cosmol-viewer 0.1.5.dev6__tar.gz → 0.1.5.dev8__tar.gz

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/Cargo.lock

@@ -222,12 +222,6 @@ dependencies = [
  "x11rb",
 ]
 
-[[package]]
-name = "arc-swap"
-version = "1.7.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "69f7f8c3906b62b754cd5326047894316021dcfe5a194c8ea52bdd94934a3457"
-
 [[package]]
 name = "arg_enum_proc_macro"
 version = "0.3.4"
@@ -529,6 +523,12 @@ version = "0.22.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
 
+[[package]]
+name = "base64ct"
+version = "1.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "55248b47b0caf0546f7988906588779981c43bb1bc9d0c44087278f80cdb44ba"
+
 [[package]]
 name = "bincode"
 version = "2.0.1"
@@ -753,6 +753,18 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "chrono"
+version = "0.4.42"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "145052bdd345b87320e369255277e3fb5152762ad123a901ef5c262dd38fe8d2"
+dependencies = [
+ "iana-time-zone",
+ "num-traits",
+ "serde",
+ "windows-link 0.2.1",
+]
+
 [[package]]
 name = "clipboard-win"
 version = "5.4.1"
@@ -876,15 +888,19 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer"
-version = "0.1.5-nightly.5"
+version = "0.1.5-nightly.8"
 dependencies = [
  "cosmol_viewer_core",
+ "serde",
+ "serde_json",
 ]
 
 [[package]]
 name = "cosmol_viewer_core"
-version = "0.1.5-nightly.5"
+version = "0.1.5-nightly.8"
 dependencies = [
+ "base64",
+ "base64ct",
  "bytemuck",
  "eframe",
  "egui-winit",
@@ -899,6 +915,7 @@ dependencies = [
  "serde",
  "serde_json",
  "serde_repr",
+ "serde_with",
  "wide",
 ]
 
@@ -912,17 +929,17 @@ dependencies = [
  "eframe",
  "egui_extras",
  "pyo3",
- "pyo3-log",
  "serde_json",
 ]
 
 [[package]]
 name = "cosmol_viewer_wasm"
-version = "0.1.5-nightly.5"
+version = "0.1.5-nightly.8"
 dependencies = [
  "base64",
  "cosmol_viewer_core",
  "eframe",
+ "flate2",
  "gloo-timers",
  "log",
  "pyo3",
@@ -980,6 +997,51 @@ version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f27ae1dd37df86211c42e150270f82743308803d90a6f6e6651cd730d5e1732f"
 
+[[package]]
+name = "darling"
+version = "0.21.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9cdf337090841a411e2a7f3deb9187445851f91b309c0c0a29e05f74a00a48c0"
+dependencies = [
+ "darling_core",
+ "darling_macro",
+]
+
+[[package]]
+name = "darling_core"
+version = "0.21.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1247195ecd7e3c85f83c8d2a366e4210d588e802133e1e355180a9870b517ea4"
+dependencies = [
+ "fnv",
+ "ident_case",
+ "proc-macro2",
+ "quote",
+ "strsim",
+ "syn",
+]
+
+[[package]]
+name = "darling_macro"
+version = "0.21.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d38308df82d1080de0afee5d069fa14b0326a88c14f15c5ccda35b4a6c414c81"
+dependencies = [
+ "darling_core",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "deranged"
+version = "0.5.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ececcb659e7ba858fb4f10388c250a7252eb0a27373f1a72b8748afdd248e587"
+dependencies = [
+ "powerfmt",
+ "serde_core",
+]
+
 [[package]]
 name = "dispatch"
 version = "0.2.0"
@@ -1049,6 +1111,12 @@ version = "0.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d8b14ccef22fc6f5a8f4d7d768562a182c04ce9a3b3157b91390b52ddfdf1a76"
 
+[[package]]
+name = "dyn-clone"
+version = "1.0.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d0881ea181b1df73ff77ffaaf9c7544ecc11e82fba9b5f27b262a3c73a332555"
+
 [[package]]
 name = "ecolor"
 version = "0.33.2"
@@ -1413,6 +1481,12 @@ dependencies = [
  "miniz_oxide",
 ]
 
+[[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"
@@ -1746,6 +1820,12 @@ dependencies = [
  "zerocopy",
 ]
 
