cosmol-viewer 0.2.0.dev4__tar.gz → 0.2.0.dev5__tar.gz

{cosmol_viewer-0.2.0.dev4 → cosmol_viewer-0.2.0.dev5}/Cargo.lock

@@ -236,9 +236,9 @@ dependencies = [
 
 [[package]]
 name = "az"
-version = "1.2.1"
+version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b7e4c2464d97fe331d41de9d5db0def0a96f4d823b8b32a2efd503578988973"
+checksum = "be5eb007b7cacc6c660343e96f650fedf4b5a77512399eb952ca6642cf8d13f7"
 
 [[package]]
 name = "base64"
@@ -420,9 +420,9 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.2.53"
+version = "1.2.54"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "755d2fce177175ffca841e9a06afdb2c4ab0f593d53b4dee48147dfaade85932"
+checksum = "6354c81bbfd62d9cfa9cb3c773c2b7b2a3a482d569de977fd0e961f6e7c00583"
 dependencies = [
  "find-msvc-tools",
  "jobserver",
@@ -589,17 +589,18 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer"
-version = "0.2.0-nightly.4"
+version = "0.2.0-nightly.5"
 dependencies = [
  "cosmol_viewer_core",
 ]
 
 [[package]]
 name = "cosmol_viewer_core"
-version = "0.2.0-nightly.4"
+version = "0.2.0-nightly.5"
 dependencies = [
  "base64",
  "bytemuck",
+ "dashmap",
  "eframe",
  "egui-winit",
  "egui_extras",
@@ -611,7 +612,6 @@ dependencies = [
  "regex",
  "serde",
  "serde_json",
- "serde_repr",
  "thiserror 2.0.18",
  "wide",
 ]
@@ -632,7 +632,7 @@ dependencies = [
 
 [[package]]
 name = "cosmol_viewer_wasm"
-version = "0.2.0-nightly.4"
+version = "0.2.0-nightly.5"
 dependencies = [
  "base64",
  "cosmol_viewer_core",
@@ -703,6 +703,20 @@ version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f27ae1dd37df86211c42e150270f82743308803d90a6f6e6651cd730d5e1732f"
 
+[[package]]
+name = "dashmap"
+version = "6.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5041cc499144891f3790297212f32a74fb938e5136a14943f338ef9e0ae276cf"
+dependencies = [
+ "cfg-if",
+ "crossbeam-utils",
+ "hashbrown 0.14.5",
+ "lock_api",
+ "once_cell",
+ "parking_lot_core",
+]
+
 [[package]]
 name = "dispatch"
 version = "0.2.0"
@@ -1057,9 +1071,9 @@ checksum = "8591b0bcc8a98a64310a2fae1bb3e9b8564dd10e381e6e28010fde8e8e8568db"
 
 [[package]]
 name = "fixed"
-version = "1.29.0"
+version = "1.30.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "707070ccf8c4173548210893a0186e29c266901b71ed20cd9e2ca0193dfe95c3"
+checksum = "c566da967934c6c7ee0458a9773de9b2a685bd2ce26a3b28ddfc740e640182f5"
 dependencies = [
  "az",
  "bytemuck",
@@ -1234,9 +1248,9 @@ dependencies = [
 
 [[package]]
 name = "glam"
-version = "0.30.10"
+version = "0.31.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "19fc433e8437a212d1b6f1e68c7824af3aed907da60afa994e7f542d18d12aa9"
+checksum = "74a4d85559e2637d3d839438b5b3d75c31e655276f9544d72475c36b92fabbed"
 dependencies = [
  "bytemuck",
  "serde_core",
@@ -1353,6 +1367,12 @@ dependencies = [
  "byteorder",
 ]
 
+[[package]]
+name = "hashbrown"
+version = "0.14.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
+
 [[package]]
 name = "hashbrown"
 version = "0.16.1"
@@ -1541,7 +1561,7 @@ dependencies = [
  "rgb",
  "tiff",
  "zune-core 0.5.1",
- "zune-jpeg 0.5.10",
+ "zune-jpeg 0.5.11",
 ]
 
