cosmol-viewer 0.1.1.dev3__tar.gz → 0.1.1.dev4__tar.gz

{cosmol_viewer-0.1.1.dev3 → cosmol_viewer-0.1.1.dev4}/Cargo.lock

@@ -699,7 +699,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer"
-version = "0.1.1-nightly.3"
+version = "0.1.1-nightly.4"
 dependencies = [
  "bytemuck",
  "cosmol_viewer_core",
@@ -717,7 +717,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer_core"
-version = "0.1.1-nightly.3"
+version = "0.1.1-nightly.4"
 dependencies = [
  "bytemuck",
  "eframe",
@@ -731,7 +731,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer_gui"
-version = "0.1.1-nightly.3"
+version = "0.1.1-nightly.4"
 dependencies = [
  "bytemuck",
  "cosmol_viewer_core",
@@ -765,7 +765,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer_wasm"
-version = "0.1.1-nightly.3"
+version = "0.1.1-nightly.4"
 dependencies = [
  "cosmol_viewer_core",
  "eframe",
@@ -3160,7 +3160,7 @@ dependencies = [
 
 [[package]]
 name = "test"
-version = "0.1.1-nightly.3"
+version = "0.1.1-nightly.4"
 dependencies = [
  "cosmol_viewer",
  "cosmol_viewer_core",

{cosmol_viewer-0.1.1.dev3 → cosmol_viewer-0.1.1.dev4}/Cargo.toml

@@ -1,6 +1,6 @@
 [workspace.package]
 edition = "2024"
-version = "0.1.1-nightly.3"
+version = "0.1.1-nightly.4"
 authors = ["9028 wjt@cosmol.org"]
 repository = "https://github.com/COSMol-repl/COSMol-viewer"
 homepage = "https://github.com/COSMol-repl/COSMol-viewer"

cosmol_viewer-0.1.1.dev4/PKG-INFO

@@ -0,0 +1,58 @@
+Metadata-Version: 2.4
+Name: cosmol-viewer
+Version: 0.1.1.dev4
+Summary: Molecular visualization tools
+Author-email: 95028 <wjt@cosmol.org>
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# COSMol-viewer
+
+A high-performance molecular visualization library built with Rust and WebGPU, designed for seamless integration into Python workflows.
+
+- ⚡ Fast: Native-speed rendering powered by Rust and GPU acceleration
+
+- 🧬 Flexible: Load molecules from .sdf, .pdb, and dynamically update 3D structures
+
+- 📓 Notebook-friendly: Fully supports Jupyter and Google Colab — ideal for education, research, and live demos
+
+- 🔁 Real-time updates: Update molecular coordinates on-the-fly for simulations or animations
+
+- 🎨 Customizable: Control styles, camera, and rendering settings programmatically
+
+# Installation
+
+install with
+```sh
+pip install cosmol-viewer==0.1.1.dev4
+```
+
+# Usage
+
+python:
+```python
+from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
+
+# === Step 1: Load and render a molecule ===
+with open("molecule.sdf", "r") as f:
+    sdf = f.read()
+    mol = Molecules(parse_sdf(sdf)).centered()
+
+scene = Scene.create_viewer()
+scene.scale(0.1)
+scene.add_shape(mol, "mol")
+
+viewer = Viewer.render(scene)  # Launch the viewer
+
+# === Step 2: Update the same molecule dynamically ===
+import time
+
+for i in range(1, 10):  # Simulate multiple frames
+    with open(f"frames/frame_{i}.sdf", "r") as f:
+        sdf = f.read()
+        updated_mol = Molecules(parse_sdf(sdf)).centered()
+
+    scene.update_shape("mol", updated_mol)
+    viewer.update(scene)
+
+    time.sleep(0.033)  # ~30 FPS
+```

{cosmol_viewer-0.1.1.dev3 → cosmol_viewer-0.1.1.dev4}/crates/core/src/shader/canvas.rs

@@ -39,7 +39,6 @@ impl Canvas {
         // 正值表示向上滚动，通常是“缩小”，负值是放大
         if scroll_delta != 0.0 {
             self.camera_state.scale *= (1.0 + scroll_delta * 0.001).clamp(0.1, 10.0);
-            println!("scale {:?}", self.camera_state.scale);
         }
 
         self.camera_state = rotate_camera(self.camera_state, response.drag_motion());
@@ -289,15 +288,13 @@ impl Shader {
         for mesh in scene_data._get_meshes() {
             self.vertex3d
                 .extend(mesh.vertices.iter().enumerate().map(|(i, pos)| {
-                    let mut j = i;
-                    j = i % 50;
                     Vertex3d {
                         position: *pos,
                         normal: mesh.normals[i],
                         color: mesh
                             .colors
                             .as_ref()
-                            .and_then(|colors| colors.get(j))
+                            .and_then(|colors| colors.get(i))
                             .unwrap_or(&[1.0, 1.0, 1.0, 1.0])
                             .clone(),
                     }
@@ -524,7 +521,7 @@ pub fn rotate_camera(mut camera_state: CameraState, drag_motion: Vec2) -> Camera
 pub struct Vertex3d {
     pub position: [f32; 3],
     pub normal: [f32; 3],
-    pub color: [f32; 4], // 可选颜色属性
+    pub color: [f32; 4],
 }
 
