cosmol-viewer 0.1.0__tar.gz → 0.1.1__tar.gz

{cosmol_viewer-0.1.0 → cosmol_viewer-0.1.1}/Cargo.lock

@@ -431,6 +431,15 @@ version = "0.22.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
 
+[[package]]
+name = "bincode"
+version = "1.3.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad"
+dependencies = [
+ "serde",
+]
+
 [[package]]
 name = "bit-set"
 version = "0.8.0"
@@ -688,40 +697,78 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "cosmol_viewer"
+version = "0.1.1"
+dependencies = [
+ "bytemuck",
+ "cosmol_viewer_core",
+ "eframe",
+ "egui_extras",
+ "hex",
+ "ipc-channel",
+ "serde",
+ "serde_json",
+ "sha2",
+ "wasm-bindgen-futures",
+ "web-sys",
+]
+
 [[package]]
 name = "cosmol_viewer_core"
-version = "0.1.0"
+version = "0.1.1"
 dependencies = [
  "bytemuck",
  "eframe",
  "egui_extras",
  "glam",
+ "once_cell",
+ "serde",
+ "serde_json",
+ "serde_repr",
+ "wasm-bindgen-futures",
+ "web-sys",
+]
+
+[[package]]
+name = "cosmol_viewer_gui"
+version = "0.1.1"
+dependencies = [
+ "bytemuck",
+ "cosmol_viewer_core",
+ "eframe",
+ "egui_extras",
+ "ipc-channel",
  "serde",
+ "serde_json",
+ "wasm-bindgen-futures",
+ "web-sys",
 ]
 
 [[package]]
 name = "cosmol_viewer_python"
-version = "0.1.0"
+version = "0.0.0"
 dependencies = [
  "base64 0.22.1",
  "cosmol_viewer_core",
  "eframe",
  "egui_extras",
- "glam",
+ "hex",
+ "ipc-channel",
  "pyo3",
  "serde_json",
+ "sha2",
  "uuid",
  "wasm-bindgen",
 ]
 
 [[package]]
 name = "cosmol_viewer_wasm"
-version = "0.1.0"
+version = "0.1.1"
 dependencies = [
  "cosmol_viewer_core",
  "eframe",
  "egui_extras",
- "glam",
  "log",
  "serde_json",
  "wasm-bindgen",
@@ -747,6 +794,15 @@ dependencies = [
  "cfg-if",
 ]
 
+[[package]]
+name = "crossbeam-channel"
+version = "0.5.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "82b8f8f868b36967f9606790d1903570de9ceaf870a7bf9fbbd3016d636a2cb2"
+dependencies = [
+ "crossbeam-utils",
+]
+
 [[package]]
 name = "crossbeam-utils"
 version = "0.8.21"
@@ -1132,6 +1188,12 @@ version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "98de4bbd547a563b716d8dfa9aad1cb19bfab00f4fa09a6a4ed21dbcf44ce9c4"
 
+[[package]]
+name = "fnv"
+version = "1.0.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
+
 [[package]]
 name = "foldhash"
 version = "0.1.5"
@@ -1603,6 +1665,24 @@ version = "2.0.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f4c7245a08504955605670dbf141fceab975f15ca21570696aebe9d2e71576bd"
 
+[[package]]
+name = "ipc-channel"
+version = "0.20.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5b1c98b70019c830a1fc39cecfe1f60ff99c4122f0a189697c810c90ec545c14"
+dependencies = [
+ "bincode",
+ "crossbeam-channel",
+ "fnv",
+ "libc",
+ "mio",
+ "rand 0.9.1",
+ "serde",
+ "tempfile",
+ "uuid",
+ "windows",
+]
+
 [[package]]
 name = "itoa"
 version = "1.0.15"
@@ -1826,6 +1906,17 @@ dependencies = [
  "simd-adler32",
 ]
 
