synth-nmr 0.2.0

NMR spectroscopy calculations for protein structures

synth-nmr

NMR spectroscopy calculations for protein structures

A lightweight, standalone Python package for calculating NMR observables from protein structures. Originally extracted from the synth-pdb package to provide a focused toolkit that works with any protein structure source.

Features

• NOE Calculations: Synthetic NOE distance restraints
• Relaxation Rates: R1, R2, and heteronuclear NOE predictions
• Chemical Shifts: SPARTA-lite based predictions with ring current corrections
• J-Couplings: Karplus equation for scalar couplings
• NEF I/O: Read and write NMR Exchange Format files
• Secondary Structure: Automatic classification for enhanced predictions

Installation

pip install synth-nmr

For improved performance with JIT compilation:

pip install synth-nmr[performance]

Quick Start

import biotite.structure.io as strucio
from synth_nmr import (
    calculate_synthetic_noes,
    calculate_relaxation_rates,
    predict_chemical_shifts,
    calculate_hn_ha_coupling
)

# Load a protein structure
structure = strucio.load_structure("protein.pdb")

# Calculate NOEs
noes = calculate_synthetic_noes(structure, cutoff=5.0)

# Predict relaxation rates
relaxation = calculate_relaxation_rates(
    structure,
    field_strength=600.0,  # MHz
    temperature=298.0,      # K
    correlation_time=5.0    # ns
)

# Predict chemical shifts
shifts = predict_chemical_shifts(structure)

# Calculate J-couplings
j_couplings = calculate_hn_ha_coupling(structure)

Requirements

• Python ≥ 3.8
• NumPy ≥ 1.20
• Biotite ≥ 0.35.0
• Numba ≥ 0.55.0 (optional, for performance)

Documentation

Core Functions

calculate_synthetic_noes(structure, cutoff=5.0)

Calculate synthetic NOE distance restraints.

Parameters:

• structure: biotite AtomArray
• cutoff: Distance cutoff in Ångströms (default: 5.0)

Returns: Dictionary of NOE restraints

calculate_relaxation_rates(structure, field_strength, temperature, correlation_time)

Predict NMR relaxation rates (R1, R2, heteronuclear NOE).

Parameters:

• structure: biotite AtomArray
• field_strength: Spectrometer frequency in MHz
• temperature: Temperature in Kelvin
• correlation_time: Molecular correlation time in nanoseconds

Returns: Dictionary of relaxation rates per residue

predict_chemical_shifts(structure)

Predict chemical shifts using SPARTA-lite with ring current corrections.

Parameters:

• structure: biotite AtomArray

Returns: Dictionary of chemical shifts by residue and atom type

calculate_hn_ha_coupling(structure)

Calculate ³J(HN-Hα) couplings using the Karplus equation.

Parameters:

• structure: biotite AtomArray

Returns: Dictionary of J-coupling values per residue

Use Cases

• Structure Validation: Compare predicted vs experimental NMR data
• MD Analysis: Calculate NMR observables from molecular dynamics trajectories
• Protein Design: Predict NMR properties of designed structures
• Data Integration: Generate synthetic NMR data for machine learning

Compatibility

Works with protein structures from any source:

• PDB files
• AlphaFold predictions
• Molecular dynamics simulations
• De novo structure generation (e.g., synth-pdb)

Citation

If you use synth-nmr in your research, please cite:

@software{synth_nmr,
  author = {Elkins, George},
  title = {synth-nmr: NMR spectroscopy calculations for protein structures},
  year = {2026},
  url = {https://github.com/elkins/synth-nmr}
}

License

MIT License - see LICENSE file for details

Related Projects

• synth-pdb - Synthetic protein structure generation
• Biotite - Computational biology toolkit

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Support

For issues and questions, please use the GitHub issue tracker.