+[[package]]
+name = "hashbrown"
+version = "0.12.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888"
+
 [[package]]
 name = "hashbrown"
 version = "0.15.5"
@@ -1788,6 +1868,30 @@ version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dfa686283ad6dd069f105e5ab091b04c62850d3e4cf5d67debad1933f55023df"
 
+[[package]]
+name = "iana-time-zone"
+version = "0.1.64"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "33e57f83510bb73707521ebaffa789ec8caf86f9657cad665b092b581d40e9fb"
+dependencies = [
+ "android_system_properties",
+ "core-foundation-sys",
+ "iana-time-zone-haiku",
+ "js-sys",
+ "log",
+ "wasm-bindgen",
+ "windows-core 0.61.2",
+]
+
+[[package]]
+name = "iana-time-zone-haiku"
+version = "0.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f31827a206f56af32e590ba56d5d2d085f558508192593743f16b2306495269f"
+dependencies = [
+ "cc",
+]
+
 [[package]]
 name = "icu_collections"
 version = "2.1.1"
@@ -1869,6 +1973,12 @@ dependencies = [
  "zerovec",
 ]
 
+[[package]]
+name = "ident_case"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b9e0384b61958566e926dc50660321d12159025e767c18e043daf26b70104c39"
+
 [[package]]
 name = "idna"
 version = "1.1.0"
@@ -1930,6 +2040,17 @@ version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e7c5cedc30da3a610cac6b4ba17597bdf7152cf974e8aab3afb3d54455e371c8"
 
+[[package]]
+name = "indexmap"
+version = "1.9.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99"
+dependencies = [
+ "autocfg",
+ "hashbrown 0.12.3",
+ "serde",
+]
+
 [[package]]
 name = "indexmap"
 version = "2.12.1"
@@ -1938,6 +2059,8 @@ checksum = "0ad4bb2b565bca0645f4d68c5c9af97fba094e9791da685bf83cb5f3ce74acf2"
 dependencies = [
  "equivalent",
  "hashbrown 0.16.1",
+ "serde",
+ "serde_core",
 ]
 
 [[package]]
@@ -2279,7 +2402,7 @@ dependencies = [
  "half",
  "hashbrown 0.16.1",
  "hexf-parse",
- "indexmap",
+ "indexmap 2.12.1",
  "libm",
  "log",
  "num-traits",
@@ -2379,6 +2502,12 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "num-conv"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9"
+
 [[package]]
 name = "num-derive"
 version = "0.4.2"
@@ -2956,6 +3085,12 @@ dependencies = [
  "zerovec",
 ]
 
+[[package]]
+name = "powerfmt"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391"
+
 [[package]]
 name = "ppv-lite86"
 version = "0.2.21"
@@ -3053,17 +3188,6 @@ dependencies = [
  "pyo3-build-config",
 ]
 
-[[package]]
-name = "pyo3-log"
-version = "0.13.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2f8bae9ad5ba08b0b0ed2bb9c2bdbaeccc69cafca96d78cf0fbcea0d45d122bb"
-dependencies = [
- "arc-swap",
- "log",
- "pyo3",
-]
-
 [[package]]
 name = "pyo3-macros"
 version = "0.27.1"
@@ -3282,6 +3406,26 @@ dependencies = [
  "bitflags 2.10.0",
 ]
 
+[[package]]
+name = "ref-cast"
+version = "1.0.25"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f354300ae66f76f1c85c5f84693f0ce81d747e2c3f21a45fef496d89c960bf7d"
+dependencies = [
+ "ref-cast-impl",
+]
+
+[[package]]
+name = "ref-cast-impl"
+version = "1.0.25"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b7186006dcb21920990093f30e3dea63b7d6e977bf1256be20c3563a5db070da"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "regex"
 version = "1.12.2"
@@ -3391,6 +3535,30 @@ dependencies = [
  "winapi-util",
 ]
 
+[[package]]
+name = "schemars"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4cd191f9397d57d581cddd31014772520aa448f65ef991055d7f61582c65165f"
+dependencies = [
+ "dyn-clone",
+ "ref-cast",
+ "serde",
+ "serde_json",
+]
+
+[[package]]
+name = "schemars"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9558e172d4e8533736ba97870c4b2cd63f84b382a3d6eb063da41b91cce17289"
+dependencies = [
+ "dyn-clone",
+ "ref-cast",
+ "serde",
+ "serde_json",
+]
+
 [[package]]
 name = "scoped-tls"
 version = "1.0.1"
@@ -3470,6 +3638,37 @@ dependencies = [
  "syn",
 ]
 
