rust-sasa-python 0.2.3__tar.gz → 0.2.5__tar.gz

{rust_sasa_python-0.2.3 → rust_sasa_python-0.2.5}/Cargo.lock

@@ -659,7 +659,7 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa-python"
-version = "0.2.3"
+version = "0.2.5"
 dependencies = [
  "nalgebra",
  "pdbtbx",

{rust_sasa_python-0.2.3 → rust_sasa_python-0.2.5}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "rust-sasa-python"
-version = "0.2.3"
+version = "0.2.5"
 edition = "2024"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

{rust_sasa_python-0.2.3 → rust_sasa_python-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rust-sasa-python
-Version: 0.2.3
+Version: 0.2.5
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -20,7 +20,7 @@ A high-performance **Python library** for computing SASA (Solvent Accessible Sur
 
 ## Features
 
-- 🦀 **Pure Rust Backend**: Leverages Rust's performance and safety.
+- 🦀 **Powered by [RustSASA](https://github.com/maxall41/RustSASA)**: Leverages Rust's performance and safety.
 - ⚡️ **Ludicrous Speed**: **46X** faster than Biopython, **7X** faster than Freesasa.
 - 🐍 **Pythonic Interface**: Clean, intuitive API.
 - 🔧 **Configurable**: Customizable probe radius and sampling points.

{rust_sasa_python-0.2.3 → rust_sasa_python-0.2.5}/README.md

@@ -4,7 +4,7 @@ A high-performance **Python library** for computing SASA (Solvent Accessible Sur
 
 ## Features
 
-- 🦀 **Pure Rust Backend**: Leverages Rust's performance and safety.
+- 🦀 **Powered by [RustSASA](https://github.com/maxall41/RustSASA)**: Leverages Rust's performance and safety.
 - ⚡️ **Ludicrous Speed**: **46X** faster than Biopython, **7X** faster than Freesasa.
 - 🐍 **Pythonic Interface**: Clean, intuitive API.
 - 🔧 **Configurable**: Customizable probe radius and sampling points.

{rust_sasa_python-0.2.3 → rust_sasa_python-0.2.5}/src/lib.rs

@@ -4,9 +4,12 @@ use pyo3::exceptions::PyRuntimeError;
 use pyo3::prelude::*;
 use rust_sasa::options::SASAOptions;
 use rust_sasa::{Atom, SASAProcessor, calculate_sasa_internal as calculate_sasa_internal_internal};
-use rust_sasa::{AtomLevel, ChainLevel, ProteinLevel, ResidueLevel}; // As in long long
+use rust_sasa::{AtomLevel, ChainLevel, ProteinLevel, ResidueLevel};
+use simd::simd_sum; // As in long long
 use std::collections::HashMap;
 
+mod simd;
+
 #[pyclass]
 #[derive(Clone)]
 pub struct Protein {
@@ -302,10 +305,11 @@ pub fn calculate_sasa_internal(
 ) -> PyResult<Vec<f32>> {
     let atoms: Vec<Atom> = atoms_in
         .into_iter()
-        .map(|(pos, radius, index)| Atom {
+        .enumerate()
+        .map(|(index, (pos, radius, parent_id))| Atom {
             position: Point3::new(pos.0, pos.1, pos.2),
             id: index,
-            parent_id: None,
+            parent_id: Some(parent_id as isize),
             radius,
         })
         .collect();
@@ -337,13 +341,13 @@ fn calculate_sasa_internal_at_residue_level(
 
     let mut residue_sasa = Vec::new();
     for (parent_id, sasa_values) in residue_groups {
-        let local_sum = sasa_values.iter().sum::<f32>();
+        let local_sum = simd_sum(sasa_values.as_slice());
 
         residue_sasa.push(Residue {
             chain_id: "UNK".to_string(),
             residue_name: "UNK".to_string(),
             residue_number: parent_id as u32,
-            sasa: local_sum / sasa_values.len() as f32,
+            sasa: local_sum,
         });
     }
 

rust_sasa_python-0.2.5/src/simd.rs

@@ -0,0 +1,33 @@
+const LANES: usize = 16;
+#[allow(clippy::needless_range_loop)]
+pub fn simd_sum(values: &[f32]) -> f32 {
+    let chunks = values.chunks_exact(LANES);
+    let remainder = chunks.remainder();
+
+    let sum = chunks.fold([0.0f32; LANES], |mut acc, chunk| {
+        let chunk: [f32; LANES] = chunk.try_into().unwrap();
+        for i in 0..LANES {
+            acc[i] += chunk[i];
+        }
+        acc
+    });
+
+    let remainder: f32 = remainder.iter().copied().sum();
+
+    let mut reduced = 0.0f32;
+    for i in 0..LANES {
+        reduced += sum[i];
+    }
+    reduced + remainder
+}
+
+pub(crate) fn serialize_chain_id(s: &str) -> isize {
+    let mut result = 0;
+    for c in s.chars() {
+        if c.is_ascii_alphabetic() {
+            let position = c.to_ascii_uppercase() as isize - 64;
+            result = result * 10 + position;
+        }
+    }
+    result
+}