rust-sasa-python 0.1.0__tar.gz → 0.1.1__tar.gz

{rust_sasa_python-0.1.0 → rust_sasa_python-0.1.1}/Cargo.lock

@@ -197,6 +197,12 @@ version = "2.0.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5"
 
+[[package]]
+name = "lazy_static"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
+
 [[package]]
 name = "libc"
 version = "0.2.153"
@@ -249,9 +255,9 @@ dependencies = [
 
 [[package]]
 name = "nalgebra"
-version = "0.32.5"
+version = "0.33.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3ea4908d4f23254adda3daa60ffef0f1ac7b8c3e9a864cf3cc154b251908a2ef"
+checksum = "3c4b5f057b303842cf3262c27e465f4c303572e7f6b0648f60e16248ac3397f4"
 dependencies = [
  "approx",
  "matrixmultiply",
@@ -265,13 +271,13 @@ dependencies = [
 
 [[package]]
 name = "nalgebra-macros"
-version = "0.2.1"
+version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "91761aed67d03ad966ef783ae962ef9bbaca728d2dd7ceb7939ec110fffad998"
+checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc"
 dependencies = [
  "proc-macro2 1.0.81",
  "quote 1.0.36",
- "syn 1.0.109",
+ "syn",
 ]
 
 [[package]]
@@ -433,7 +439,7 @@ dependencies = [
  "proc-macro2 1.0.81",
  "pyo3-macros-backend",
  "quote 1.0.36",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
@@ -446,7 +452,7 @@ dependencies = [
  "proc-macro2 1.0.81",
  "pyo3-build-config",
  "quote 1.0.36",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
@@ -526,10 +532,11 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa"
-version = "0.2.1"
+version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "882f4821fadbd616f60dd5029e52f28279573df38380e80409422050e42b00b1"
+checksum = "e558f2e471a933b98a3218e604c6761ff1ebe7434b1a326d39c0338054651d5e"
 dependencies = [
+ "lazy_static",
  "nalgebra",
  "pdbtbx",
  "rayon",
@@ -539,7 +546,7 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa-python"
-version = "0.1.0"
+version = "0.1.1"
 dependencies = [
  "pdbtbx",
  "pyo3",
@@ -593,14 +600,14 @@ checksum = "11bd257a6541e141e42ca6d24ae26f7714887b47e89aa739099104c7e4d3b7fc"
 dependencies = [
  "proc-macro2 1.0.81",
  "quote 1.0.36",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
 name = "simba"
-version = "0.8.1"
+version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "061507c94fc6ab4ba1c9a0305018408e312e17c041eb63bef8aa726fa33aceae"
+checksum = "b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa"
 dependencies = [
  "approx",
  "num-complex",
@@ -617,23 +624,23 @@ checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
 
 [[package]]
 name = "snafu"
-version = "0.8.2"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "75976f4748ab44f6e5332102be424e7c2dc18daeaf7e725f2040c3ebb133512e"
+checksum = "2b835cb902660db3415a672d862905e791e54d306c6e8189168c7f3d9ae1c79d"
 dependencies = [
  "snafu-derive",
 ]
 
 [[package]]
 name = "snafu-derive"
-version = "0.8.2"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b4b19911debfb8c2fb1107bc6cb2d61868aaf53a988449213959bb1b5b1ed95f"
+checksum = "38d1e02fca405f6280643174a50c942219f0bbf4dbf7d480f1dd864d6f211ae5"
 dependencies = [
  "heck",
  "proc-macro2 1.0.81",
  "quote 1.0.36",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
@@ -651,17 +658,6 @@ version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a8f112729512f8e442d81f95a8a7ddf2b7c6b8a1a6f509a95864142b30cab2d3"
 
-[[package]]
-name = "syn"
-version = "1.0.109"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
-dependencies = [
- "proc-macro2 1.0.81",
- "quote 1.0.36",
- "unicode-ident",
-]
-
 [[package]]
 name = "syn"
 version = "2.0.60"