+[[package]]
+name = "serde_with"
+version = "3.16.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4fa237f2807440d238e0364a218270b98f767a00d3dada77b1c53ae88940e2e7"
+dependencies = [
+ "base64",
+ "chrono",
+ "hex",
+ "indexmap 1.9.3",
+ "indexmap 2.12.1",
+ "schemars 0.9.0",
+ "schemars 1.1.0",
+ "serde_core",
+ "serde_json",
+ "serde_with_macros",
+ "time",
+]
+
+[[package]]
+name = "serde_with_macros"
+version = "3.16.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "52a8e3ca0ca629121f70ab50f95249e5a6f925cc0f6ffe8256c45b728875706c"
+dependencies = [
+ "darling",
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "sharded-slab"
 version = "0.1.7"
@@ -3641,6 +3840,12 @@ version = "0.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6637bab7722d379c8b41ba849228d680cc12d0a45ba1fa2b48f2a30577a06731"
 
+[[package]]
+name = "strsim"
+version = "0.11.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
+
 [[package]]
 name = "syn"
 version = "2.0.111"
@@ -3754,6 +3959,37 @@ dependencies = [
  "zune-jpeg 0.4.21",
 ]
 
+[[package]]
+name = "time"
+version = "0.3.44"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "91e7d9e3bb61134e77bde20dd4825b97c010155709965fedf0f49bb138e52a9d"
+dependencies = [
+ "deranged",
+ "itoa",
+ "num-conv",
+ "powerfmt",
+ "serde",
+ "time-core",
+ "time-macros",
+]
+
+[[package]]
+name = "time-core"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "40868e7c1d2f0b8d73e4a8c7f0ff63af4f6d19be117e90bd73eb1d62cf831c6b"
+
+[[package]]
+name = "time-macros"
+version = "0.2.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "30cfb0125f12d9c277f35663a0a33f8c30190f4e4574868a330595412d34ebf3"
+dependencies = [
+ "num-conv",
+ "time-core",
+]
+
 [[package]]
 name = "tiny-skia"
 version = "0.11.4"
@@ -3804,7 +4040,7 @@ version = "0.23.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6485ef6d0d9b5d0ec17244ff7eb05310113c3f316f2d14200d4de56b3cb98f8d"
 dependencies = [
- "indexmap",
+ "indexmap 2.12.1",
  "toml_datetime",
  "toml_parser",
  "winnow",
@@ -4301,7 +4537,7 @@ dependencies = [
  "cfg_aliases",
  "document-features",
  "hashbrown 0.16.1",
- "indexmap",
+ "indexmap 2.12.1",
  "log",
  "naga",
  "once_cell",

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/Cargo.toml

@@ -1,6 +1,6 @@
 [workspace.package]
 edition = "2024"
-version = "0.1.5-nightly.5"
+version = "0.1.5-nightly.8"
 authors = ["9028 wjt@cosmol.org"]
 repository = "https://github.com/COSMol-repl/COSMol-viewer"
 homepage = "https://github.com/COSMol-repl/COSMol-viewer"
@@ -13,8 +13,8 @@ resolver = "2"
 members = ["crates/python"]
 
 [workspace.dependencies]
-cosmol_viewer = { version = "0.1.5-nightly.5", path = "cosmol_viewer"}
-cosmol_viewer_core = { version = "0.1.5-nightly.5", path = "crates/core" }
+cosmol_viewer = { version = "0.1.5-nightly.8", path = "cosmol_viewer"}
+cosmol_viewer_core = { version = "0.1.5-nightly.8", path = "crates/core" }
 
 pyo3 = { version = "0.27.1", features = ["extension-module", "abi3-py37"] }
 eframe = { version = "0.33.2", features = ["wayland","x11"] }

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.1.5.dev6
+Version: 0.1.5.dev8
 Summary: Molecular visualization tools
 Author-email: 95028 <wjt@cosmol.org>
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/core/Cargo.toml

