoms.len() != other.atoms.len() {
+            logger.error(format!(
+                "Interpolation aborted: atom count differs (self: {}, other: {}). \
+                Smooth interpolation requires scenes with identical atom structures.",
+                self.atoms.len(),
+                other.atoms.len()
+            ));
+            panic!("Smooth interpolation requires matching atom structures.");
+        }
+
+        // 检查键数量是否匹配（可选，根据需要）
+        if self.bonds.len() != other.bonds.len() {
+            logger.error(format!(
+                "Interpolation aborted: bond topology differs (self: {}, other: {}). \
+                Smooth interpolation cannot proceed with different bonding graphs.",
+                self.bonds.len(),
+                other.bonds.len()
+            ));
+            panic!("Smooth interpolation requires matching bond topology.");
+        }
+
         // 原子坐标插值
         let atoms: Vec<[f32; 3]> = self
             .atoms
@@ -192,11 +216,9 @@ impl Molecules {
         }
     }
 
-    /// 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 {
+    pub fn get_center(&self) -> [f32; 3] {
         if self.atoms.is_empty() {
-            return self;
+            return [0.0; 3];
         }
 
         // 1. 累加所有原子坐标
@@ -213,16 +235,27 @@ impl Molecules {
         center[1] /= count;
         center[2] /= count;
 
-        // 3. 所有原子坐标减去中心
-        for pos in &mut self.atoms {
-            pos[0] -= center[0];
-            pos[1] -= center[1];
-            pos[2] -= center[2];
+        center
+    }
+
+    /// 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 {
+        let center = self.get_center();
+        for atom in &mut self.atoms {
+            atom[0] -= center[0];
+            atom[1] -= center[1];
+            atom[2] -= center[2];
         }
 
         self
     }
 
+    pub fn reset_color(mut self) -> Self {
+        self.style_mut().color = None;
+        self
+    }
+
     pub fn to_mesh(&self, scale: f32) -> MeshData {
         return MeshData::default();
 
@@ -480,22 +513,26 @@ impl IntoInstanceGroups for Molecules {
             let d = 0.22;
 
             // 颜色和半径与原来一致
-            let color_a = match self
-                .atom_types
-                .get(a as usize)
-                .unwrap_or(&AtomType::Unknown)
-            {
-                AtomType::C => [0.75, 0.75, 0.75],
-                other => other.color(),
-            };
-            let color_b = match self
-                .atom_types
-                .get(b as usize)
-                .unwrap_or(&AtomType::Unknown)
-            {
-                AtomType::C => [0.75, 0.75, 0.75],
-                other => other.color(),
-            };
+            let color_a = self.style.color.unwrap_or(
+                match self
+                    .atom_types
+                    .get(a as usize)
+                    .unwrap_or(&AtomType::Unknown)
+                {
+                    AtomType::C => [0.75, 0.75, 0.75],
+                    other => other.color(),
+                },
+            );
+            let color_b = self.style.color.unwrap_or(
+                match self
+                    .atom_types
+                    .get(b as usize)
+                    .unwrap_or(&AtomType::Unknown)
+                {
+                    AtomType::C => [0.75, 0.75, 0.75],
+                    other => other.color(),
+                },
+            );
 
             // 根据键类型生成多个 stick
             let (num_sticks, radius) = match bond_type {

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/shapes/sphere.rs

@@ -3,7 +3,9 @@ use serde::{Deserialize, Serialize};
 use crate::{
     Shape,
     scene::{Instance, InstanceGroups, Scene, SphereInstance},
-    utils::{Interaction, Interpolatable, IntoInstanceGroups, MeshData, VisualShape, VisualStyle},
+    utils::{
+        Interaction, Interpolatable, IntoInstanceGroups, Logger, MeshData, VisualShape, VisualStyle,
+    },
 };
 
 use once_cell::sync::Lazy;
@@ -31,7 +33,7 @@ pub struct Sphere {
 }
 
 impl Interpolatable for Sphere {
-    fn interpolate(&self, other: &Self, t: f32) -> Self {
+    fn interpolate(&self, other: &Self, t: f32, logger: impl Logger) -> Self {
         Self {
             center: [
                 self.center[0] * (1.0 - t) + other.center[0] * t,

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/shapes/stick.rs

@@ -7,7 +7,7 @@ use crate::{
     Shape,
     scene::{Scene, StickInstance},
     shapes::sphere::MeshTemplate,
-    utils::{Interaction, Interpolatable, MeshData, VisualShape, VisualStyle},
+    utils::{Interaction, Interpolatable, Logger, MeshData, VisualShape, VisualStyle},
 };
 
 static STICK_TEMPLATE_CACHE: Lazy<Mutex<HashMap<u32, MeshTemplate>>> =
@@ -25,7 +25,7 @@ pub struct Stick {
 }
 
 impl Interpolatable for Stick {
-    fn interpolate(&self, other: &Self, t: f32) -> Self {
+    fn interpolate(&self, other: &Self, t: f32, logger: impl Logger) -> Self {
         Self {
             start: [
                 self.start[0] * (1.0 - t) + other.start[0] * t,