+[[package]]
+name = "mio"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "78bed444cc8a2160f01cbcf811ef18cac863ad68ae8ca62092e8db51d51c761c"
+dependencies = [
+ "libc",
+ "wasi 0.11.1+wasi-snapshot-preview1",
+ "windows-sys 0.59.0",
+]
+
 [[package]]
 name = "naga"
 version = "24.0.0"
@@ -2318,7 +2409,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3c80231409c20246a13fddb31776fb942c38553c51e871f8cbd687a4cfb5843d"
 dependencies = [
  "phf_shared",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -2579,8 +2670,18 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404"
 dependencies = [
  "libc",
- "rand_chacha",
- "rand_core",
+ "rand_chacha 0.3.1",
+ "rand_core 0.6.4",
+]
+
+[[package]]
+name = "rand"
+version = "0.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9fbfd9d094a40bf3ae768db9361049ace4c0e04a4fd6b359518bd7b73a73dd97"
+dependencies = [
+ "rand_chacha 0.9.0",
+ "rand_core 0.9.3",
 ]
 
 [[package]]
@@ -2590,7 +2691,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88"
 dependencies = [
  "ppv-lite86",
- "rand_core",
+ "rand_core 0.6.4",
+]
+
+[[package]]
+name = "rand_chacha"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb"
+dependencies = [
+ "ppv-lite86",
+ "rand_core 0.9.3",
 ]
 
 [[package]]
@@ -2602,6 +2713,15 @@ dependencies = [
  "getrandom 0.2.16",
 ]
 
+[[package]]
+name = "rand_core"
+version = "0.9.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "99d9a13982dcf210057a8a78572b2217b667c3beacbf3a0d8b454f6f82837d38"
+dependencies = [
+ "getrandom 0.3.3",
+]
+
 [[package]]
 name = "raw-window-handle"
 version = "0.6.2"
@@ -2805,6 +2925,17 @@ dependencies = [
  "digest",
 ]
 
+[[package]]
+name = "sha2"
+version = "0.10.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a7507d819769d01a365ab707794a4084392c824f54a7a6a7862f8c3d0892b283"
+dependencies = [
+ "cfg-if",
+ "cpufeatures",
+ "digest",
+]
+
 [[package]]
 name = "shlex"
 version = "1.3.0"
@@ -3027,12 +3158,12 @@ dependencies = [
 
 [[package]]
 name = "test"
-version = "0.1.0"
+version = "0.1.1"
 dependencies = [
+ "cosmol_viewer",
  "cosmol_viewer_core",
  "eframe",
  "egui_extras",
- "glam",
 ]
 
 [[package]]
@@ -4242,7 +4373,7 @@ dependencies = [
  "hex",
  "nix",
  "ordered-stream",
- "rand",
+ "rand 0.8.5",
  "serde",
  "serde_repr",
  "sha1",

cosmol_viewer-0.1.1/Cargo.toml

@@ -0,0 +1,22 @@
+[workspace.package]
+edition = "2024"
+version = "0.1.1"
+authors = ["9028 wjt@cosmol.org"]
+repository = "https://github.com/COSMol-repl/COSMol-viewer"
+homepage = "https://github.com/COSMol-repl/COSMol-viewer"
+keywords = ["molecular", "visualization"]
+
+[workspace]
+resolver = "2"
+members = ["crates/python"]
+
+[workspace.dependencies]
+cosmol_viewer = {path = "cosmol_viewer"}
+cosmol_viewer_core = { path = "crates/core" }
+eframe = { version = "0.31.1"}
+egui_extras = { version = "0.31.1", features = ["svg"] }
+serde = { version = "1.0.219" , features = ["derive"] }
+serde_json = "1.0.140"
+sha2 = "0.10.9"
+hex = "0.4.3"
+ipc-channel = "0.20.0"

cosmol_viewer-0.1.1/PKG-INFO

@@ -0,0 +1,57 @@
+Metadata-Version: 2.4
+Name: cosmol-viewer
+Version: 0.1.1
+Summary: Molecular visualization tools
+Author-email: 95028 <wjt@cosmol.org>
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Repository, https://github.com/COSMol-repl/COSMol-viewer
+
+# 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
+
+```sh
+pip install cosmol-viewer==0.1.1
+```
+
+# Usage
+
+```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()
+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/crates/core/Cargo.toml