@@ -11,7 +11,9 @@ eframe.workspace = true
 serde_json.workspace = true
 egui_extras.workspace = true
 serde.workspace = true
+base64.workspace = true
 glam = { version = "0.30.8" , features = ["serde", "bytemuck"] }
+serde_with = { version = "3.16.1", features = ["base64"] }
 regex = "1.12.2"
 na_seq = "0.3.6"
 bytemuck = "1.24.0"
@@ -21,6 +23,7 @@ half = "2.7.1"
 wide = "0.8.3"
 kiddo = "5.2.2"
 image = "0.25.8"
+base64ct = { version = "1.8.0", features = ["alloc"] }
 
 [target.'cfg(not(target_arch = "wasm32"))'.dependencies]
 egui-winit.workspace = true

cosmol_viewer-0.1.5.dev6/crates/core/src/parser/compute_secondary_structure.rs → cosmol_viewer-0.1.5.dev8/crates/core/src/parser/DSSP.rs

@@ -1,3 +1,15 @@
+// DSSP secondary structure assignment
+//
+// Ported and adapted from ChimeraX:
+// https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/CompSS.cpp
+//
+// Original ChimeraX code (c) 2004-2025 Regents of the University of California.
+// Licensed under a BSD-style license; see the original repository for details.
+//
+// Original DSSP algorithm:
+// Kabsch & Sander, Biopolymers 22:2577-2637 (1983)
+// https://doi.org/10.1002/bip.360221211
+
 use crate::parser::mmcif::Residue;
 use crate::parser::mmcif::SecondaryStructure;
 use glam::Vec3;

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/core/src/parser/mmcif.rs

@@ -1,4 +1,4 @@
-use crate::parser::compute_secondary_structure::SecondaryStructureCalculator;
+use crate::parser::DSSP::SecondaryStructureCalculator;
 use crate::utils::vec_f16_scaled;
 pub use crate::utils::{Logger, RustLogger};
 use glam::Vec3;
@@ -630,14 +630,10 @@ pub struct Residue {
     pub sns: usize, // PDB numbering or sequential
 
     // Minimum for cartoon backbone
-    #[serde(with = "vec_f16_scaled")]
-    pub c: Vec3, // or pseudo-CB for glycine
-    #[serde(with = "vec_f16_scaled")]
-    pub n: Vec3, // C-alpha coordinates
-    #[serde(with = "vec_f16_scaled")]
-    pub ca: Vec3, // C-alpha coordinates
-    #[serde(with = "vec_f16_scaled")]
-    pub o: Vec3, // C-alpha coordinates
+    pub c: Vec3,         // or pseudo-CB for glycine
+    pub n: Vec3,         // C-alpha coordinates
+    pub ca: Vec3,        // C-alpha coordinates
+    pub o: Vec3,         // C-alpha coordinates
     pub h: Option<Vec3>, // C-alpha coordinates
 
     // Secondary structure tag

cosmol_viewer-0.1.5.dev8/crates/core/src/parser/mod.rs

@@ -0,0 +1,3 @@
+pub mod DSSP;
+pub mod mmcif;
+pub mod sdf;

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/core/src/scene.rs

@@ -67,7 +67,7 @@ impl InstanceGroups {
     }
 }
 
-#[derive(Deserialize, Serialize, Clone)]
+#[derive(Deserialize, Serialize, Debug, Clone)]
 pub struct Scene {
     pub background_color: [f32; 3],
     pub camera_state: CameraState,

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/core/src/shapes/molecules.rs

@@ -54,11 +54,11 @@ pub enum BondType {
 
 #[derive(Serialize, Deserialize, Debug, Clone)]
 pub struct Molecules {
-    atom_types: Vec<String>,
+    pub atom_types: Vec<String>,
     #[serde(with = "vec_f16_scaled::vec")]
-    atoms: Vec<Vec3>,
-    bond_types: Vec<BondType>,
-    bonds: Vec<[usize; 2]>,
+    pub atoms: Vec<Vec3>,
+    pub bond_types: Vec<BondType>,
+    pub bonds: Vec<[usize; 2]>,
     pub quality: u32,
 
     pub style: VisualStyle,

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/core/src/shapes/protein.rs

@@ -6,13 +6,15 @@ use crate::parser::mmcif::ResidueType;
 use crate::parser::mmcif::SecondaryStructure;
 use crate::shapes::protein::ResidueType::AminoAcid;
 use crate::utils::{MeshData, VisualShape, VisualStyle};
+use crate::utils::{deserialize_bits, serialize_bits};
 use bytemuck::{Pod, Zeroable};
 use glam::{Quat, Vec3, Vec4};
 use na_seq::AtomTypeInRes;
 use serde::{Deserialize, Serialize};
+use serde_with::{base64::Base64, serde_as};
 use wide::f32x8;
 