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/core/src/utils.rs

@@ -6,6 +6,27 @@ use crate::{
     shapes::{Molecules, Sphere, Stick},
 };
 
+pub trait Logger: Send + Sync + Copy {
+    fn log(&self, message: impl std::fmt::Display);
+    fn error(&self, message: impl std::fmt::Display);
+    fn warn(&self, message: impl std::fmt::Display);
+}
+
+#[derive(Clone, Copy)]
+pub struct RustLogger;
+
+impl Logger for RustLogger {
+    fn log(&self, message: impl std::fmt::Display) {
+        println!("[LOG] {}", message);
+    }
+    fn warn(&self, message: impl std::fmt::Display) {
+        eprintln!("[WARN] {}", message);
+    }
+    fn error(&self, message: impl std::fmt::Display) {
+        eprintln!("[ERROR] {}", message);
+    }
+}
+
 #[derive(Serialize, Deserialize, Debug, Clone, Default, Copy)]
 pub struct VisualStyle {
     pub color: Option<[f32; 3]>,
@@ -25,7 +46,7 @@ pub struct Interaction {
 
 pub trait Interpolatable {
     /// t ∈ [0.0, 1.0]，返回两个实例之间的插值
-    fn interpolate(&self, other: &Self, t: f32) -> Self;
+    fn interpolate(&self, other: &Self, t: f32, logger: impl Logger) -> Self;
 }
 
 // -------------------- 图元结构体 --------------------------
@@ -53,11 +74,13 @@ pub struct InstanceData {
 }
 
 impl Interpolatable for Shape {
-    fn interpolate(&self, other: &Self, t: f32) -> Self {
+    fn interpolate(&self, other: &Self, t: f32, logger: impl Logger) -> Self {
         match (self, other) {
-            (Shape::Sphere(a), Shape::Sphere(b)) => Shape::Sphere(a.interpolate(b, t)),
-            (Shape::Stick(a), Shape::Stick(b)) => Shape::Stick(a.interpolate(b, t)),
-            (Shape::Molecules(a), Shape::Molecules(b)) => Shape::Molecules(a.interpolate(b, t)),
+            (Shape::Sphere(a), Shape::Sphere(b)) => Shape::Sphere(a.interpolate(b, t, logger)),
+            (Shape::Stick(a), Shape::Stick(b)) => Shape::Stick(a.interpolate(b, t, logger)),
+            (Shape::Molecules(a), Shape::Molecules(b)) => {
+                Shape::Molecules(a.interpolate(b, t, logger))
+            }
             _ => self.clone(), // 如果类型不匹配，可以选择不插值或做默认处理
         }
     }
@@ -75,7 +98,7 @@ impl IntoInstanceGroups for Shape {
                 let m_groups = m.to_instance_group(scale);
                 groups.merge(m_groups);
             }
-            _ => {},
+            _ => {}
         }
         groups
     }

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/python/cosmol_viewer.pyi

@@ -1,4 +1,4 @@
-from typing import Optional, Union, List 
+from typing import Optional, Union, List
 
 def parse_sdf(
     sdf: str,
@@ -201,7 +201,7 @@ class Viewer:
           - loops: Number of loops to repeat (-1 for infinite).
           - width: The viewport width in pixels.
           - height: The viewport height in pixels.
-          - smooth: Whether to smooth the animation by 
+          - smooth: Whether to smooth the animation by
             interpolating between frames.
 
         # Returns
@@ -306,10 +306,12 @@ class Molecules:
     """
 
     def __init__(self, molecule_data: "MoleculeData") -> None: ...
+    def get_center(self) -> List[float]: ...
     def centered(self) -> "Molecules": ...
     def color(self, color: List[float]) -> "Molecules": ...
     def color_rgba(self, color: List[float]) -> "Molecules": ...
     def opacity(self, opacity: float) -> "Molecules": ...
+    def reset_color(self) -> "Molecules": ...
 
 class MoleculeData:
     """

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/python/src/shapes.rs

@@ -7,13 +7,13 @@ use pyo3::{PyRefMut, pyclass, pymethods};
 
 #[pyclass(name = "Sphere")]
 /// Sphere(center: [f32; 3], radius: f32)
-/// 
+///
 /// A sphere in the scene.
-/// 
+///
 /// # Arguments
 /// * `center` - The center of the sphere.
 /// * `radius` - The radius of the sphere.
-/// 
+///
 /// # Examples
 /// ```
 /// scene = Scene()
@@ -21,7 +21,7 @@ use pyo3::{PyRefMut, pyclass, pymethods};
 /// scene.add_shape(sphere, id)
 /// viewer = Viewer.render(scene)
 /// ```
-/// 
+///
 #[derive(Clone)]
 pub struct PySphere {
     pub inner: Sphere,
@@ -123,6 +123,10 @@ impl PyMolecules {
         }
     }
 
