cosmol-viewer 0.1.5.dev6__tar.gz → 0.1.5.dev7__tar.gz

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev7}/Cargo.lock

@@ -879,6 +879,8 @@ name = "cosmol_viewer"
 version = "0.1.5-nightly.5"
 dependencies = [
  "cosmol_viewer_core",
+ "serde",
+ "serde_json",
 ]
 
 [[package]]

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.1.5.dev6
+Version: 0.1.5.dev7
 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/crates/core/src/parser/compute_secondary_structure.rs → cosmol_viewer-0.1.5.dev7/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.dev7}/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;

cosmol_viewer-0.1.5.dev7/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.dev7}/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.dev7}/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>
@@ -266,7 +266,7 @@ 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
@@ -303,31 +303,41 @@ 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)
         }
     }
 }

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev7}/crates/wasm/src/lib.rs

@@ -8,7 +8,7 @@ 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;

{cosmol_viewer-0.1.5.dev6 → cosmol_viewer-0.1.5.dev7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cosmol-viewer"
-version = "0.1.5.dev6"
+version = "0.1.5.dev7"
 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;