-#[derive(Serialize, Deserialize, Debug, Clone)]
+#[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Protein {
     pub chains: Vec<Chain>,
     pub center: Vec3,

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/core/src/utils.rs

@@ -200,7 +200,7 @@ pub struct Frames {
 
 use half::f16;
 use serde::{Deserializer, Serializer};
-pub mod vec_f16_scaled {
+pub mod vec_f16 {
     use super::*;
 
     pub fn serialize<S, T>(v: &T, s: S) -> Result<S::Ok, S::Error>
@@ -208,11 +208,7 @@ pub mod vec_f16_scaled {
         S: Serializer,
         T: IntoF32Slice,
     {
-        let bits: Vec<u16> = v
-            .as_f32_slice()
-            .iter()
-            .map(|x| f16::from_f32(*x).to_bits())
-            .collect();
+        let bits: Vec<u32> = v.as_f32_slice().iter().map(|x| x.to_bits()).collect();
         bits.serialize(s)
     }
 
@@ -266,7 +262,7 @@ pub mod vec_f16_scaled {
     }
 }
 
-pub mod vec_f16_scaled_scaled {
+pub mod vec_f16_scaled {
     use super::*;
 
     // 你可以选择固定系数，或者运行时传
@@ -303,35 +299,139 @@ pub mod vec_f16_scaled_scaled {
     pub mod vec {
         use super::*;
 
-        // ---- Vec2 ----
-        pub fn serialize<S, T>(v: &T, s: S) -> Result<S::Ok, S::Error>
+        pub fn serialize<S, T>(v: &Vec<T>, s: S) -> Result<S::Ok, S::Error>
         where
             S: Serializer,
             T: IntoF32Slice,
         {
-            let bits: Vec<u16> = v
-                .as_f32_slice()
+            let bits: Vec<Vec<u16>> = v
                 .iter()
-                .map(|x| f16::from_f32(x * SCALE).to_bits())
+                .map(|v| {
+                    let floats: Vec<f32> = v.as_f32_slice().iter().map(|x| x * SCALE).collect();
+                    floats
+                        .into_iter()
+                        .map(|x| f16::from_f32(x).to_bits())
+                        .collect()
+                })
                 .collect();
             bits.serialize(s)
         }
 
-        pub fn deserialize<'de, D, T>(d: D) -> Result<T, D::Error>
+        pub fn deserialize<'de, D, T>(d: D) -> Result<Vec<T>, D::Error>
         where
             D: Deserializer<'de>,
             T: FromF32Slice,
         {
-            let bits: Vec<u16> = Vec::<u16>::deserialize(d)?;
-            let floats: Vec<f32> = bits
-                .iter()
-                .map(|b| f16::from_bits(*b).to_f32() / SCALE)
+            let bits: Vec<Vec<u16>> = Vec::<Vec<u16>>::deserialize(d)?;
+            let out = bits
+                .into_iter()
+                .map(|v| {
+                    let floats: Vec<f32> = v
+                        .iter()
+                        .map(|b| f16::from_bits(*b).to_f32() / SCALE)
+                        .collect();
+                    T::from_f32_slice(&floats)
+                })
                 .collect();
-            Ok(T::from_f32_slice(&floats))
+            Ok(out)
         }
     }
 }
 
