rust-sasa-python 0.2.0__tar.gz → 0.2.2__tar.gz

{rust_sasa_python-0.2.0 → rust_sasa_python-0.2.2}/.github/workflows/CI.yml

@@ -138,6 +138,7 @@ jobs:
     name: Release
     runs-on: ubuntu-latest
     needs: [linux, windows, macos, sdist, test]
+    if: startsWith(github.ref, 'refs/tags/v')
     steps:
       - uses: actions/download-artifact@v4
       - name: Publish to PyPI

{rust_sasa_python-0.2.0 → rust_sasa_python-0.2.2}/Cargo.lock

@@ -659,8 +659,9 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa-python"
-version = "0.2.0"
+version = "0.2.2"
 dependencies = [
+ "nalgebra",
  "pdbtbx",
  "pyo3",
  "rust-sasa",

{rust_sasa_python-0.2.0 → rust_sasa_python-0.2.2}/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "rust-sasa-python"
-version = "0.2.0"
-edition = "2021"
+version = "0.2.2"
+edition = "2024"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
@@ -12,3 +12,4 @@ crate-type = ["cdylib"]
 pdbtbx = "0.12.0"
 pyo3 = "0.25.1"
 rust-sasa = "0.3.2"
+nalgebra = "0.33.2"

{rust_sasa_python-0.2.0 → rust_sasa_python-0.2.2}/DOCS.md

@@ -84,6 +84,41 @@ atom_results = sasa.calculate_atom_sasa("protein.pdb")
 chain_results = sasa.calculate_chain_sasa("protein.pdb")
 ```
 
+### Low-level Functions
+
+For advanced use cases where you need to calculate SASA for custom atom sets:
+
+**`calculate_sasa_internal(atoms_in: list[tuple[tuple[float, float, float], float, int]], probe_radius: float, n_points: int) -> list[float]`**
+
+Calculate SASA for a set of atoms directly without PDB file parsing.
+
+**Parameters:**
+- `atoms_in`: List of tuples, each containing:
+  - Atom coordinates as `(x, y, z)` tuple of floats
+  - Atom radius as float
+  - Atom index as int
+- `probe_radius`: Probe sphere radius in Ångströms
+- `n_points`: Number of points for surface sampling
+
+**Returns:**
+- List of SASA values (floats) corresponding to each input atom
+
+**Example:**
+```python
+import rust_sasa_python as sasa
+
+# Define atoms: [(coordinates, radius, index), ...]
+atoms = [
+    ((0.0, 0.0, 0.0), 1.7, 0),    # Carbon atom
+    ((2.0, 0.0, 0.0), 1.2, 1),    # Hydrogen atom
+    ((0.0, 2.0, 0.0), 1.55, 2),   # Nitrogen atom
+]
+
+# Calculate SASA
+sasa_values = sasa.calculate_sasa_internal(atoms, probe_radius=1.4, n_points=100)
+print(f"SASA values: {sasa_values}")
+```
+
 ## Usage Examples
 
 ### Basic Usage

{rust_sasa_python-0.2.0 → rust_sasa_python-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rust-sasa-python
-Version: 0.2.0
+Version: 0.2.2
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

rust_sasa_python-0.2.2/rust-sasa-python.pyi

@@ -0,0 +1,151 @@
+"""Type stubs for rust_sasa_python module."""
+
+from typing import List
+
+class Protein:
+    """Protein-level SASA results."""
+
+    total: float
+    polar: float
+    non_polar: float
+
+class Residue:
+    """Residue-level SASA results."""
+
+    chain_id: str
+    residue_name: str
+    residue_number: int
+    sasa: float
+
+class Chain:
+    """Chain-level SASA results."""
+
+    chain_id: str
+    sasa: float
+
+class SASACalculator:
+    """SASA calculator with configurable parameters."""
+
+    def __init__(self, pdb_path: str) -> None:
+        """Initialize SASA calculator with PDB file path.
+
+        Args:
+            pdb_path: Path to PDB or mmCIF file
+
+        """
+
+    def with_probe_radius(self, radius: float) -> SASACalculator:
+        """Set the probe radius for SASA calculation.
+
+        Args:
+            radius: Probe sphere radius in Ångströms (default: 1.4)
+
+        Returns:
+            Self for method chaining
+
+        """
+
+    def with_n_points(self, points: int) -> SASACalculator:
+        """Set the number of points for surface sampling.
+
+        Args:
+            points: Number of sampling points (default: 100)
+
+        Returns:
+            Self for method chaining
+
+        """
+
+    def calculate_protein(self) -> Protein:
+        """Calculate SASA at the protein level.
+
+        Returns:
+            Protein: Object containing total, polar, and non-polar SASA values
+
+        """
+
+    def calculate_chain(self) -> List[Chain]:
+        """Calculate SASA at the chain level.
