bmdms-np

BMDMS-NP is a database that encompasses ESI MS/MS mass spectra of natural compounds, especially plant secondary metabolites. At present, the database contains 288,939 MS/MS spectra of 2,739 natural compounds that are commercially available.

Dependencies

1. Anaconda for python 3.7 and create & activate a virtual environment

2. JRE 8.0

3. Numpy

    conda install -c anaconda numpy
   

4. SQLAlchemy

    conda install -c anaconda sqlalchemy	
   

5. Pymysql

    conda install -c anaconda pymysql
   

6. Scikit Learn

    conda install scikit-learn
   

7. Pymzml

    conda install -c bioconda pymzml
   

8. RDKit

    conda install -c rdkit rdkit
   

9. Jpype1

    conda install -c conda-forge jpype1
   

10. PyFingerprint

    pip install git+git://github.com/hcji/PyFingerprint@master
    

11. Matplotlib-venn (optional)

    conda install -c conda-forge matplotlib-venn
    

12. Clone the code

    git clone https://github.com/chalbori/bmdms-np.git
    

Usage

• To access to the BMDMS-NP spectra, please follow this slide.
• To check molecular structures of compounds included in database, SDFiles in the folder out/sdfs/ are being provided.
• Take sample/search_block.py as examples for running as described in the file.
• To parse all spectral records to MSP format file, please run sample/retrieve_records.py