+// pub mod vec_binary {
+//     use super::*;
+//     use base64::{Engine, engine::general_purpose::STANDARD as b64};
+//     use serde::{Deserialize, Deserializer, Serialize, Serializer};
+
+//     // -------------------------------------------------------
+//     // 单个 Vec2 / Vec3：无损（f32 -> u32 bits）
+//     // -------------------------------------------------------
+//     pub fn serialize<S, T>(v: &T, s: S) -> Result<S::Ok, S::Error>
+//     where
+//         S: Serializer,
+//         T: IntoF32Slice,
+//     {
+//         let bits: Vec<u32> = v.as_f32_slice().iter().map(|x| x.to_bits()).collect();
+//         bits.serialize(s)
+//     }
+
+//     pub fn deserialize<'de, D, T>(d: D) -> Result<T, D::Error>
+//     where
+//         D: Deserializer<'de>,
+//         T: FromF32Slice,
+//     {
+//         let bits: Vec<u32> = Vec::<u32>::deserialize(d)?;
+//         let floats: Vec<f32> = bits.iter().map(|b| f32::from_bits(*b)).collect();
+//         Ok(T::from_f32_slice(&floats))
+//     }
+
+//     // ==========================================================
+//     // Vec<T>：base64 无损存储（高压缩），不使用 f16
+//     // ==========================================================
+//     pub mod vec {
+//         use super::*;
+
+//         pub fn serialize<S, T>(v: &Vec<T>, s: S) -> Result<S::Ok, S::Error>
+//         where
+//             S: Serializer,
+//             T: IntoF32Slice,
+//         {
+//             // 1. flatten 成连续 f32
+//             let mut floats = Vec::<f32>::new();
+//             for item in v {
+//                 floats.extend_from_slice(item.as_f32_slice());
+//             }
+
+//             // 2. f32 -> u32 bits -> bytes
+//             let mut bytes = Vec::<u8>::new();
+//             for f in floats {
+//                 bytes.extend_from_slice(&f.to_bits().to_le_bytes());
+//             }
+
+//             // 3. base64
+//             let encoded = b64.encode(bytes);
+
+//             s.serialize_str(&encoded)
+//         }
+
+//         pub fn deserialize<'de, D, T>(d: D) -> Result<Vec<T>, D::Error>
+//         where
+//             D: Deserializer<'de>,
+//             T: FromF32Slice,
+//         {
+//             // 1. base64 decode
+//             let encoded = String::deserialize(d)?;
+//             let bytes = b64
+//                 .decode(encoded.as_bytes())
+//                 .map_err(serde::de::Error::custom)?;
+
+//             if bytes.len() % 4 != 0 {
+//                 return Err(serde::de::Error::custom("byte length not aligned"));
+//             }
+
+//             // 2. bytes -> u32 bits -> f32
+//             let mut floats = Vec::<f32>::new();
+//             for chunk in bytes.chunks_exact(4) {
+//                 let bits = u32::from_le_bytes(chunk.try_into().unwrap());
+//                 floats.push(f32::from_bits(bits));
+//             }
+
+//             // 3. 按 T::dim() 重建 T
+//             let dim = T::dim();
+//             if floats.len() % dim != 0 {
+//                 return Err(serde::de::Error::custom("dimension mismatch"));
+//             }
+
+//             let mut out = Vec::<T>::new();
+//             for chunk in floats.chunks(dim) {
+//                 out.push(T::from_f32_slice(chunk));
+//             }
+
+//             Ok(out)
+//         }
+//     }
+// }
+
 // ====== Trait definitions ======
 
 pub trait IntoF32Slice {
@@ -380,3 +480,64 @@ impl FromF32Slice for Vec4 {
         Self::new(v[0], v[1], v[2], v[3])
     }
 }
+
+use base64::{Engine, engine::general_purpose::STANDARD as B64};
+use bytemuck::Pod;
+
+pub mod vec_compact {
+    use super::*;
+
+    pub fn serialize<T, S>(data: &[T], serializer: S) -> Result<S::Ok, S::Error>
+    where
+        S: Serializer,
+        T: Pod,
+    {
+        if data.is_empty() {
+            return serializer.serialize_str("");
+        }
+
+        // 直接 cast 成字节流，最快方式（零拷贝！）
+        let bytes = bytemuck::cast_slice(data);
+        let encoded = B64.encode(bytes);
+        serializer.serialize_str(&encoded)
+    }
+
+    pub fn deserialize<'de, T, D>(deserializer: D) -> Result<Vec<T>, D::Error>
+    where
+        D: Deserializer<'de>,
+        T: Pod,
+    {
+        let s = String::deserialize(deserializer)?;
+        if s.is_empty() {
+            return Ok(Vec::new());
+        }
+
+        let bytes = B64.decode(&s).map_err(serde::de::Error::custom)?;
+        if bytes.len() % std::mem::size_of::<T>() != 0 {
+            return Err(serde::de::Error::custom("length not aligned to type size"));
+        }
+
+        // 安全 + 零拷贝
+        Ok(bytemuck::pod_collect_to_vec(&bytes))
+    }
+}
+
+pub fn serialize_bits<S>(v: &Vec3, serializer: S) -> Result<S::Ok, S::Error>
+where
+    S: Serializer,
+{
+    let bits: [u32; 3] = [v.x.to_bits(), v.y.to_bits(), v.z.to_bits()];
+    bits.serialize(serializer)
+}
+
+pub fn deserialize_bits<'de, D>(deserializer: D) -> Result<Vec3, D::Error>
+where
+    D: Deserializer<'de>,
+{
+    let bits: [u32; 3] = Deserialize::deserialize(deserializer)?;
+    Ok(Vec3::new(
+        f32::from_bits(bits[0]),
+        f32::from_bits(bits[1]),
+        f32::from_bits(bits[2]),
+    ))
+}