 [[package]]
@@ -1567,7 +1587,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7714e70437a7dc3ac8eb7e6f8df75fd8eb422675fc7678aff7364301092b1017"
 dependencies = [
  "equivalent",
- "hashbrown",
+ "hashbrown 0.16.1",
 ]
 
 [[package]]
@@ -1749,9 +1769,9 @@ dependencies = [
 
 [[package]]
 name = "libm"
-version = "0.2.15"
+version = "0.2.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f9fbbcab51052fe104eb5e5d351cf728d30a5be1fe14d9be8a3b097481fb97de"
+checksum = "b6d2cec3eae94f9f509c767b45932f1ada8350c4bdb85af2fcab4a3c14807981"
 
 [[package]]
 name = "libredox"
@@ -1895,7 +1915,7 @@ dependencies = [
  "cfg_aliases",
  "codespan-reporting",
  "half",
- "hashbrown",
+ "hashbrown 0.16.1",
  "hexf-parse",
  "indexmap",
  "libm",
@@ -2561,9 +2581,9 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.105"
+version = "1.0.106"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "535d180e0ecab6268a3e718bb9fd44db66bbbc256257165fc699dadf70d16fe7"
+checksum = "8fd00f0bb2e90d81d1044c2b32617f68fcb9fa3bb7640c23e9c748e53fb30934"
 dependencies = [
  "unicode-ident",
 ]
@@ -2717,9 +2737,9 @@ dependencies = [
 
 [[package]]
 name = "quote"
-version = "1.0.43"
+version = "1.0.44"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc74d9a594b72ae6656596548f56f667211f8a97b3d4c3d467150794690dc40a"
+checksum = "21b2ebcf727b7760c461f091f9f0f539b77b8e87f2fd88131e7f1b433b3cece4"
 dependencies = [
  "proc-macro2",
 ]
@@ -3045,9 +3065,9 @@ checksum = "b39cdef0fa800fc44525c84ccb54a029961a8215f9619753635a9c0d2538d46d"
 
 [[package]]
 name = "safe_arch"
-version = "0.9.3"
+version = "1.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "629516c85c29fe757770fa03f2074cf1eac43d44c02a3de9fc2ef7b0e207dfdd"
+checksum = "1f7caad094bd561859bcd467734a720c3c1f5d1f338995351fefe2190c45efed"
 dependencies = [
  "bytemuck",
 ]
@@ -3122,17 +3142,6 @@ dependencies = [
  "zmij",
 ]
 
-[[package]]
-name = "serde_repr"
-version = "0.1.20"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "175ee3e80ae9982737ca543e96133087cbd9a485eecc3bc4de9c1a37b47ea59c"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn",
-]
-
 [[package]]
 name = "serde_spanned"
 version = "1.0.4"
@@ -3662,9 +3671,9 @@ checksum = "b6c140620e7ffbb22c2dee59cafe6084a59b5ffc27a8859a5f0d494b5d52b6be"
 
 [[package]]
 name = "uuid"
-version = "1.19.0"
+version = "1.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2e054861b4bd027cd373e18e8d8d8e6548085000e41290d95ce0c373a654b4a"
+checksum = "ee48d38b119b0cd71fe4141b30f5ba9c7c5d9f4e7a3a8b4a674e4b6ef789976f"
 dependencies = [
  "getrandom 0.3.4",
  "js-sys",
@@ -3972,7 +3981,7 @@ dependencies = [
  "cfg-if",
  "cfg_aliases",
  "document-features",
- "hashbrown",
+ "hashbrown 0.16.1",
  "log",
  "portable-atomic",
  "profiling",
@@ -3997,7 +4006,7 @@ dependencies = [
  "bytemuck",
  "cfg_aliases",
  "document-features",
- "hashbrown",
+ "hashbrown 0.16.1",
  "indexmap",
  "log",
  "naga",
@@ -4059,9 +4068,9 @@ dependencies = [
 