+
+        Returns:
+            List[Chain]: List of chain-level SASA results
+
+        """
+
+    def calculate_residue(self) -> List[Residue]:
+        """Calculate SASA at the residue level.
+
+        Returns:
+            List[Residue]: List of residue-level SASA results
+
+        """
+
+    def calculate_atom(self) -> List[float]:
+        """Calculate SASA at the atom level.
+
+        Returns:
+            List[float]: List of atom-level SASA values
+
+        """
+
+# Convenience functions
+def calculate_protein_sasa(pdb_path: str) -> Protein:
+    """Calculate protein-level SASA for a PDB file.
+
+    Args:
+        pdb_path: Path to PDB or mmCIF file
+
+    Returns:
+        Protein: Object containing total, polar, and non-polar SASA values
+
+    """
+
+def calculate_residue_sasa(pdb_path: str) -> List[Residue]:
+    """Calculate residue-level SASA for a PDB file.
+
+    Args:
+        pdb_path: Path to PDB or mmCIF file
+
+    Returns:
+        List[Residue]: List of residue-level SASA results
+
+    """
+
+def calculate_atom_sasa(pdb_path: str) -> List[float]:
+    """Calculate atom-level SASA for a PDB file.
+
+    Args:
+        pdb_path: Path to PDB or mmCIF file
+
+    Returns:
+        List[float]: List of atom-level SASA values
+
+    """
+
+def calculate_chain_sasa(pdb_path: str) -> List[Chain]:
+    """Calculate chain-level SASA for a PDB file.
+
+    Args:
+        pdb_path: Path to PDB or mmCIF file
+
+    Returns:
+        List[Chain]: List of chain-level SASA results
+
+    """
+
+def calculate_sasa_internal(
+    atoms_in: list[tuple[tuple[float, float, float], float, int]],
+    probe_radius: float,
+    n_points: int,
+) -> list[float]:
+    """Calculate SASA for a set of atoms.
+
+    Args:
+        atoms_in: List of atom coordinates, radii, and indices
+        probe_radius: Probe radius
+        n_points: Number of points on the sphere
+
+    Returns:
+        List[float]: List of SASA values
+
+    """

{rust_sasa_python-0.2.0 → rust_sasa_python-0.2.2}/src/lib.rs

@@ -1,8 +1,10 @@
+use nalgebra::Point3;
 use pdbtbx;
 use pyo3::exceptions::PyRuntimeError;
 use pyo3::prelude::*;
 use rust_sasa::options::SASAOptions;
-use rust_sasa::{AtomLevel, ChainLevel, ProteinLevel, ResidueLevel};
+use rust_sasa::{Atom, calculate_sasa_internal as calculate_sasa_internal_internal};
+use rust_sasa::{AtomLevel, ChainLevel, ProteinLevel, ResidueLevel}; // As in long long
 
 #[pyclass]
 #[derive(Clone)]
@@ -291,6 +293,29 @@ pub fn calculate_chain_sasa(pdb_path: String) -> PyResult<Vec<Chain>> {
     SASACalculator::new(pdb_path).calculate_chain()
 }
 
+#[pyfunction]
+pub fn calculate_sasa_internal(
+    atoms_in: Vec<((f32, f32, f32), f32, usize)>,
+    probe_radius: f32,
+    n_points: usize,
+) -> PyResult<Vec<f32>> {
+    let atoms: Vec<Atom> = atoms_in
+        .into_iter()
+        .map(|(pos, radius, index)| Atom {
+            position: Point3::new(pos.0, pos.1, pos.2),
+            id: index,
+            parent_id: None,
+            radius,
+        })
+        .collect();
+    Ok(calculate_sasa_internal_internal(
+        atoms.as_slice(),
+        probe_radius,
+        n_points,
+        true,
+    ))
+}
+
 #[pymodule]
 fn rust_sasa_python(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<SASACalculator>()?;
@@ -303,6 +328,7 @@ fn rust_sasa_python(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_function(wrap_pyfunction!(calculate_residue_sasa, m)?)?;
     m.add_function(wrap_pyfunction!(calculate_atom_sasa, m)?)?;
     m.add_function(wrap_pyfunction!(calculate_chain_sasa, m)?)?;
+    m.add_function(wrap_pyfunction!(calculate_sasa_internal, m)?)?;
 
     Ok(())
 }

{rust_sasa_python-0.2.0 → rust_sasa_python-0.2.2}/uv.lock

@@ -84,7 +84,7 @@ wheels = [
 
 [[package]]
 name = "rust-sasa-python"
-version = "0.2.0"
+version = "0.2.1"
 source = { editable = "." }
 
 [package.optional-dependencies]

rust_sasa_python-0.2.0/test.py

@@ -1,6 +0,0 @@
-import rust_sasa_python as sasa
-
-# Simple calculation - use convenience function
-calculator = sasa.SASACalculator("example.cif").with_n_points(960)
-residues = calculator.calculate_residue()
-print(residues)