@@ -0,0 +1,17 @@
+[package]
+name = "cosmol_viewer_core"
+version.workspace = true
+edition = "2024"
+publish = false
+
+[dependencies]
+eframe.workspace = true
+serde_json.workspace = true
+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-0.1.1/crates/core/src/lib.rs

@@ -0,0 +1,72 @@
+mod shader;
+use std::{
+    sync::{Arc, Mutex},
+};
+
+pub mod utils;
+pub mod parser;
+pub use eframe::egui;
+
+use eframe::egui::{Color32, Stroke};
+
+use shader::Canvas;
+
+pub use crate::utils::{Shape};
+pub mod shapes;
+use crate::{scene::Scene};
+
+pub mod scene;
+
+pub struct AppWrapper(pub Arc<Mutex<Option<App>>>);
+
+impl eframe::App for AppWrapper {
+    fn update(&mut self, ctx: &egui::Context, frame: &mut eframe::Frame) {
+        if let Some(app) = &mut *self.0.lock().unwrap() {
+            app.update(ctx, frame);
+        }
+    }
+}
+
+pub struct App {
+    canvas: Canvas,
+    gl: Option<Arc<eframe::glow::Context>>,
+    pub ctx: egui::Context,
+}
+
+impl App {
+    pub fn new(cc: &eframe::CreationContext<'_>, scene: Scene) -> Self {
+        let gl = cc.gl.clone();
+        let canvas = Canvas::new(gl.as_ref().unwrap().clone(), scene).unwrap();
+        App {
+            gl,
+            canvas,
+            ctx: cc.egui_ctx.clone(),
+        }
+    }
+
+    pub fn update_scene(&mut self, scene: Scene) {
+        self.canvas.update_scene(scene);
+    }
+}
+
+impl eframe::App for App {
+    fn update(&mut self, ctx: &egui::Context, _frame: &mut eframe::Frame) {
+        egui_extras::install_image_loaders(ctx);
+        egui::CentralPanel::default()
+            .frame(
+                egui::Frame::default()
+                    .fill(Color32::from_rgb(48, 48, 48))
+                    .inner_margin(0.0)
+                    .outer_margin(0.0)
+                    .stroke(Stroke::new(0.0, Color32::from_rgb(30, 200, 30))),
+            )
+            .show(ctx, |ui| {
+                ui.set_width(ui.available_width());
+                ui.set_height(ui.available_height());
+
+                self.canvas.custom_painting(ui);
+            });
+    }
+}
+
+

