edref 3.5.0

Electron Diffraction Refinement Engine - SHELXL-compatible crystallographic refinement for 3D ED/microED

EDref v3

Electron Diffraction Refinement Engine - A Python library for crystallographic structure refinement compatible with SHELXL.

Overview

EDref is a modular implementation of least-squares crystallographic refinement on F². It can reproduce SHELXL's kinematic refinement workflow and supports both X-ray and electron diffraction data.

Installation

# Development installation
cd EDref_v3
pip install -e .

# With development dependencies
pip install -e ".[dev]"

Quick Start

from edref import (
    InsFileReader, HklFileReader,
    SpaceGroup,
    calculate_reciprocal_cell,
    calculate_structure_factor,
    merge_reflections,
    calculate_R1,
)

# Load structure
ins = InsFileReader("structure.ins").read()
hkl = HklFileReader("structure.hkl").read()

# Setup
reciprocal = calculate_reciprocal_cell(ins.cell)
spacegroup = SpaceGroup(ins.latt, ins.symm)

# Merge reflections
merged = merge_reflections(hkl.reflections, spacegroup)

# Calculate structure factors
for refl in merged[:5]:
    Fc = calculate_structure_factor(
        refl.h, refl.k, refl.l,
        ins.atoms, ins.sfac,
        spacegroup, reciprocal,
        ins.wavelength
    )
    print(f"({refl.h},{refl.k},{refl.l}): |Fc|² = {abs(Fc)**2:.2f}")

Package Structure

src/edref/
├── core/           # Crystallographic fundamentals
│   ├── crystallography.py   # Unit cell, d-spacing
│   ├── symmetry.py          # Space group operations
│   ├── scattering.py        # Atomic scattering factors
│   └── structure_factors.py # F(hkl) calculation
├── io/             # File I/O
│   ├── formats.py          # Data classes
│   └── shelxl.py           # SHELXL file readers
├── refinement/     # Least-squares refinement
│   ├── weighting.py        # SHELXL weighting scheme
│   └── statistics.py       # R-factors, GooF
└── analysis/       # Data processing
    └── merging.py          # Reflection merging

Key Features

• SHELXL-compatible: Reproduces SHELXL kinematic refinement
• Type hints: Full type annotations for better IDE support
• Modular design: Use only the components you need
• No hard-coded paths: All paths are parameters
• Electron diffraction: Supports custom SFAC coefficients

Validated Against SHELXL

• Aspirin (P2₁/c, 21 atoms): R1 within 0.32% of SHELXL
• Structure factors: Correlation > 0.9999 with SHELXL .fcf

Command-Line Interface

EDref includes a CLI for running refinements:

# Run EDref refinement
edref structure.ins --edref

# Run SHELXL for comparison
edref structure.ins --shelxl

# Run both and compare results
edref structure.ins --compare

# With resolution cutoff
edref structure.ins --compare --resolution 99 0.8

Requirements

• Python >= 3.10
• NumPy >= 1.21
• SciPy >= 1.7
• Matplotlib >= 3.5

Documentation

• Full Manual - Complete API reference and examples
• Contributing Guide - How to contribute
• Citation - How to cite EDref

License

MIT License - see LICENSE for details