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/python/Cargo.toml

@@ -12,7 +12,6 @@ serde_json.workspace = true
 base64.workspace = true
 eframe.workspace = true
 pyo3.workspace = true
-pyo3-log = "0.13.2"
 
 [lib]
 name = "cosmol_viewer"
@@ -22,3 +21,11 @@ crate-type = ["cdylib"]
 default = []
 wayland = ["cosmol_viewer_core/wayland"]
 x11 = ["cosmol_viewer_core/x11"]
+
+[profile.release]
+lto = "fat"              # 以前叫 "full"，现在推荐写 fat
+codegen-units = 1        # 必须和 fat LTO 一起开才有效
+panic = "abort"          # 二进制体积暴降，Python 侧反正会接管 panic
+strip = "symbols"        # 去掉 debug symbols
+opt-level = "z"          # 体积党终极选择，速度损失 <1%
+incremental = false

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/wasm/Cargo.toml

@@ -18,7 +18,9 @@ web-sys = { version = "0.3.82", features = ["HtmlCanvasElement", "console","Wind
 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 }
+base64 = { workspace = true }
+flate2 = "1.1.5"
+
 
 [features]
 default = ["wasm"]
@@ -34,12 +36,33 @@ wasm = [
 
 js_bridge = [
     "pyo3",
-    "base64",
     "uuid",
 ]
 
 [lib]
 crate-type = ["rlib", "cdylib"]
 
+[package.metadata.wasm-pack.profile.dev]
+wasm-opt = false
+
+[package.metadata.wasm-pack.profile.dev.wasm-bindgen]
+debug-js-glue = true
+demangle-name-section = true
+dwarf-debug-info = true
+
 [package.metadata.wasm-pack.profile.release]
-# wasm-opt = false
+wasm-opt = [
+  "-O4",
+  "--enable-simd",
+  "--enable-bulk-memory",
+  "--enable-mutable-globals",
+  "--zero-filled-memory",
+  "--strip-producers",
+  "--vacuum",
+]
+
+[package.metadata.wasm-pack.profile.release.wasm-bindgen]
+debug-js-glue = false
+demangle-name-section = false
+dwarf-debug-info = false
+split-linked-modules = true

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/crates/wasm/src/lib.rs

@@ -1,14 +1,16 @@
+use base64::Engine;
 #[cfg(feature = "wasm")]
 use cosmol_viewer_core::App;
 use cosmol_viewer_core::scene::Scene;
 use cosmol_viewer_core::utils::Logger;
 #[cfg(feature = "js_bridge")]
 use serde::Serialize;
+use std::io::Write;
 use std::sync::Arc;
 use std::sync::Mutex;
 
 #[cfg(not(target_arch = "wasm32"))]
-const VERSION: &str = env!("CARGO_PKG_VERSION"); // crate 当前版本号
+const VERSION: &str = env!("CARGO_PKG_VERSION");
 
 #[cfg(feature = "wasm")]
 use web_sys::HtmlCanvasElement;
@@ -91,8 +93,7 @@ impl WasmViewer {
             height = height
         );
 
-        let scene_json = serde_json::to_string(scene).unwrap();
-        let escaped = serde_json::to_string(&scene_json).unwrap();
+        let escaped = serde_json::to_string(&compress_json(&scene)).unwrap();
 
         let combined_js = format!(
             r#"
@@ -167,14 +168,13 @@ impl WasmViewer {
             height = height
         );
 
