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.
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Anaconda for python 3.7 and create & activate a virtual environment
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JRE 8.0
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Numpy
conda install -c anaconda numpy
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SQLAlchemy
conda install -c anaconda sqlalchemy
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Pymysql
conda install -c anaconda pymysql
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Scikit Learn
conda install scikit-learn
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Pymzml
conda install -c bioconda pymzml
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RDKit
conda install -c rdkit rdkit
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Jpype1
conda install -c conda-forge jpype1
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PyFingerprint
pip install git+git://github.com/hcji/PyFingerprint@master
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Matplotlib-venn (optional)
conda install -c conda-forge matplotlib-venn
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Clone the code
git clone https://github.com/chalbori/bmdms-np.git
- 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