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

1. Guinier Analysis: Extract Radius of Gyration ($R_g$) and forward scattering $I(0)$.
2. Crystallinity Analysis: Detect Bragg peaks and calculate Crystallinity Index (CI).
3. 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 for oligomer.exe.
• scripts/analyze_batch.py: CLI tool for bulk processing.