 [[package]]
 name = "wide"
-version = "0.8.3"
+version = "1.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "13ca908d26e4786149c48efcf6c0ea09ab0e06d1fe3c17dc1b4b0f1ca4a7e788"
+checksum = "ac11b009ebeae802ed758530b6496784ebfee7a87b9abfbcaf3bbe25b814eb25"
 dependencies = [
  "bytemuck",
  "safe_arch",
@@ -4532,18 +4541,18 @@ dependencies = [
 
 [[package]]
 name = "zerocopy"
-version = "0.8.33"
+version = "0.8.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "668f5168d10b9ee831de31933dc111a459c97ec93225beb307aed970d1372dfd"
+checksum = "71ddd76bcebeed25db614f82bf31a9f4222d3fbba300e6fb6c00afa26cbd4d9d"
 dependencies = [
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.8.33"
+version = "0.8.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2c7962b26b0a8685668b671ee4b54d007a67d4eaf05fda79ac0ecf41e32270f1"
+checksum = "d8187381b52e32220d50b255276aa16a084ec0a9017a0ca2152a1f55c539758d"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -4606,9 +4615,9 @@ dependencies = [
 
 [[package]]
 name = "zmij"
-version = "1.0.15"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "94f63c051f4fe3c1509da62131a678643c5b6fbdc9273b2b79d4378ebda003d2"
+checksum = "02aae0f83f69aafc94776e879363e9771d7ecbffe2c7fbb6c14c5e00dfe88439"
 
 [[package]]
 name = "zune-core"
@@ -4642,9 +4651,9 @@ dependencies = [
 
 [[package]]
 name = "zune-jpeg"
-version = "0.5.10"
+version = "0.5.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ea2db9186c0a6ad1aa7012046f3fadc8db9001691b367c510f5867f17f975752"
+checksum = "2959ca473aae96a14ecedf501d20b3608d2825ba280d5adb57d651721885b0c2"
 dependencies = [
  "zune-core 0.5.1",
 ]

{cosmol_viewer-0.2.0.dev4 → cosmol_viewer-0.2.0.dev5}/Cargo.toml

@@ -1,6 +1,6 @@
 [workspace.package]
 edition = "2024"
-version = "0.2.0-nightly.4"
+version = "0.2.0-nightly.5"
 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 = "0.2.0-nightly.4", path = "cosmol_viewer"}
-cosmol_viewer_core = { version = "0.2.0-nightly.4", path = "crates/core" }
+cosmol_viewer = { version = "0.2.0-nightly.5", path = "cosmol_viewer"}
+cosmol_viewer_core = { version = "0.2.0-nightly.5", path = "crates/core" }
 
 pyo3 = { version = "0.27.2", features = ["extension-module", "abi3-py310"] }
 eframe = { version = "0.33.3", features = ["wayland","x11","glow"], default-features = false }

{cosmol_viewer-0.2.0.dev4 → cosmol_viewer-0.2.0.dev5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.2.0.dev4
+Version: 0.2.0.dev5
 Summary: Molecular visualization tools
 Author-email: 95028 <wjt@cosmol.org>
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM

{cosmol_viewer-0.2.0.dev4 → cosmol_viewer-0.2.0.dev5}/crates/core/Cargo.toml

@@ -14,13 +14,13 @@ serde.workspace = true
 base64.workspace = true
 thiserror.workspace = true
 
-glam = { version = "0.30.10" , features = ["serde", "bytemuck"] }
+glam = { version = "0.31.0" , features = ["serde", "bytemuck"] }
+dashmap = "6.1.0"
 regex = "1.12.2"
 na_seq = "0.3.12"
 bytemuck = "1.24.0"
-serde_repr = "0.1.20"
 once_cell = "1.21.3"
-wide = "0.8.3"
+wide = "1.1.1"
 kiddo = "5.2.4"
 image = "0.25.9"
 

{cosmol_viewer-0.2.0.dev4 → cosmol_viewer-0.2.0.dev5}/crates/core/src/parser/sdf.rs

@@ -15,6 +15,7 @@ pub struct Sdf {
     pub ident: String,
     pub metadata: HashMap<String, String>,
     pub atoms: Vec<AtomGeneric>,
+    pub atoms_weight: Option<Vec<Option<f32>>>,
     pub bonds: Vec<BondGeneric>,
     pub chains: Vec<ChainGeneric>,
     pub residues: Vec<ResidueGeneric>,
@@ -48,6 +49,8 @@ impl Sdf {
         let mut atoms = Vec::new();
         let mut bonds = Vec::new();
 
