cosmol-viewer 0.1.1.dev2__tar.gz → 0.1.1.dev4__tar.gz

{cosmol_viewer-0.1.1.dev2 → cosmol_viewer-0.1.1.dev4}/Cargo.lock

@@ -699,7 +699,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer"
-version = "0.1.1-nightly.2"
+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.2"
+version = "0.1.1-nightly.4"
 dependencies = [
  "bytemuck",
  "eframe",
@@ -731,7 +731,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer_gui"
-version = "0.1.1-nightly.2"
+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.2"
+version = "0.1.1-nightly.4"
 dependencies = [
  "cosmol_viewer_core",
  "eframe",
@@ -3160,7 +3160,7 @@ dependencies = [
 
 [[package]]
 name = "test"
-version = "0.1.1-nightly.2"
+version = "0.1.1-nightly.4"
 dependencies = [
  "cosmol_viewer",
  "cosmol_viewer_core",

{cosmol_viewer-0.1.1.dev2 → cosmol_viewer-0.1.1.dev4}/Cargo.toml

@@ -1,6 +1,6 @@
 [workspace.package]
 edition = "2024"
-version = "0.1.1-nightly.2"
+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.dev2 → cosmol_viewer-0.1.1.dev4}/crates/core/src/parser/sdf.rs

@@ -14,7 +14,7 @@ pub struct Atom {
 }
 
 pub type Molecule = Vec<Atom>;
-pub type MoleculeData  = Vec<Molecule>;
+pub type MoleculeData = Vec<Molecule>;
 
 #[derive(Default)]
 pub struct ParserOptions {
@@ -23,7 +23,7 @@ pub struct ParserOptions {
     pub onemol: bool,
 }
 
-pub fn parse_sdf(sdf: &str, options: &ParserOptions) -> MoleculeData  {
+pub fn parse_sdf(sdf: &str, options: &ParserOptions) -> MoleculeData {
     let lines: Vec<&str> = sdf.lines().collect();
     if lines.len() > 3 && lines[3].len() > 38 {
         let version = lines[3][34..39].trim();
@@ -36,7 +36,22 @@ pub fn parse_sdf(sdf: &str, options: &ParserOptions) -> MoleculeData  {
     }
 }
 
-fn parse_v2000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData  {
+fn parse_v2000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData {
+    let model_count = count_models(&lines);
+    // 多个分子但用户没开启
+    if model_count > 0 && !options.multimodel {
+        panic!(
+            "Found multiple molecules but 'multimodel' is false. Please enable 'multimodel = true' to parse all molecules."
+        );
+    }
+
+    // 用户开启了但其实只有一个
+    if model_count == 0 && options.multimodel {
+        panic!(
+            "Only one molecule found, but 'multimodel = true' was set. Consider setting 'multimodel = false' to avoid confusion."
+        );
+    }
+
     let mut molecules = vec![vec![]];
     let mut current = 0;
 
@@ -80,10 +95,21 @@ fn parse_v2000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData  {
 
         for i in 0..bond_count {
             let line = lines[offset + i];
-            let from = line[0..3].trim().parse::<usize>().unwrap_or(0).saturating_sub(1);
-            let to = line[3..6].trim().parse::<usize>().unwrap_or(0).saturating_sub(1);
+            let from = line[0..3]
+                .trim()
+                .parse::<usize>()
+                .unwrap_or(0)
+                .saturating_sub(1);
+            let to = line[3..6]
+                .trim()
+                .parse::<usize>()
+                .unwrap_or(0)
+                .saturating_sub(1);
             let order = line[6..].trim().parse::<f32>().unwrap_or(1.0);
-            if let (Some(f), Some(t)) = (serial_to_index.get(from).and_then(|x| *x), serial_to_index.get(to).and_then(|x| *x)) {
+            if let (Some(f), Some(t)) = (
+                serial_to_index.get(from).and_then(|x| *x),
+                serial_to_index.get(to).and_then(|x| *x),
+            ) {
                 molecules[current][f].bonds.push(t);
                 molecules[current][f].bond_order.push(order);
                 molecules[current][t].bonds.push(f);
@@ -109,7 +135,23 @@ fn parse_v2000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData  {
     molecules
 }
 
