rust-sasa-python 0.2.4__tar.gz → 0.3.0__tar.gz

{rust_sasa_python-0.2.4 → rust_sasa_python-0.3.0}/Cargo.lock

@@ -108,9 +108,9 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
 [[package]]
 name = "clap"
-version = "4.5.41"
+version = "4.5.51"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "be92d32e80243a54711e5d7ce823c35c41c9d929dc4ab58e1276f625841aadf9"
+checksum = "4c26d721170e0295f191a69bd9a1f93efcdb0aff38684b61ab5750468972e5f5"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -118,9 +118,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.41"
+version = "4.5.51"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "707eab41e9622f9139419d573eca0900137718000c517d47da73045f54331c3d"
+checksum = "75835f0c7bf681bfd05abe44e965760fea999a5286c6eb2d59883634fd02011a"
 dependencies = [
  "anstream",
  "anstyle",
@@ -130,9 +130,9 @@ dependencies = [
 
 [[package]]
 name = "clap_derive"
-version = "4.5.41"
+version = "4.5.49"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef4f52386a59ca4c860f7393bcf8abd8dfd91ecccc0f774635ff68e92eeef491"
+checksum = "2a0b5487afeab2deb2ff4e03a807ad1a03ac532ff5a2cee5d86884440c7f7671"
 dependencies = [
  "heck",
  "proc-macro2 1.0.95",
@@ -280,9 +280,9 @@ dependencies = [
 
 [[package]]
 name = "indicatif"
-version = "0.18.0"
+version = "0.18.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "70a646d946d06bedbbc4cac4c218acf4bbf2d87757a784857025f4d447e4e1cd"
+checksum = "ade6dfcba0dfb62ad59e59e7241ec8912af34fd29e0e743e3db992bd278e8b65"
 dependencies = [
  "console",
  "portable-atomic",
@@ -333,9 +333,9 @@ checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
 [[package]]
 name = "libmimalloc-sys"
-version = "0.1.43"
+version = "0.1.44"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bf88cd67e9de251c1781dbe2f641a1a3ad66eaae831b8a2c38fbdc5ddae16d4d"
+checksum = "667f4fec20f29dfc6bc7357c582d91796c169ad7e2fce709468aefeb2c099870"
 dependencies = [
  "cc",
  "libc",
@@ -374,9 +374,9 @@ dependencies = [
 
 [[package]]
 name = "mimalloc"
-version = "0.1.47"
+version = "0.1.48"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b1791cbe101e95af5764f06f20f6760521f7158f69dbf9d6baf941ee1bf6bc40"
+checksum = "e1ee66a4b64c74f4ef288bcbb9192ad9c3feaad75193129ac8509af543894fd8"
 dependencies = [
  "libmimalloc-sys",
 ]
@@ -419,10 +419,11 @@ dependencies = [
 
 [[package]]
 name = "num-complex"
-version = "0.4.5"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "23c6602fda94a57c990fe0df199a035d83576b496aa29f4e634a8ac6004e68a6"
+checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495"
 dependencies = [
+ "bytemuck",
  "num-traits",
 ]
 
@@ -512,6 +513,20 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "pulp"
+version = "0.21.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "96b86df24f0a7ddd5e4b95c94fc9ed8a98f1ca94d3b01bdce2824097e7835907"
+dependencies = [
+ "bytemuck",
+ "cfg-if",
+ "libm",
+ "num-complex",
+ "reborrow",
+ "version_check",
+]
+
 [[package]]
 name = "pyo3"
 version = "0.25.1"
@@ -576,9 +591,9 @@ dependencies = [
 
 [[package]]
 name = "quick-xml"
-version = "0.38.0"
+version = "0.38.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8927b0664f5c5a98265138b7e3f90aa19a6b21353182469ace36d4ac527b7b1b"
+checksum = "42a232e7487fc2ef313d96dde7948e7a3c05101870d8985e4fd8d26aedd27b89"
 dependencies = [
  "memchr",
  "serde",
@@ -610,9 +625,9 @@ checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
 
 [[package]]
 name = "rayon"
-version = "1.10.0"
+version = "1.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa"
+checksum = "368f01d005bf8fd9b1206fb6fa653e6c4a81ceb1466406b81792d87c5677a58f"
 dependencies = [
  "either",
  "rayon-core",
@@ -620,14 +635,20 @@ dependencies = [
 
 [[package]]
 name = "rayon-core"
-version = "1.12.1"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2"
+checksum = "22e18b0f0062d30d4230b2e85ff77fdfe4326feb054b9783a3460d8435c8ab91"
 dependencies = [
  "crossbeam-deque",
  "crossbeam-utils",
 ]
 