+        let mut atoms_weight: Option<Vec<Option<f32>>> = None;
+
         if is_v2000 {
             // ============================
             // V2000 parsing
@@ -137,6 +140,7 @@ impl Sdf {
             // --- find counts ---
             let mut n_atoms = 0usize;
             let mut n_bonds = 0usize;
+            let mut atoms_weight_: Vec<Option<f32>> = Vec::new();
 
             while i < lines.len() {
                 let line = lines[i];
@@ -162,6 +166,17 @@ impl Sdf {
                 let y = cols[5].parse::<f64>().unwrap();
                 let z = cols[6].parse::<f64>().unwrap();
 
+                // ---- parse WEIGHT if exists ----
+                let mut weight: Option<f32> = None;
+
+                for col in cols.iter().skip(7) {
+                    if let Some(v) = col.strip_prefix("WEIGHT=") {
+                        if let Ok(w) = v.parse::<f32>() {
+                            weight = Some(w);
+                        }
+                    }
+                }
+
                 let element = match Element::from_letter(element_str) {
                     Ok(element) => element,
                     Err(_) => Element::Other,
@@ -175,9 +190,13 @@ impl Sdf {
                     ..Default::default()
                 });
 
+                atoms_weight_.push(weight);
+
                 i += 1;
             }
 
+            atoms_weight = Some(atoms_weight_);
+
             // --- find bond begin ---
             while i < lines.len() && !lines[i].starts_with("M  V30 BEGIN BOND") {
                 i += 1;
@@ -227,6 +246,7 @@ impl Sdf {
         Ok(Self {
             ident,
             metadata: HashMap::new(),
+            atoms_weight,
             atoms,
             bonds,
             chains,

{cosmol_viewer-0.2.0.dev4 → cosmol_viewer-0.2.0.dev5}/crates/core/src/scene.rs

@@ -1,3 +1,4 @@
+use crate::utils::InstanceGroups;
 use crate::utils::Logger;
 use glam::Mat3;
 use glam::Mat4;
@@ -13,60 +14,9 @@ use crate::{
     utils::{self, Interpolatable, IntoInstanceGroups, ToMesh},
 };
 
-pub enum Instance {
-    Sphere(SphereInstance),
-}
-
-#[repr(C)]
-#[derive(Clone, Copy, bytemuck::Pod, bytemuck::Zeroable, Debug)]
-pub struct SphereInstance {
-    pub position: [f32; 3],
-    pub radius: f32,
-    pub color: [f32; 4],
-}
-
-impl SphereInstance {
-    pub fn new(position: [f32; 3], radius: f32, color: [f32; 4]) -> Self {
-        Self {
-            position,
-            radius,
-            color,
-        }
-    }
-}
-
-#[repr(C)]
-#[derive(Clone, Copy, bytemuck::Pod, bytemuck::Zeroable, Debug)]
-pub struct StickInstance {
-    pub start: [f32; 3],
-    pub end: [f32; 3],
-    pub radius: f32,
-    pub color: [f32; 4],
-}
-
-impl StickInstance {
-    pub fn new(start: [f32; 3], end: [f32; 3], radius: f32, color: [f32; 4]) -> Self {
-        Self {
-            start,
-            end,
-            radius,
-            color,
-        }
-    }
-}
-
-#[derive(Clone, Default)]
-pub struct InstanceGroups {
-    pub spheres: Vec<SphereInstance>,
-    pub sticks: Vec<StickInstance>,
-}
-
-impl InstanceGroups {
-    pub fn merge(&mut self, mut other: InstanceGroups) {
-        self.spheres.append(&mut other.spheres);
-        self.sticks.append(&mut other.sticks);
-    }
-}
+// pub enum Instance {
+//     Sphere(SphereInstance),
+// }
 
 #[derive(Serialize, Deserialize, Debug, Clone)]
 pub struct Scene {