cosmol-viewer 0.1.0__tar.gz → 0.1.1.dev2__tar.gz

{cosmol_viewer-0.1.0 → cosmol_viewer-0.1.1.dev2}/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"
@@ -688,35 +697,75 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "cosmol_viewer"
+version = "0.1.1-nightly.2"
+dependencies = [
+ "bytemuck",
+ "cosmol_viewer_core",
+ "eframe",
+ "egui_extras",
+ "glam",
+ "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-nightly.2"
+dependencies = [
+ "bytemuck",
+ "eframe",
+ "egui_extras",
+ "glam",
+ "serde",
+ "serde_json",
+ "wasm-bindgen-futures",
+ "web-sys",
+]
+
+[[package]]
+name = "cosmol_viewer_gui"
+version = "0.1.1-nightly.2"
 dependencies = [
  "bytemuck",
+ "cosmol_viewer_core",
  "eframe",
  "egui_extras",
  "glam",
+ "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-nightly.2"
 dependencies = [
  "cosmol_viewer_core",
  "eframe",
@@ -747,6 +796,15 @@ 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 +1190,12 @@ 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 +1667,24 @@ 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 +1908,17 @@ 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 +2411,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3c80231409c20246a13fddb31776fb942c38553c51e871f8cbd687a4cfb5843d"
 dependencies = [
  "phf_shared",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -2579,8 +2672,18 @@ 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 +2693,17 @@ 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 +2715,15 @@ 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 +2927,17 @@ 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"
@@ -3027,8 +3160,9 @@ dependencies = [
 
 [[package]]
 name = "test"
-version = "0.1.0"
+version = "0.1.1-nightly.2"
 dependencies = [
+ "cosmol_viewer",
  "cosmol_viewer_core",
  "eframe",
  "egui_extras",
@@ -4242,7 +4376,7 @@ dependencies = [
  "hex",
  "nix",
  "ordered-stream",
- "rand",
+ "rand 0.8.5",
  "serde",
  "serde_repr",
  "sha1",

cosmol_viewer-0.1.1.dev2/Cargo.toml

@@ -0,0 +1,22 @@
+[workspace.package]
+edition = "2024"
+version = "0.1.1-nightly.2"
+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"] }
+glam = { version = "0.30.3" , features = ["serde"] }
+serde_json = "1.0.140"
+sha2 = "0.10.9"
+hex = "0.4.3"
+ipc-channel = "0.20.0"

{cosmol_viewer-0.1.0 → cosmol_viewer-0.1.1.dev2}/PKG-INFO

@@ -1,5 +1,5 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.1.0
+Version: 0.1.1.dev2
 Summary: Molecular visualization tools
 Author-email: 95028 <wjt@cosmol.org>

{cosmol_viewer-0.1.0/cosmol_viewer_core → cosmol_viewer-0.1.1.dev2/crates/core}/Cargo.toml

@@ -2,10 +2,14 @@
 name = "cosmol_viewer_core"
 version.workspace = true
 edition = "2024"
+publish = false
 
 [dependencies]
 eframe.workspace = true
+serde_json.workspace = true
 glam.workspace = true
 egui_extras.workspace = true
 serde = { version = "1.0.219" , features = ["derive"] }
 bytemuck = "1.23.1"
+web-sys = "0.3.77"
+wasm-bindgen-futures = "0.4.50"

cosmol_viewer-0.1.1.dev2/crates/core/src/lib.rs

@@ -0,0 +1,72 @@
+mod shader;
+use std::{
+    sync::{Arc, Mutex},
+};
+
+pub mod utils;
+pub mod parser;
+
+use eframe::egui::{self, 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 {
+    // #[cfg(not(target_arch = "wasm32"))]
+    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.dev2/crates/core/src/parser/mod.rs

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

cosmol_viewer-0.1.1.dev2/crates/core/src/parser/sdf.rs

@@ -0,0 +1,197 @@
+#[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 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 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(),
+    }
+}

cosmol_viewer-0.1.1.dev2/crates/core/src/scene.rs

@@ -0,0 +1,63 @@
+use std::collections::HashMap;
+
+use serde::{Deserialize, Serialize};
+
+use crate::{shader::CameraState, utils::{self, ToMesh}, Shape};
+
+
+#[derive(Deserialize, Serialize, Clone)]
+pub struct Scene {
+    pub background_color: [f32; 3],
+    pub camera_state: CameraState,
+    pub named_shapes: HashMap<String, Shape>,
+    pub unnamed_shapes: Vec<Shape>,
+    pub scale: f32,
+}
+
+impl Scene {
+    pub fn _get_meshes(&self) -> Vec<utils::MeshData> {
+        self.named_shapes
+            .values()
+            .chain(self.unnamed_shapes.iter())
+            .map(|s| s.to_mesh(self.scale))
+            .collect()
+    }
+
+    pub fn new() -> Self {
+        Scene {
+            background_color: [1.0, 1.0, 1.0],
+            camera_state: CameraState::new(1.0),
+            named_shapes: HashMap::new(),
+            unnamed_shapes: Vec::new(),
+            scale: 1.0,
+        }
+    }
+
+    pub fn scale(&mut self, scale: f32) {
+        self.scale = scale;
+    }
+
+    pub fn add_shape<S: Into<Shape>>(&mut self, shape: S, id: Option<&str>) {
+        let shape = shape.into();
+        if let Some(id) = id {
+            self.named_shapes.insert(id.into(), shape);
+        } else {
+            self.unnamed_shapes.push(shape);
+        }
+    }
+
+    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) {
+            *existing_shape = shape;
+        } else {
+            panic!("Shape with ID '{}' not found", id);
+        }
+    }
+}