{rust_sasa_python-0.1.0 → rust_sasa_python-0.1.1}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "rust-sasa-python"
-version = "0.1.0"
+version = "0.1.1"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -11,4 +11,4 @@ crate-type = ["cdylib"]
 [dependencies]
 pdbtbx = "0.11.0"
 pyo3 = "0.20.0"
-rust-sasa = "0.2.1"
+rust-sasa = "0.2.3"

rust_sasa_python-0.1.1/DOCS.md

@@ -0,0 +1,51 @@
+# Documentation
+
+## Functions
+
+### `calculate_sasa_at_protein_level`
+
+Signature: calculate_sasa_at_protein_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>)
+
+Returns: tuple (GLOBAL_SASA,Non-polar total SASA,Polar total SASA) as f32
+Example:
+
+```python
+import rust_sasa_python
+rust_sasa_python.calculate_sasa_at_protein_level("path_to_pdb_file.pdb") # Also supports mmCIF files!
+```
+
+### `calculate_sasa_at_residue_level`
+
+Signature: calculate_sasa_at_residue_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>)
+
+Returns: list of tuples <({CHAIN*ID}*{RESIDUE*NAE}*{RESIDUE_INDEX},SASA VALUE as f32)>
+Example:
+
+```python
+import rust_sasa_python
+rust_sasa_python.calculate_sasa_at_residue_level("path_to_pdb_file.pdb") # Also supports mmCIF files!
+```
+
+### `calculate_sasa_at_atom_level`
+
+Signature: calculate_sasa_at_atom_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>)
+
+Returns: array of SASA values for each atom
+Example:
+
+```python
+import rust_sasa_python
+rust_sasa_python.calculate_sasa_at_atom_level("path_to_pdb_file.pdb") # Also supports mmCIF files!
+```
+
+### `calculate_sasa_at_chain_level`
+
+Signature: calculate_sasa_at_chain_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>)
+
+Returns: array of SASA values for each chain
+Example:
+
+```python
+import rust_sasa_python
+rust_sasa_python.calculate_sasa_at_chain_level("path_to_pdb_file.pdb") # Also supports mmCIF files!
+```

rust_sasa_python-0.1.1/PKG-INFO

@@ -0,0 +1,46 @@
+Metadata-Version: 2.3
+Name: rust-sasa-python
+Version: 0.1.1
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+License-File: LICENSE.md
+Summary: An ultra-fast package for computing Solvent Accessible Surface Area (SASA/ASA) for proteins
+Author: Max Campbell
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# rust-sasa-python
+
+rust-sasa-python is a Python library for computing SASA (Solvent Accessible Surface Area) far faster than biopython and other packages.
+See [RustSasa](https://github.com/maxall41/RustSASA) for more info.
+
+## Features:
+- 🦀 Backend written in Pure Rust
+- ⚡️ 3X Faster than Biopython and ~120% faster than Freesasa
+- 🐍 Quick drop-in replacement for Biopython
+
+## Usage
+
+You can now utilize RustSasa within Python to speed up your scripts! Take a look at [rust-sasa-python](https://github.com/maxall41/rust-sasa-python)!
+
+Installation:
+```
+pip install rust-sasa-python
+```
+Example:
+```python
+from rust_sasa_python import calculate_sasa_at_residue_level
+residue_sasa_values = calculate_sasa_at_residue_level("path_to_pdb_file.pdb") # Also supports mmCIF files!
+```
+See full docs [here](https://github.com/maxall41/rust-sasa-python/blob/main/DOCS.md)
+
+## Benchmarking
+Benchmarks were performed on an M2 Apple Mac with 8GB of RAM and 8 Cores with the protein AF-A0A2K5XT84-F1 (AlphaFold).
+
+- Biopython: ~150ms
+
+- Freesasa: ~90ms
+
+- RustSASA: ~40ms
+

rust_sasa_python-0.1.1/README.md

@@ -0,0 +1,33 @@
+# rust-sasa-python
+
+rust-sasa-python is a Python library for computing SASA (Solvent Accessible Surface Area) far faster than biopython and other packages.
+See [RustSasa](https://github.com/maxall41/RustSASA) for more info.
+
+## Features:
+- 🦀 Backend written in Pure Rust
+- ⚡️ 3X Faster than Biopython and ~120% faster than Freesasa
+- 🐍 Quick drop-in replacement for Biopython
+
+## Usage
+
+You can now utilize RustSasa within Python to speed up your scripts! Take a look at [rust-sasa-python](https://github.com/maxall41/rust-sasa-python)!
+
+Installation:
+```
+pip install rust-sasa-python
+```
+Example:
+```python
+from rust_sasa_python import calculate_sasa_at_residue_level
+residue_sasa_values = calculate_sasa_at_residue_level("path_to_pdb_file.pdb") # Also supports mmCIF files!
+```
+See full docs [here](https://github.com/maxall41/rust-sasa-python/blob/main/DOCS.md)
+
+## Benchmarking
+Benchmarks were performed on an M2 Apple Mac with 8GB of RAM and 8 Cores with the protein AF-A0A2K5XT84-F1 (AlphaFold).
+
+- Biopython: ~150ms
+
+- Freesasa: ~90ms
+
+- RustSASA: ~40ms