-        let frames_json = serde_json::to_string(&Frames {
+        let frames = &Frames {
             frames,
             interval,
             loops,
             smooth,
-        })
-        .unwrap();
-        let escaped = serde_json::to_string(&frames_json).unwrap();
+        };
+        let escaped = serde_json::to_string(&compress_json(&frames)).unwrap();
 
         let combined_js = format!(
             r#"
@@ -228,8 +228,7 @@ impl WasmViewer {
     pub fn call<T: Serialize>(&self, py: Python, name: &str, input: T) -> () {
         use pyo3::types::PyAnyMethods;
 
-        let input_json = serde_json::to_string(&input).unwrap();
-        let escaped = serde_json::to_string(&input_json).unwrap();
+        let escaped = serde_json::to_string(&compress_json(&input)).unwrap();
         let combined_js = format!(
             r#"
 (async function() {{
@@ -345,8 +344,13 @@ impl WebHandle {
         _canvas: HtmlCanvasElement,
         scene_json: String,
     ) -> Result<(), JsValue> {
-        let _scene: Scene = serde_json::from_str(&scene_json)
-            .map_err(|e| JsValue::from_str(&format!("Scene parse error: {}", e)))?;
+        // let _scene: Scene = serde_json::from_str(&scene_json)
+        //     .map_err(|e| JsValue::from_str(&format!("Scene parse error: {}", e)))?;
+
+        let _scene: Scene =
+            decompress_json(&scene_json).map_err(|e| JsValue::from_str(&e.to_string()))?;
+
+        println!("{:?}", _scene);
 
         #[cfg(target_arch = "wasm32")]
         {
@@ -375,8 +379,8 @@ impl WebHandle {
 
     #[wasm_bindgen]
     pub async fn update_scene(&mut self, scene_json: String) -> Result<(), JsValue> {
-        let scene: Scene = serde_json::from_str(&scene_json)
-            .map_err(|e| JsValue::from_str(&format!("Scene parse error: {}", e)))?;
+        let scene: Scene =
+            decompress_json(&scene_json).map_err(|e| JsValue::from_str(&e.to_string()))?;
 
         let mut app_guard = self.app.lock().unwrap();
         if let Some(app) = &mut *app_guard {
@@ -399,8 +403,8 @@ impl WebHandle {
         {
             use cosmol_viewer_core::utils::Frames;
 
-            let frames: Frames = serde_json::from_str(&_frames_json)
-                .map_err(|e| JsValue::from_str(&format!("Frames parse error: {}", e)))?;
+            let frames: Frames =
+                decompress_json(&_frames_json).map_err(|e| JsValue::from_str(&e.to_string()))?;
 
             let app = Arc::clone(&self.app);
             let _ = self
@@ -426,3 +430,29 @@ impl WebHandle {
         Some("The returned value is omitted!".to_string())
     }
 }
+
+use base64::engine::general_purpose::STANDARD as B64;
+use flate2::{Compression, read::GzDecoder, write::GzEncoder};
+use serde::ser::Error;
+use std::io::Read;
+/// 把 JSON 压缩成 base64 字符串（用于发送）
+pub fn compress_json<T: serde::Serialize>(value: &T) -> String {
+    let json = serde_json::to_string(value).unwrap();
+    let mut e = GzEncoder::new(Vec::new(), Compression::best());
+    e.write_all(json.as_bytes()).unwrap();
+    B64.encode(e.finish().unwrap())
+}
+
+// 把 base64 字符串解压成目标类型（用于接收）
+pub fn decompress_json<T: for<'de> serde::Deserialize<'de>>(
+    s: &str,
+) -> Result<T, serde_json::Error> {
+    let bytes = B64
+        .decode(s)
+        .map_err(|_| serde_json::Error::custom("base64 error"))?;
+    let mut d = GzDecoder::new(&bytes[..]);
+    let mut json = String::new();
+    d.read_to_string(&mut json)
+        .map_err(|_| serde_json::Error::custom("gzip error"))?;
+    serde_json::from_str(&json)
+}

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev8}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cosmol-viewer"
-version = "0.1.5.dev6"
+version = "0.1.5.dev8"
 description = "Molecular visualization tools"
 authors = [{name = "95028", email = "wjt@cosmol.org"}]
 readme = "README.md"

cosmol_viewer-0.1.5.dev6/crates/core/src/parser/mod.rs

@@ -1,3 +0,0 @@
-pub mod compute_secondary_structure;
-pub mod mmcif;
-pub mod sdf;