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strux_rs-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: strux-rs
+Version: 0.1.0
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Summary: A performance-engineered structural biology library in Rust
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# strux-rs
+
+[![Language](https://img.shields.io/badge/Language-Rust-orange.svg)]()
+[![Python Bindings](https://img.shields.io/badge/Python-PyO3_/_Maturin-blue.svg)]()
+[![License](https://img.shields.io/badge/License-MIT-green.svg)]()
+
+> **strux-rs** is a blazingly fast, performance-engineered structural biology library written in Rust, offering direct, zero-copy Python bindings via PyO3 and NumPy.
+
+It acts as a drop-in accelerator for slow CPU-bound bottlenecks in molecular dynamics (MD) analysis and generative structural biology pipelines.
+
+---
+
+## Performance Speedups
+
+Benchmark performed on a **21-frame trajectory** of a designed E3 ubiquitin ligase binder containing **1,924 atoms per frame**:
+
+| Task | Python (Pure/NumPy) | Rust (`strux-rs`) | Speedup |
+| :--- | :--- | :--- | :--- |
+| **PDB Trajectory Parsing** | 0.0781s | 0.0513s | **1.5x** |
+| **Radius of Gyration ($R_g$)** | 0.000140s | 0.000009s | **16.0x** |
+| **Raw RMSD** | 0.000037s | 0.000008s | **4.5x** |
+| **Kabsch Aligned RMSD** | 0.004737s | 0.000019s | **255.6x** |
+| **RMSF** | 0.000601s | 0.000131s | **4.6x** |
+| **Interface Contacts (5.0Å)** | 0.026400s | 0.000500s | **55.5x** |
+
+### Core Optimization Features
+* **SVD-based Kabsch Alignment (~255x faster)**: Mathematical alignment centered at centroids, computing covariance matrices, and executing reflection-corrected Singular Value Decomposition (SVD) using optimized SIMD-capable `nalgebra` structures.
+* **Spatial Hashing Cell Lists (~55x faster)**: Bypasses naive $O(N_A \times N_B)$ double-loop contact mapping. It indexes coordinate grids into cubical voxels and wraps boundary cells under Periodic Boundary Conditions (PBC) using minimum image conventions.
+* **Multi-Threaded Trajectory Scaling**: Bypasses the Python Global Interpreter Lock (GIL) entirely. Heavy computations scale automatically across all CPU cores using `rayon`.
+
+---
+
+## Features
+
+* **Trajectory Parsing**: High-speed multi-model PDB text scanner returning a 3D NumPy array `[Frames, Atoms, 3]`.
+* **Kabsch Superposition**: RMSD alignment for coordinate superposition.
+* **Biophysical Metrics**: Radius of Gyration ($R_g$), Root Mean Square Fluctuation (RMSF), and Raw RMSD.
+* **Interface Contact Mapper**: Rapid neighbor lookup under cutoff distances supporting periodic boxes.
+
+---
+
+## Installation
+
+To build and compile `strux-rs` from source, ensure you have the Rust toolchain installed.
+
+```bash
+# Clone the repository
+git clone https://github.com/QntmSeer/strux-rs.git
+cd strux-rs
+
+# Compile and install inside your active Python environment
+pip install .
+```
+
+*For active local development:*
+```bash
+pip install maturin
+maturin develop --release
+```
+
+---
+
+## Quickstart (Python API)
+
+```python
+import numpy as np
+import strux_rs
+
+# 1. Parse a multi-model PDB trajectory into a [Frames, Atoms, 3] numpy array
+traj = strux_rs.parse_pdb("trajectory.pdb")
+print(f"Loaded trajectory with shape: {traj.shape}")
+
+# 2. Compute Radius of Gyration for the first frame
+rg = strux_rs.calculate_rg(traj[0])
+print(f"Radius of Gyration: {rg:.3f} Å")
+
+# 3. Calculate aligned RMSD using the Kabsch algorithm
+aligned_rmsd = strux_rs.calculate_rmsd_kabsch(traj[0], traj[1])
+print(f"Aligned RMSD: {aligned_rmsd:.3f} Å")
+
+# 4. Rapid interface contact mapping under Periodic Boundary Conditions (PBC)
+target = traj[0][:1023]
+binder = traj[0][1023:]
+cutoff = 5.0  # Ångstroms
+box_dims = [25.0, 25.0, 25.0]  # Periodic boundary box length
+
+contacts = strux_rs.find_interface_contacts(target, binder, cutoff, box_dims)
+print(f"Detected {len(contacts)} contact pairs at the interface.")
+```
+
+---
+
+## Repository Layout
+
+```text
+strux-rs/
+├── Cargo.toml          # Cargo configuration and dependencies (pyo3, numpy, nalgebra, rayon)
+├── benchmark.py        # Correctness and performance benchmarking suite
+├── src/
+│   ├── lib.rs          # PyO3 bindings and array conversion layer
+│   ├── pdb.rs          # Zero-allocation buffered PDB trajectory scanner
+│   ├── spatial.rs      # PBC-aware Voxel spatial hashing / Cell Lists
+│   └── analysis.rs     # Biophysical math: Rg, RMSD, SVD-Kabsch, and RMSF
+└── tests/
+    └── grueling_tests.rs # Edge-case, boundary wrapping, and degeneracy verification
+```
+
+---
+
+## License
+This project is licensed under the MIT License.
+