By name: saxs-physics description: A lightweight, physics-based toolkit for analyzing Small-Angle X-ray Scattering (SAXS) data. Calculates Rg, I(0), and Crystallinity Index without bloat.
SAXS Physics Toolkit
This skill provides a minimalist, pure-Python library for extracting physical parameters from SAXS data. Unlike complex pipelines, these scripts focus solely on the mathematical analysis.
Core Capabilities
- Guinier Analysis: Extract Radius of Gyration ($R_g$) and forward scattering $I(0)$.
- Crystallinity Analysis: Detect Bragg peaks and calculate Crystallinity Index (CI).
- Oligomer Wrapper: Simple interface to ATSAS tools (requires local installation).
Usage
1. Batch Analysis (CLI)
Run the batch analyzer on a directory of .dat files:
python skill/saxs_physics/scripts/analyze_batch.py /path/to/data --out results.csv
2. Library Usage (Python)
You can import the math functions directly in your own scripts:
from skill.saxs_physics.scripts.utils import read_dat
from skill.saxs_physics.scripts.saxs_math import calculate_guinier
q, I, err = read_dat("sample.dat")
res = calculate_guinier(q, I)
print(f"Rg = {res['Rg']} A")
Structure
scripts/saxs_math.py: Pure numpy implementation of physics equations.scripts/atsas_wrapper.py: Minimal wrapper foroligomer.exe.scripts/analyze_batch.py: CLI tool for bulk processing.