+    pub fn get_center(slf: PyRefMut<'_, Self>) -> [f32; 3] {
+        slf.inner.clone().get_center()
+    }
+
     pub fn centered(mut slf: PyRefMut<'_, Self>) -> PyRefMut<'_, Self> {
         slf.inner = slf.inner.clone().centered();
         slf
@@ -138,7 +142,6 @@ impl PyMolecules {
         slf
     }
 
-
     pub fn opacity(mut slf: PyRefMut<'_, Self>, opacity: f32) -> PyRefMut<'_, Self> {
         slf.inner = slf.inner.clone().opacity(opacity);
         slf

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/wasm/Cargo.toml

@@ -1,7 +1,6 @@
 [package]
 name = "cosmol_viewer_wasm"
-version.workspace = true
-edition = "2024"
+edition.workspace = true
 publish = false
 
 [dependencies]
@@ -12,9 +11,9 @@ log = "0.4.28"
 
 uuid = { version = "1.18.1", features = ["v4"], optional = true }
 eframe = { workspace = true, optional = true }
-wasm-bindgen-futures = { version = "0.4.54", optional = true }
-web-sys = { version = "0.3.81", features = ["HtmlCanvasElement"], optional = true }
-wasm-bindgen = { version = "0.2.104", optional = true }
+wasm-bindgen-futures = { version = "0.4.55", optional = true }
+web-sys = { version = "0.3.82", features = ["HtmlCanvasElement", "console","Window"], optional = true }
+wasm-bindgen = { version = "0.2.105", optional = true }
 gloo-timers = { version = "0.3.0", features = ["futures-core", "futures"], optional = true }
 pyo3 = { workspace = true, optional = true }
 base64 = { workspace = true, optional = true }

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/crates/wasm/src/lib.rs

@@ -1,6 +1,6 @@
 use cosmol_viewer_core::App;
 use cosmol_viewer_core::scene::Scene;
-use cosmol_viewer_core::utils::Frames;
+use cosmol_viewer_core::utils::{Frames, Logger};
 #[cfg(feature = "js_bridge")]
 use serde::Serialize;
 use std::sync::Arc;
@@ -292,11 +292,38 @@ impl WebRunner {
     }
 }
 
+#[cfg(feature = "wasm")]
+#[derive(Clone, Copy)]
+pub struct WasmLogger;
+
+#[cfg(feature = "wasm")]
+impl Logger for WasmLogger {
+    fn log(&self, message: impl std::fmt::Display) {
+        web_sys::console::log_1(&JsValue::from_str(&message.to_string()));
+    }
+
+    fn warn(&self, message: impl std::fmt::Display) {
+        web_sys::console::warn_1(&JsValue::from_str(&message.to_string()));
+    }
+
+    fn error(&self, message: impl std::fmt::Display) {
+        let msg = message.to_string();
+
+        // Send to console
+        web_sys::console::error_1(&JsValue::from_str(&msg));
+
+        // Show browser alert
+        if let Some(window) = web_sys::window() {
+            window.alert_with_message(&msg).ok();
+        }
+    }
+}
+
 #[cfg(feature = "wasm")]
 #[wasm_bindgen]
 pub struct WebHandle {
     runner: WebRunner,
-    app: Arc<Mutex<Option<App>>>,
+    app: Arc<Mutex<Option<App<WasmLogger>>>>,
 }
 
 #[cfg(feature = "wasm")]
@@ -337,7 +364,7 @@ impl WebHandle {
                     use cosmol_viewer_core::AppWrapper;
 
                     let mut guard = app.lock().unwrap();
-                    *guard = Some(App::new(cc, scene));
+                    *guard = Some(App::new(cc, scene, WasmLogger));
                     Ok(Box::new(AppWrapper(app.clone())))
                 }),
             )
@@ -384,7 +411,7 @@ impl WebHandle {
                     use cosmol_viewer_core::AppWrapper;
 
                     let mut guard = app.lock().unwrap();
-                    *guard = Some(App::new_play(cc, frames));
+                    *guard = Some(App::new_play(cc, frames, WasmLogger));
                     Ok(Box::new(AppWrapper(app.clone())))
                 }),
             )

{cosmol_viewer-0.1.4.dev3 → cosmol_viewer-0.1.5.dev1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cosmol-viewer"
-version = "0.1.4.dev3"
+version = "0.1.5.dev1"
 description = "Molecular visualization tools"
 authors = [{name = "95028", email = "wjt@cosmol.org"}]
 readme = "README.md"