synth-xtal 0.1.0

Simulate X-ray crystallography diffraction data from atomic models.

synth-xtal

synth-xtal is a lightweight Python library for simulating X-ray Crystallography diffraction data (structure factors and MTZ files) from input atomic models (PDB/mmCIF files).

Extracted from the synth-pdb ecosystem, it provides a physically grounded, education-focused engine for reciprocal space simulation.

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🧪 For Structural Biologists

• Virtual Crystallography: Generate ideal $F_{calc}$ and $\phi_{calc}$ structure factors from structural models.
• Automated Cell Generation: Transparently computes optimal bounding unit cells in $P 1$ for standalone peptides/proteins lacking periodic symmetry constraints.

🤖 For Machine Learning Researchers

• Standard Integrations: Built directly on top of gemmi and reciprocalspaceship for native FFT acceleration and robust MTZ writing.
• Multi-Model Support: Seamlessly handles NMR ensembles or MD trajectories by accurately averaging grid densities to simulate alternative conformations.
• Educational Clarity: Simple, well-commented implementation of crystallographic density mapping — easy to audit and extend.

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Features

• Diffraction Simulation: Direct generation of complex structure factors from atomic coordinates using gemmi.DensityCalculatorX.
• Ensemble Averaging: Calculates coherent scattering intensities over an ensemble of structural models.
• Pythonic Data Structures: Outputs are formatted to reciprocalspaceship.DataSet objects for seamless downstream integration with standard ML/data-science tools (Pandas).

Installation

# Basic installation
pip install synth-xtal

# Installation for contributors/developers
pip install "synth-xtal[dev,test,docs]"

Command-Line Interface (CLI)

synth-xtal provides a simple CLI for rapid simulation:

# Basic simulation (outputs to MTZ format)
synth-xtal input.pdb -o simulated.mtz

# Simulation at a specific high-resolution limit (e.g., 1.5 Å)
synth-xtal input.pdb -o simulated.mtz --resolution 1.5

# Simulation with a custom padding margin for automatically generated unit cells
synth-xtal input.pdb -o simulated.mtz --margin 15.0

CLI Arguments

• input: Path to PDB or mmCIF file.
• -o, --output: Save structure factor data to an .mtz file (Required).
• -d, --resolution: High resolution limit in Ångströms (default: 2.0).
• --margin: Margin in Ångströms for the unit cell bounding box if the input lacks a defined unit cell (default: 10.0).

Quick Start

Python API

from synth_xtal.simulator import simulate_diffraction

# Calculate MTZ from a PDB or mmCIF file
simulate_diffraction(
    input_pdb="protein.cif",
    output_mtz="simulated_data.mtz",
    d_min=2.0
)

Tutorials

Try out synth-xtal interactively in Google Colab:

• 01. Crystallography Basics:
• 02. Experimental Validation (4LZT):

Acknowledgements

synth-xtal was heavily inspired by the educational goals of the larger synth-pdb ecosystem and relies critically on:

• gemmi - for core density calculations and FFT operations.
• reciprocalspaceship - for MTZ manipulation and Pandas integration.