cosmol_viewer-0.1.1/crates/core/src/parser/mod.rs

@@ -0,0 +1,2 @@
+pub mod sdf;
+

cosmol_viewer-0.1.1/crates/core/src/parser/sdf.rs

@@ -0,0 +1,254 @@
+#[derive(Debug, Clone)]
+pub struct Atom {
+    pub atom: String,
+    pub elem: String,
+    pub x: f32,
+    pub y: f32,
+    pub z: f32,
+    pub serial: usize,
+    pub index: usize,
+    pub hetflag: bool,
+    pub bonds: Vec<usize>,
+    pub bond_order: Vec<f32>,
+    pub properties: std::collections::HashMap<String, String>,
+}
+
+pub type Molecule = Vec<Atom>;
+pub type MoleculeData = Vec<Molecule>;
+
+#[derive(Default)]
+pub struct ParserOptions {
+    pub keep_h: bool,
+    pub multimodel: bool,
+    pub onemol: bool,
+}
+
+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();
+        match version {
+            "V3000" => parse_v3000(lines, options),
+            _ => parse_v2000(lines, options),
+        }
+    } else {
+        vec![vec![]]
+    }
+}
+
+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;
+
+    while lines.len() >= 4 {
+        let header = lines[3];
+        let atom_count = header[0..3].trim().parse::<usize>().unwrap_or(0);
+        let bond_count = header[3..6].trim().parse::<usize>().unwrap_or(0);
+
+        if atom_count == 0 || lines.len() < 4 + atom_count + bond_count {
+            break;
+        }
+
+        let mut serial_to_index = vec![None; atom_count];
+        let mut offset = 4;
+        let start = molecules[current].len();
+
+        for i in 0..atom_count {
+            let line = lines[offset + i];
+            let elem = line[31..34].trim();
+            let elem_cap = capitalize(elem);
+            if elem_cap != "H" || options.keep_h {
+                let atom = Atom {
+                    atom: elem_cap.clone(),
+                    elem: elem_cap,
+                    x: line[0..10].trim().parse().unwrap_or(0.0),
+                    y: line[10..20].trim().parse().unwrap_or(0.0),
+                    z: line[20..30].trim().parse().unwrap_or(0.0),
+                    serial: start + i,
+                    index: molecules[current].len(),
+                    hetflag: true,
+                    bonds: vec![],
+                    bond_order: vec![],
+                    properties: std::collections::HashMap::new(),
+                };
+                serial_to_index[i] = Some(molecules[current].len());
+                molecules[current].push(atom);
+            }
+        }
+
+        offset += atom_count;
+
+        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 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),
+            ) {
+                molecules[current][f].bonds.push(t);
+                molecules[current][f].bond_order.push(order);
+                molecules[current][t].bonds.push(f);
+                molecules[current][t].bond_order.push(order);
+            }
+        }
+
+        let mut next_offset = offset + bond_count;
+        if options.multimodel {
+            if !options.onemol {
+                molecules.push(vec![]);
+                current += 1;
+            }
+            while next_offset < lines.len() && lines[next_offset] != "$$$$" {
+                next_offset += 1;
+            }
+            lines.drain(0..=next_offset);
+        } else {
+            break;
+        }
+    }
+
+    molecules
+}
+
+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;
+
+    while lines.len() >= 8 {
+        if !lines[4].starts_with("M  V30 BEGIN CTAB") || !lines[5].starts_with("M  V30 COUNTS") {
+            break;
+        }
+
+        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 mut offset = 7;
+
+        let mut serial_to_index = vec![None; atom_count];
+        let start = molecules[current].len();
+
+        for i in 0..atom_count {
+            let line = lines[offset + i];
+            let parts: Vec<_> = line[6..].split_whitespace().collect();
+            if parts.len() > 4 {
+                let elem_cap = capitalize(parts[1]);
+                if elem_cap != "H" || options.keep_h {
+                    let atom = Atom {
+                        atom: elem_cap.clone(),
+                        elem: elem_cap,
+                        x: parts[2].parse().unwrap_or(0.0),
+                        y: parts[3].parse().unwrap_or(0.0),
+                        z: parts[4].parse().unwrap_or(0.0),
+                        serial: start + i,
+                        index: molecules[current].len(),
+                        hetflag: true,
+                        bonds: vec![],
+                        bond_order: vec![],
+                        properties: std::collections::HashMap::new(),
+                    };
+                    serial_to_index[i] = Some(molecules[current].len());
+                    molecules[current].push(atom);
+                }
+            }
+        }
+
+        offset += atom_count + 1; // skip "END ATOM"
+        offset += 1; // BEGIN BOND
+
+        for i in 0..bond_count {
+            let line = lines[offset + i];
+            let parts: Vec<_> = line[6..].split_whitespace().collect();
+            if parts.len() > 3 {
+                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),
+                ) {
+                    molecules[current][f].bonds.push(t);
+                    molecules[current][f].bond_order.push(order);
+                    molecules[current][t].bonds.push(f);
+                    molecules[current][t].bond_order.push(order);
+                }
+            }
+        }
+
+        let mut next_offset = offset + bond_count;
+        if options.multimodel {
+            if !options.onemol {
+                molecules.push(vec![]);
+                current += 1;
+            }
+            while next_offset < lines.len() && lines[next_offset] != "$$$$" {
+                next_offset += 1;
+            }
+            lines.drain(0..=next_offset);
+        } else {
+            break;
+        }
+    }
+
+    molecules
+}
+
+fn capitalize(s: &str) -> String {
+    let mut chars = s.chars();
+    match chars.next() {
+        Some(first) => {
+            first.to_ascii_uppercase().to_string() + &chars.as_str().to_ascii_lowercase()
+        }
+        None => String::new(),
+    }
+}
+
+fn count_models(lines: &[&str]) -> usize {
+    lines.iter().filter(|line| line.trim() == "$$$$").count()
+}