-fn parse_v3000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData  {
+fn parse_v3000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData {
+    let model_count = count_models(&lines);
+
+    // 多个分子但用户没开启
+    if model_count > 0 && !options.multimodel {
+        panic!(
+            "Found multiple molecules but 'multimodel' is false. Please enable 'multimodel = true' to parse all molecules."
+        );
+    }
+
+    // 用户开启了但其实只有一个
+    if model_count == 0 && options.multimodel {
+        panic!(
+            "Only one molecule found, but 'multimodel = true' was set. Consider setting 'multimodel = false' to avoid confusion."
+        );
+    }
+
     let mut molecules = vec![vec![]];
     let mut current = 0;
 
@@ -119,8 +161,14 @@ fn parse_v3000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData  {
         }
 
         let counts: Vec<_> = lines[5][13..].split_whitespace().collect();
-        let atom_count = counts.get(0).and_then(|s| s.parse::<usize>().ok()).unwrap_or(0);
-        let bond_count = counts.get(1).and_then(|s| s.parse::<usize>().ok()).unwrap_or(0);
+        let atom_count = counts
+            .get(0)
+            .and_then(|s| s.parse::<usize>().ok())
+            .unwrap_or(0);
+        let bond_count = counts
+            .get(1)
+            .and_then(|s| s.parse::<usize>().ok())
+            .unwrap_or(0);
         let mut offset = 7;
 
         let mut serial_to_index = vec![None; atom_count];
@@ -161,7 +209,10 @@ fn parse_v3000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData  {
                 let from = parts[2].parse::<usize>().unwrap_or(0).saturating_sub(1);
                 let to = parts[3].parse::<usize>().unwrap_or(0).saturating_sub(1);
                 let order = parts[1].parse::<f32>().unwrap_or(1.0);
-                if let (Some(f), Some(t)) = (serial_to_index.get(from).and_then(|x| *x), serial_to_index.get(to).and_then(|x| *x)) {
+                if let (Some(f), Some(t)) = (
+                    serial_to_index.get(from).and_then(|x| *x),
+                    serial_to_index.get(to).and_then(|x| *x),
+                ) {
                     molecules[current][f].bonds.push(t);
                     molecules[current][f].bond_order.push(order);
                     molecules[current][t].bonds.push(f);
@@ -191,7 +242,13 @@ fn parse_v3000(mut lines: Vec<&str>, options: &ParserOptions) -> MoleculeData  {
 fn capitalize(s: &str) -> String {
     let mut chars = s.chars();
     match chars.next() {
-        Some(first) => first.to_ascii_uppercase().to_string() + &chars.as_str().to_ascii_lowercase(),
+        Some(first) => {
+            first.to_ascii_uppercase().to_string() + &chars.as_str().to_ascii_lowercase()
+        }
         None => String::new(),
     }
 }
+
+fn count_models(lines: &[&str]) -> usize {
+    lines.iter().filter(|line| line.trim() == "$$$$").count()
+}

{cosmol_viewer-0.1.1.dev2 → 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.dev2 → 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.dev2 → 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.dev2 → cosmol_viewer-0.1.1.dev4}/crates/python/src/shapes.rs

@@ -94,4 +94,9 @@ impl PyMolecules {
             inner: Molecules::new(molecule_data.inner.clone())
         }
     }
+
+    pub fn centered(mut slf: PyRefMut<'_, Self>) -> PyRefMut<'_, Self> {
+        slf.inner = slf.inner.clone().centered();
+        slf
+    }
 }

{cosmol_viewer-0.1.1.dev2 → cosmol_viewer-0.1.1.dev4}/pyproject.toml

@@ -1,8 +1,9 @@
 [project]
 name = "cosmol-viewer"
-version = "0.1.1.dev2"
+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.dev2/PKG-INFO

@@ -1,5 +0,0 @@
-Metadata-Version: 2.4
-Name: cosmol-viewer
-Version: 0.1.1.dev2
-Summary: Molecular visualization tools
-Author-email: 95028 <wjt@cosmol.org>