rust_sasa_python-0.1.1/src/lib.rs

@@ -0,0 +1,85 @@
+use pdbtbx::StrictnessLevel;
+use pyo3::prelude::*;
+use rust_sasa::{SASALevel, SASAResult};
+
+#[pyfunction]
+fn calculate_sasa_at_protein_level(
+    pdb_path: String,
+    probe_radius: Option<f32>,
+    n_points: Option<usize>,
+) -> PyResult<(f32, f32, f32)> {
+    let (pdb, _errors) = pdbtbx::open(pdb_path, StrictnessLevel::Medium).unwrap();
+    let result =
+        rust_sasa::calculate_sasa(&pdb, probe_radius, n_points, SASALevel::Protein).unwrap();
+    return match result {
+        SASAResult::Protein(v) => Ok((v.global_total, v.non_polar_total, v.polar_total)),
+        _ => panic!("This will never run"),
+    };
+}
+
+#[pyfunction]
+fn calculate_sasa_at_residue_level(
+    pdb_path: String,
+    probe_radius: Option<f32>,
+    n_points: Option<usize>,
+) -> PyResult<Vec<(String, f32)>> {
+    let (pdb, _errors) = pdbtbx::open(pdb_path, StrictnessLevel::Medium).unwrap();
+    let result =
+        rust_sasa::calculate_sasa(&pdb, probe_radius, n_points, SASALevel::Residue).unwrap();
+    return match result {
+        SASAResult::Residue(v) => {
+            let mut temp: Vec<(String, f32)> = vec![];
+            for value in v {
+                temp.push((
+                    format!("{}_{}_{}", value.chain_id, value.name, value.serial_number),
+                    value.value,
+                ))
+            }
+            Ok(temp)
+        }
+        _ => panic!("This will never run"),
+    };
+}
+
+#[pyfunction]
+fn calculate_sasa_at_atom_level(
+    pdb_path: String,
+    probe_radius: Option<f32>,
+    n_points: Option<usize>,
+) -> PyResult<Vec<f32>> {
+    let (pdb, _errors) = pdbtbx::open(pdb_path, StrictnessLevel::Medium).unwrap();
+    let result = rust_sasa::calculate_sasa(&pdb, probe_radius, n_points, SASALevel::Atom).unwrap();
+    return match result {
+        SASAResult::Atom(v) => Ok(v),
+        _ => panic!("This will never run"),
+    };
+}
+
+#[pyfunction]
+fn calculate_sasa_at_chain_level(
+    pdb_path: String,
+    probe_radius: Option<f32>,
+    n_points: Option<usize>,
+) -> PyResult<Vec<f32>> {
+    let (pdb, _errors) = pdbtbx::open(pdb_path, StrictnessLevel::Medium).unwrap();
+    let result = rust_sasa::calculate_sasa(&pdb, probe_radius, n_points, SASALevel::Chain).unwrap();
+    return match result {
+        SASAResult::Chain(v) => {
+            let mut temp: Vec<f32> = vec![];
+            for value in v {
+                temp.push(value.value)
+            }
+            Ok(temp)
+        }
+        _ => panic!("This will never run"),
+    };
+}
+
+#[pymodule]
+fn rust_sasa_python(_py: Python, m: &PyModule) -> PyResult<()> {
+    m.add_function(wrap_pyfunction!(calculate_sasa_at_protein_level, m)?)?;
+    m.add_function(wrap_pyfunction!(calculate_sasa_at_chain_level, m)?)?;
+    m.add_function(wrap_pyfunction!(calculate_sasa_at_residue_level, m)?)?;
+    m.add_function(wrap_pyfunction!(calculate_sasa_at_atom_level, m)?)?;
+    Ok(())
+}