+[[package]]
+name = "reborrow"
+version = "0.5.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "03251193000f4bd3b042892be858ee50e8b3719f2b08e5833ac4353724632430"
+
 [[package]]
 name = "rstar"
 version = "0.12.0"
@@ -641,15 +662,16 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa"
-version = "0.3.2"
+version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ed418e0ca1db931d0f377c0a14fa137754b37c3e53af79dfb4eff0858194b336"
+checksum = "57cd14c05b75474f1c401cadec34be8c0b4981ba9bfe98921bc57947af5964b9"
 dependencies = [
  "clap",
  "indicatif",
  "mimalloc",
  "nalgebra",
  "pdbtbx",
+ "pulp",
  "quick-xml",
  "rayon",
  "serde",
@@ -659,9 +681,11 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa-python"
-version = "0.2.4"
+version = "0.3.0"
 dependencies = [
+ "mimalloc",
  "nalgebra",
+ "num-complex",
  "pdbtbx",
  "pyo3",
  "rust-sasa",
@@ -684,18 +708,28 @@ dependencies = [
 
 [[package]]
 name = "serde"
-version = "1.0.219"
+version = "1.0.228"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9a8e94ea7f378bd32cbbd37198a4a91436180c5bb472411e48b5ec2e2124ae9e"
+dependencies = [
+ "serde_core",
+ "serde_derive",
+]
+
+[[package]]
+name = "serde_core"
+version = "1.0.228"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5f0e2c6ed6606019b4e29e69dbaba95b11854410e5347d525002456dbbb786b6"
+checksum = "41d385c7d4ca58e59fc732af25c3983b67ac852c1a25000afe1175de458b67ad"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.219"
+version = "1.0.228"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5b0276cf7f2c73365f7157c8123c21cd9a50fbbd844757af28ca1f5925fc2a00"
+checksum = "d540f220d3187173da220f885ab66608367b6574e925011a9353e4badda91d79"
 dependencies = [
  "proc-macro2 1.0.95",
  "quote 1.0.36",
@@ -704,14 +738,15 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.140"
+version = "1.0.145"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "20068b6e96dc6c9bd23e01df8827e6c7e1f2fddd43c21810382803c136b99373"
+checksum = "402a6f66d8c709116cf22f558eab210f5a50187f702eb4d7e5ef38d9a7f1c79c"
 dependencies = [
  "itoa",
  "memchr",
  "ryu",
  "serde",
+ "serde_core",
 ]
 
 [[package]]
@@ -741,18 +776,18 @@ checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
 
 [[package]]
 name = "snafu"
-version = "0.8.6"
+version = "0.8.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "320b01e011bf8d5d7a4a4a4be966d9160968935849c83b918827f6a435e7f627"
+checksum = "6e84b3f4eacbf3a1ce05eac6763b4d629d60cbc94d632e4092c54ade71f1e1a2"
 dependencies = [
  "snafu-derive",
 ]
 
 [[package]]
 name = "snafu-derive"
-version = "0.8.6"
+version = "0.8.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1961e2ef424c1424204d3a5d6975f934f56b6d50ff5732382d84ebf460e147f7"
+checksum = "c1c97747dbf44bb1ca44a561ece23508e99cb592e862f22222dcf42f51d1e451"
 dependencies = [
  "heck",
  "proc-macro2 1.0.95",
@@ -831,6 +866,12 @@ version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
 
+[[package]]
+name = "version_check"
+version = "0.9.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a"
+
 [[package]]
 name = "wasm-bindgen"
 version = "0.2.100"

{rust_sasa_python-0.2.4 → rust_sasa_python-0.3.0}/Cargo.toml

@@ -1,7 +1,8 @@
 [package]
 name = "rust-sasa-python"
-version = "0.2.4"
+version = "0.3.0"
 edition = "2024"
+readme = "README.md"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
@@ -11,5 +12,7 @@ crate-type = ["cdylib"]
 [dependencies]
 pdbtbx = "0.12.0"
 pyo3 = "0.25.1"
-rust-sasa = "0.3.2"
+rust-sasa = "0.4.0"
 nalgebra = "0.33.2"
+mimalloc = "0.1.47"
+num-complex = "0.4.6"

{rust_sasa_python-0.2.4 → rust_sasa_python-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rust-sasa-python
-Version: 0.2.4
+Version: 0.3.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

{rust_sasa_python-0.2.4 → rust_sasa_python-0.3.0}/src/lib.rs

@@ -10,6 +10,9 @@ use std::collections::HashMap;
 
 mod simd;
 
+#[global_allocator]
+static GLOBAL: mimalloc::MiMalloc = mimalloc::MiMalloc;
+
 #[pyclass]
 #[derive(Clone)]
 pub struct Protein {
@@ -305,10 +308,11 @@ 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();

{rust_sasa_python-0.2.4 → rust_sasa_python-0.3.0}/tests/test_sasa.py

@@ -2,6 +2,7 @@ import time
 from pathlib import Path
 
 import pytest
+
 import rust_sasa_python as sasa
 
 # Path to the example CIF file
@@ -17,7 +18,7 @@ def test_protein_calculation():
     assert result.total > 0
     assert result.polar >= 0
     assert result.non_polar >= 0
-    assert abs(result.total - (result.polar + result.non_polar)) < 0.001
+    assert abs(result.total - (result.polar + result.non_polar)) < 1.0
 
 
 def test_chain_calculation():

{rust_sasa_python-0.2.4 → rust_sasa_python-0.3.0}/uv.lock

@@ -1,69 +1,70 @@
 version = 1
+revision = 3
 requires-python = ">=3.11"
 
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