 #[repr(C)]

{cosmol_viewer-0.1.1.dev3 → cosmol_viewer-0.1.1.dev4}/crates/core/src/shapes/molecules.rs

@@ -210,10 +210,7 @@ impl Molecules {
             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();
 
-            println!("atom: {}, color: {:?}, radius: {}", i, color, radius);
-
             let mut sphere = Sphere::new(*pos, radius);
-            sphere.style = self.style; // 继承样式
             sphere.interaction = self.interaction;
             sphere = sphere.color(color);
 
@@ -226,7 +223,7 @@ impl Molecules {
             for n in mesh.normals {
                 normals.push(n.map(|x| x * scale));
             }
-            for c in mesh.colors.unwrap_or_default() {
+            for c in mesh.colors.unwrap() {
                 colors.push(c);
             }
             for idx in mesh.indices {
@@ -243,8 +240,8 @@ impl Molecules {
             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.style = self.style;
             stick.interaction = self.interaction;
+            stick = stick.color([0.5, 0.5, 0.5]);
 
             let mesh = stick.to_mesh(1.0);
 
@@ -254,7 +251,7 @@ impl Molecules {
             for n in mesh.normals {
                 normals.push(n.map(|x| x * scale));
             }
-            for c in mesh.colors.unwrap_or_default() {
+            for c in mesh.colors.unwrap() {
                 colors.push(c);
             }
             for idx in mesh.indices {

cosmol_viewer-0.1.1.dev4/crates/python/README.md

@@ -0,0 +1,51 @@
+# COSMol-viewer
+
+A high-performance molecular visualization library built with Rust and WebGPU, designed for seamless integration into Python workflows.
+
+- ⚡ Fast: Native-speed rendering powered by Rust and GPU acceleration
+
+- 🧬 Flexible: Load molecules from .sdf, .pdb, and dynamically update 3D structures
+
+- 📓 Notebook-friendly: Fully supports Jupyter and Google Colab — ideal for education, research, and live demos
+
+- 🔁 Real-time updates: Update molecular coordinates on-the-fly for simulations or animations
+
+- 🎨 Customizable: Control styles, camera, and rendering settings programmatically
+
+# Installation
+
+install with
+```sh
+pip install cosmol-viewer==0.1.1.dev4
+```
+
+# Usage
+
+python:
+```python
+from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
+
+# === Step 1: Load and render a molecule ===
+with open("molecule.sdf", "r") as f:
+    sdf = f.read()
+    mol = Molecules(parse_sdf(sdf)).centered()
+
+scene = Scene.create_viewer()
+scene.scale(0.1)
+scene.add_shape(mol, "mol")
+
+viewer = Viewer.render(scene)  # Launch the viewer
+
+# === Step 2: Update the same molecule dynamically ===
+import time
+
+for i in range(1, 10):  # Simulate multiple frames
+    with open(f"frames/frame_{i}.sdf", "r") as f:
+        sdf = f.read()
+        updated_mol = Molecules(parse_sdf(sdf)).centered()
+
+    scene.update_shape("mol", updated_mol)
+    viewer.update(scene)
+
+    time.sleep(0.033)  # ~30 FPS
+```

{cosmol_viewer-0.1.1.dev3 → cosmol_viewer-0.1.1.dev4}/crates/python/src/lib.rs

@@ -138,8 +138,6 @@ impl Viewer {
 
     #[staticmethod]
     pub fn render(scene: &Scene, py: Python) -> Self {
-        println!("scene {}", serde_json::to_string(&scene.inner).unwrap());
-
         let env_type = detect_runtime_env(py).unwrap();
         match env_type {
             RuntimeEnv::Colab | RuntimeEnv::Jupyter => {

{cosmol_viewer-0.1.1.dev3 → cosmol_viewer-0.1.1.dev4}/pyproject.toml

@@ -1,8 +1,9 @@
 [project]
 name = "cosmol-viewer"
-version = "0.1.1.dev3"
+version = "0.1.1.dev4"
 description = "Molecular visualization tools"
 authors = [{name = "95028", email = "wjt@cosmol.org"}]
+repository = "https://github.com/COSMol-repl/COSMol-viewer"
 
 [build-system]
 requires = ["maturin>=1.0,<2.0"]

cosmol_viewer-0.1.1.dev3/PKG-INFO

@@ -1,5 +0,0 @@
-Metadata-Version: 2.4
-Name: cosmol-viewer
-Version: 0.1.1.dev3
-Summary: Molecular visualization tools
-Author-email: 95028 <wjt@cosmol.org>