{rust_sasa_python-0.1.0 → rust_sasa_python-0.1.1}/test.py

@@ -4,7 +4,8 @@ from Bio.PDB.SASA import ShrakeRupley
 from Bio.PDB.MMCIFParser import MMCIFParser
 
 start = time.time()
-rust_sasa_python.calculate_sasa_at_residue_level("example.cif")
+v = rust_sasa_python.calculate_sasa_at_residue_level("example.cif")
+print(v)
 end = time.time()
 print("Time for RustSasa:")
 print(end - start)

rust_sasa_python-0.1.0/PKG-INFO

@@ -1,16 +0,0 @@
-Metadata-Version: 2.3
-Name: rust-sasa-python
-Version: 0.1.0
-Classifier: Programming Language :: Rust
-Classifier: Programming Language :: Python :: Implementation :: CPython
-Classifier: Programming Language :: Python :: Implementation :: PyPy
-License-File: LICENSE.md
-Summary: An ultra-fast package for computing Solvent Accessible Surface Area (SASA/ASA) for proteins
-Author: Max Campbell
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
-
-# rust-sasa-python
-
-rust-sasa-python is a tool for computing SASA (Solvent Accessible Surface Area) far faster than biopython and other packages.
-See [RustSasa](https://github.com/maxall41/RustSASA) for more info.

rust_sasa_python-0.1.0/README.md

@@ -1,4 +0,0 @@
-# rust-sasa-python
-
-rust-sasa-python is a tool for computing SASA (Solvent Accessible Surface Area) far faster than biopython and other packages.
-See [RustSasa](https://github.com/maxall41/RustSASA) for more info.

rust_sasa_python-0.1.0/src/lib.rs

@@ -1,78 +0,0 @@
-use pdbtbx::StrictnessLevel;
-use pyo3::prelude::*;
-use rust_sasa::{SASALevel, SASAResult};
-
-#[pyfunction]
-fn calculate_sasa_at_protein_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>) -> PyResult<f32> {
-    let (mut pdb, _errors) = pdbtbx::open(
-        pdb_path,
-        StrictnessLevel::Medium
-    ).unwrap();
-    let result = rust_sasa::calculate_sasa(&pdb,probe_radius,n_points,SASALevel::Protein).unwrap();
-    return match result {
-        SASAResult::Protein(v) => Ok(v),
-        _ => panic!("This will never run")
-    };
-}
-
-#[pyfunction]
-fn calculate_sasa_at_residue_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>) -> PyResult<Vec<f32>> {
-    let (mut pdb, _errors) = pdbtbx::open(
-        pdb_path,
-        StrictnessLevel::Medium
-    ).unwrap();
-    let result = rust_sasa::calculate_sasa(&pdb,probe_radius,n_points,SASALevel::Residue).unwrap();
-    return match result {
-        SASAResult::Residue(v) => {
-            let mut temp : Vec<f32> = vec![];
-            for value in v {
-                temp.push(value.value)
-            }
-            Ok(temp)
-        },
-        _ => panic!("This will never run")
-    };
-}
-
-#[pyfunction]
-fn calculate_sasa_at_atom_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>) -> PyResult<Vec<f32>> {
-    let (mut pdb, _errors) = pdbtbx::open(
-        pdb_path,
-        StrictnessLevel::Medium
-    ).unwrap();
-    let result = rust_sasa::calculate_sasa(&pdb,probe_radius,n_points,SASALevel::Atom).unwrap();
-    return match result {
-        SASAResult::Atom(v) => {
-            Ok(v)
-        },
-        _ => panic!("This will never run")
-    };
-}
-
-#[pyfunction]
-fn calculate_sasa_at_chain_level(pdb_path: String,probe_radius: Option<f32>,n_points: Option<usize>) -> PyResult<Vec<f32>> {
-    let (mut pdb, _errors) = pdbtbx::open(
-        pdb_path,
-        StrictnessLevel::Medium
-    ).unwrap();
-    let result = rust_sasa::calculate_sasa(&pdb,probe_radius,n_points,SASALevel::Chain).unwrap();
-    return match result {
-        SASAResult::Chain(v) => {
-            let mut temp : Vec<f32> = vec![];
-            for value in v {
-                temp.push(value.value)
-            }
-            Ok(temp)
-        },
-        _ => panic!("This will never run")
-    };
-}
-
-#[pymodule]
-fn rust_sasa_python(_py: Python, m: &PyModule) -> PyResult<()> {
-    m.add_function(wrap_pyfunction!(calculate_sasa_at_protein_level, m)?)?;
-    m.add_function(wrap_pyfunction!(calculate_sasa_at_chain_level, m)?)?;
-    m.add_function(wrap_pyfunction!(calculate_sasa_at_residue_level, m)?)?;
-    m.add_function(wrap_pyfunction!(calculate_sasa_at_atom_level, m)?)?;
-    Ok(())
-}