NMReDATA is a standard format for representing NMR spectroscopy data, including chemical structures, peak assignments, and raw spectral data. NMR-ML is an XML-based format for representing NMR data in a standardized way. This tool allows for conversion between these formats, enabling interoperability between different NMR data processing systems. It's features include:

• Convert NMReDATA files (SDF format) to NMR-ML format
• Convert NMReDATA zip archives containing SDF files and raw spectral data to NMR-ML
• Convert NMR-ML files back to NMReDATA format
• Process raw NMR data from various vendors (Bruker, Varian/Agilent)
• Extract peak lists and assignments from NMReDATA files
• Generate synthetic spectra from peak lists

Installation:

Prerequisites

The following dependencies are required:

• Python 3.6+
• RDKit
• NumPy
• Matplotlib (for visualization)
• Additional dependencies in related repositories:
• nmr-pred (for prediction)
• magmet (for processing raw NMR data)
• nmr_ml (for NMR-ML creation and extraction)

Setup

1. Download the nmrML repository, and related repositories:

   git clone https://github.com/tsajed/nmr-pred
   git clone magmet-repository-url

2. Install Python dependencies:

   pip install rdkit numpy matplotlib

3. Ensure the directory structure is maintained as expected by the scripts:

   parent-directory/
   ├── nmredata/           # This repository
   ├── nmr-pred/           # For NMR prediction
   ├── magmet/             # For processing raw NMR data
   │   ├── setting
   │   ├── settings_update.txt
   │   └── solvent_lib/
   └── nmr_ml/
       ├── nmrml_creator.py
       └── nmrml_extract.py

Usage:

Converting NMReDATA SDF to NMR-ML

To convert a single NMReDATA SDF file to NMR-ML:

python nmredata_to_nmrml.py  [output_dir [output_file_basename]]

Example:

python nmredata_to_nmrml.py compound.nmredata.sdf output_folder compound

Converting NMReDATA ZIP to NMR-ML

To convert a zipped NMReDATA file (containing SDF and raw data) to NMR-ML:

python nmredata_zip_to_nmrml.py  [extract_dir output_dir output_basename]

Example:

python nmredata_zip_to_nmrml.py compound.zip extract_folder output_folder compound

Converting NMR-ML to NMReDATA

To convert an NMR-ML file to NMReDATA format:

python nmrml_to_nmredata.py --input  [--tmp ] [--base ] [--output ]

Example:

python nmrml_to_nmredata.py --input compound.nmrML --tmp temp_folder --base compound --output compound_nmredata.zip

Algorithm Details:

NMReDATA to NMR-ML Conversion

1. Reading NMReDATA:Parse the SDF file using RDKit, extract molecule structure, assignments, peak information, and raw data if available
2. Extracting Spin System:Build a spin system matrix from assignments, extract chemical shifts and J couplings
3. Processing Raw Data:Detect data format (Bruker, Varian), process with magmet to get spectra and peak lists
4. Generating NMR-ML:Create NMR-ML files per spectrum type, include structure, assignments, and data

NMR-ML to NMReDATA Conversion

1. Extracting from NMR-ML:Parse file to extract structure, peaks, metadata, and generate JSONs
2. Creating NMReDATA:Build SDF with tags and package with spectral data

Supported Spectrum Types:

• 1D-1H NMR
• 1D-13C NMR
• 2D-1H-13C-HSQC
• 2D-1H-13C-HMBC
• 2D-1H-1H-COSY
• 2D-1H-1H-TOCSY
• 2D-1H-1H-ROESY/NOESY

File Formats:

NMReDATA

• SDF file containing molecular structure and NMR tags
• Optional raw spectral data files
• All files can be zipped together

NMR-ML

• XML-based format with: ul li Molecular structure li Acquisition parameters li Processing parameters li Peak lists and assignments li Spectral data (optional)

Example:

The example directory contains a sample implementation for ethanol:

cd example
python construct_example_nmredata.py

This creates:

• nmredata.sdf: NMReDATA file for ethanol
• Ethanol_nmredata.zip: ZIP archive with SDF and simulated data

Troubleshooting:

• Missing dependencies:Ensure all repositories are cloned and properly placed
• Path issues:Verify raw data paths
• Format detection:If automatic detection fails, set manually

References:

• NMReDATA Initiative
• NMR-ML Format

License:

This project is licensed under the MIT License - see the LICENSE file for details.